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Buenrostro Lab Publications

Featured Publications

• Papathanasiou S, Mynhier NA, Liu S, Brunette G, Stokasimov E, Jacob E, Li L, Comenho C, van Steensel B, Buenrostro JD, Zhang CZ, Pellman D. 2023. Heritable transcriptional defects from aberrations of nuclear architecture. Nature. 619(7968):184-192. Pubmed: 37286600 DOI:10.1038/s41586-023-06157-7 Papathanasiou S, Mynhier NA, Liu S, Brunette G, Stokasimov E, Jacob E, Li L, Comenho C, van Steensel B, Buenrostro JD, Zhang CZ, Pellman D. 2023. Heritable transcriptional defects from aberrations of nuclear architecture. Nature. 619(7968):184-192. Pubmed: 37286600 DOI:10.1038/s41586-023-06157-7 Transcriptional heterogeneity due to plasticity of the epigenetic state of chromatin contributes to tumour evolution, metastasis and drug resistance. However, the mechanisms that cause this epigenetic variation are incompletely understood. Here we identify micronuclei and chromosome bridges, aberrations in the nucleus common in cancer, as sources of heritable transcriptional suppression. Using a combination of approaches, including long-term live-cell imaging and same-cell single-cell RNA sequencing (Look-Seq2), we identified reductions in gene expression in chromosomes from micronuclei. With heterogeneous penetrance, these changes in gene expression can be heritable even after the chromosome from the micronucleus has been re-incorporated into a normal daughter cell nucleus. Concomitantly, micronuclear chromosomes acquire aberrant epigenetic chromatin marks. These defects may persist as variably reduced chromatin accessibility and reduced gene expression after clonal expansion from single cells. Persistent transcriptional repression is strongly associated with, and may be explained by, markedly long-lived DNA damage. Epigenetic alterations in transcription may therefore be inherently coupled to chromosomal instability and aberrations in nuclear architecture. © 2023. The Author(s). Read Abstract
• Cheong JG, Ravishankar A, Sharma S, Parkhurst CN, Grassmann SA, Wingert CK, Laurent P, Ma S, Paddock L, Miranda IC, Karakaslar EO, Nehar-Belaid D, Thibodeau A, Bale MJ, Kartha VK, Yee JK, Mays MY, Jiang C, Daman AW, Martinez de Paz A, Ahimovic D, Ramos V, Lercher A, Nielsen E, Alvarez-Mulett S, Zheng L, Earl A, Yallowitz A, Robbins L, LaFond E, Weidman KL, Racine-Brzostek S, Yang HS, Price DR, Leyre L, Rendeiro AF, Ravichandran H, Kim J, Borczuk AC, Rice CM, Jones RB, Schenck EJ, Kaner RJ, Chadburn A, Zhao Z, Pascual V, Elemento O, Schwartz RE, Buenrostro JD, Niec RE, Barrat FJ, Lief L, Sun JC, Ucar D, Josefowicz SZ. 2023. Epigenetic memory of coronavirus infection in innate immune cells and their progenitors. Cell. 186(18):3882-3902.e24. Pubmed: 37597510 DOI:S0092-8674(23)00796-1 Cheong JG, Ravishankar A, Sharma S, Parkhurst CN, Grassmann SA, Wingert CK, Laurent P, Ma S, Paddock L, Miranda IC, Karakaslar EO, Nehar-Belaid D, Thibodeau A, Bale MJ, Kartha VK, Yee JK, Mays MY, Jiang C, Daman AW, Martinez de Paz A, Ahimovic D, Ramos V, Lercher A, Nielsen E, Alvarez-Mulett S, Zheng L, Earl A, Yallowitz A, Robbins L, LaFond E, Weidman KL, Racine-Brzostek S, Yang HS, Price DR, Leyre L, Rendeiro AF, Ravichandran H, Kim J, Borczuk AC, Rice CM, Jones RB, Schenck EJ, Kaner RJ, Chadburn A, Zhao Z, Pascual V, Elemento O, Schwartz RE, Buenrostro JD, Niec RE, Barrat FJ, Lief L, Sun JC, Ucar D, Josefowicz SZ. 2023. Epigenetic memory of coronavirus infection in innate immune cells and their progenitors. Cell. 186(18):3882-3902.e24. Pubmed: 37597510 DOI:S0092-8674(23)00796-1 Inflammation can trigger lasting phenotypes in immune and non-immune cells. Whether and how human infections and associated inflammation can form innate immune memory in hematopoietic stem and progenitor cells (HSPC) has remained unclear. We found that circulating HSPC, enriched from peripheral blood, captured the diversity of bone marrow HSPC, enabling investigation of their epigenomic reprogramming following coronavirus disease 2019 (COVID-19). Alterations in innate immune phenotypes and epigenetic programs of HSPC persisted for months to 1 year following severe COVID-19 and were associated with distinct transcription factor (TF) activities, altered regulation of inflammatory programs, and durable increases in myelopoiesis. HSPC epigenomic alterations were conveyed, through differentiation, to progeny innate immune cells. Early activity of IL-6 contributed to these persistent phenotypes in human COVID-19 and a mouse coronavirus infection model. Epigenetic reprogramming of HSPC may underlie altered immune function following infection and be broadly relevant, especially for millions of COVID-19 survivors. Copyright © 2023 Elsevier Inc. All rights reserved. Read Abstract
• Mangiameli SM, Chen H, Earl AS, Dobkin JA, Lesman D, Buenrostro JD, Chen F. 2023. Photoselective sequencing: microscopically guided genomic measurements with subcellular resolution. Nature methods. 20(5):686-694. Pubmed: 37106232 DOI:10.1038/s41592-023-01845-8 Mangiameli SM, Chen H, Earl AS, Dobkin JA, Lesman D, Buenrostro JD, Chen F. 2023. Photoselective sequencing: microscopically guided genomic measurements with subcellular resolution. Nature methods. 20(5):686-694. Pubmed: 37106232 DOI:10.1038/s41592-023-01845-8 In biological systems, spatial organization and function are interconnected. Here we present photoselective sequencing, a new method for genomic and epigenomic profiling within morphologically distinct regions. Starting with an intact biological specimen, photoselective sequencing uses targeted illumination to selectively unblock a photocaged fragment library, restricting the sequencing-based readout to microscopically identified spatial regions. We validate photoselective sequencing by measuring the chromatin accessibility profiles of fluorescently labeled cell types within the mouse brain and comparing with published data. Furthermore, by combining photoselective sequencing with a computational strategy for decomposing bulk accessibility profiles, we find that the oligodendrocyte-lineage-cell population is relatively enriched for oligodendrocyte-progenitor cells in the cortex versus the corpus callosum. Finally, we leverage photoselective sequencing at the subcellular scale to identify features of chromatin that are correlated with positioning at the nuclear periphery. These results collectively demonstrate that photoselective sequencing is a flexible and generalizable platform for exploring the interplay of spatial structures with genomic and epigenomic properties. © 2023. The Author(s), under exclusive licence to Springer Nature America, Inc. Read Abstract
• Joung J, Ma S, Tay T, Geiger-Schuller KR, Kirchgatterer PC, Verdine VK, Guo B, Arias-Garcia MA, Allen WE, Singh A, Kuksenko O, Abudayyeh OO, Gootenberg JS, Fu Z, Macrae RK, Buenrostro JD, Regev A, Zhang F. 2023. A transcription factor atlas of directed differentiation. Cell. 186(1):209-229.e26. Pubmed: 36608654 DOI:S0092-8674(22)01470-2 Joung J, Ma S, Tay T, Geiger-Schuller KR, Kirchgatterer PC, Verdine VK, Guo B, Arias-Garcia MA, Allen WE, Singh A, Kuksenko O, Abudayyeh OO, Gootenberg JS, Fu Z, Macrae RK, Buenrostro JD, Regev A, Zhang F. 2023. A transcription factor atlas of directed differentiation. Cell. 186(1):209-229.e26. Pubmed: 36608654 DOI:S0092-8674(22)01470-2 Transcription factors (TFs) regulate gene programs, thereby controlling diverse cellular processes and cell states. To comprehensively understand TFs and the programs they control, we created a barcoded library of all annotated human TF splice isoforms (>3,500) and applied it to build a TF Atlas charting expression profiles of human embryonic stem cells (hESCs) overexpressing each TF at single-cell resolution. We mapped TF-induced expression profiles to reference cell types and validated candidate TFs for generation of diverse cell types, spanning all three germ layers and trophoblasts. Targeted screens with subsets of the library allowed us to create a tailored cellular disease model and integrate mRNA expression and chromatin accessibility data to identify downstream regulators. Finally, we characterized the effects of combinatorial TF overexpression by developing and validating a strategy for predicting combinations of TFs that produce target expression profiles matching reference cell types to accelerate cellular engineering efforts. Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved. Read Abstract
• Kartha VK, Duarte FM, Hu Y, Ma S, Chew JG, Lareau CA, Earl A, Burkett ZD, Kohlway AS, Lebofsky R, Buenrostro JD. 2022. Functional inference of gene regulation using single-cell multi-omics. Cell genomics. 2(9). Pubmed: 36204155 DOI:10.1016/j.xgen.2022.100166 Kartha VK, Duarte FM, Hu Y, Ma S, Chew JG, Lareau CA, Earl A, Burkett ZD, Kohlway AS, Lebofsky R, Buenrostro JD. 2022. Functional inference of gene regulation using single-cell multi-omics. Cell genomics. 2(9). Pubmed: 36204155 DOI:10.1016/j.xgen.2022.100166 Cells require coordinated control over gene expression when responding to environmental stimuli. Here we apply scATAC-seq and single-cell RNA sequencing (scRNA-seq) in resting and stimulated human blood cells. Collectively, we generate ~91,000 single-cell profiles, allowing us to probe the cis-regulatory landscape of the immunological response across cell types, stimuli, and time. Advancing tools to integrate multi-omics data, we develop functional inference of gene regulation (FigR), a framework to computationally pair scA-TAC-seq with scRNA-seq cells, connect distal cis-regulatory elements to genes, and infer gene-regulatory networks (GRNs) to identify candidate transcription factor (TF) regulators. Utilizing these paired multi-omics data, we define domains of regulatory chromatin (DORCs) of immune stimulation and find that cells alter chromatin accessibility and gene expression at timescales of minutes. Construction of the stimulation GRN elucidates TF activity at disease-associated DORCs. Overall, FigR enables elucidation of regulatory interactions across single-cell data, providing new opportunities to understand the function of cells within tissues. Read Abstract
• Ana Uzquiano, Amanda J Kedaigle, Martina Pigoni, Bruna Paulsen, Xian Adiconis, Kwanho Kim, Tyler Faits, Surya Nagaraja, Noelia Antón-Bolaños, Chiara Gerhardinger, Ashley Tucewicz, Evan Murray, Xin Jin, Jason Buenrostro, Fei Chen, Silvia Velasco, Aviv Regev, Joshua Z Levin, Paola Arlotta. 2022. Proper acquisition of cell class identity in organoids allows definition of fate specification programs of the human cerebral cortex. Cell. 185(20):3770-3788.e27. DOI:10.1016/j.cell.2022.09.010 Ana Uzquiano, Amanda J Kedaigle, Martina Pigoni, Bruna Paulsen, Xian Adiconis, Kwanho Kim, Tyler Faits, Surya Nagaraja, Noelia Antón-Bolaños, Chiara Gerhardinger, Ashley Tucewicz, Evan Murray, Xin Jin, Jason Buenrostro, Fei Chen, Silvia Velasco, Aviv Regev, Joshua Z Levin, Paola Arlotta. 2022. Proper acquisition of cell class identity in organoids allows definition of fate specification programs of the human cerebral cortex. Cell. 185(20):3770-3788.e27. DOI:10.1016/j.cell.2022.09.010

All Publications

• 2025

• Yuan WC, Earl AS, Ma S, Alcedo K, Russell JO, Duarte FM, Chu YT, Chang PC, Chen HY, Chi HH, Zhu Q, Rodriguez-Fraticelli AE, Patel SH, Lee YR, Buenrostro JD, Camargo FD. 2025. HBO1 functions as an epigenetic barrier to hepatocyte plasticity and reprogramming during liver injury. Cell stem cell. 32(6):990-1005.e8. Pubmed: 40403721 DOI:S1934-5909(25)00177-8 Yuan WC, Earl AS, Ma S, Alcedo K, Russell JO, Duarte FM, Chu YT, Chang PC, Chen HY, Chi HH, Zhu Q, Rodriguez-Fraticelli AE, Patel SH, Lee YR, Buenrostro JD, Camargo FD. 2025. HBO1 functions as an epigenetic barrier to hepatocyte plasticity and reprogramming during liver injury. Cell stem cell. 32(6):990-1005.e8. Pubmed: 40403721 DOI:S1934-5909(25)00177-8 Hepatocytes can reprogram into biliary epithelial cells (BECs) during liver injury, but the underlying epigenetic mechanisms remain poorly understood. Here, we define the chromatin dynamics of this process using single-cell ATAC-seq and identify YAP/TEAD activation as a key driver of chromatin remodeling. An in vivo CRISPR screen highlights the histone acetyltransferase HBO1 as a critical barrier to reprogramming. HBO1 is recruited by YAP to target loci, where it promotes histone H3 lysine 14 acetylation (H3K14ac) and engages the chromatin reader zinc-finger MYND-type containing 8 (ZMYND8) to suppress YAP/TEAD-driven transcription. Loss of HBO1 accelerates chromatin remodeling, enhances YAP binding, and enables a more complete hepatocyte-to-BEC transition. Our findings position HBO1 as an epigenetic brake that restrains YAP-mediated reprogramming, suggesting that targeting HBO1 may enhance hepatocyte plasticity for liver regeneration. Copyright © 2025 Elsevier Inc. All rights reserved. Read Abstract
• Hingerl JC, Martens LD, Karollus A, Manz T, Buenrostro JD, Theis FJ, Gagneur J. 2025. scooby: Modeling multi-modal genomic profiles from DNA sequence at single-cell resolution. bioRxiv : the preprint server for biology. Pubmed: 39345504 DOI:10.1101/2024.09.19.613754 Hingerl JC, Martens LD, Karollus A, Manz T, Buenrostro JD, Theis FJ, Gagneur J. 2025. scooby: Modeling multi-modal genomic profiles from DNA sequence at single-cell resolution. bioRxiv : the preprint server for biology. Pubmed: 39345504 DOI:10.1101/2024.09.19.613754 Understanding how regulatory DNA elements shape gene expression across individual cells is a fundamental challenge in genomics. Joint RNA-seq and epigenomic profiling provides opportunities to build unifying models of gene regulation capturing sequence determinants across steps of gene expression. However, current models, developed primarily for bulk omics data, fail to capture the cellular heterogeneity and dynamic processes revealed by single-cell multi-modal technologies. Here, we introduce scooby, the first framework to model scRNA-seq coverage and scATAC-seq insertion profiles along the genome from sequence at single-cell resolution. For this, we leverage the pre-trained multi-omics profile predictor Borzoi as a foundation model, equip it with a cell-specific decoder, and fine-tune its sequence embeddings. Specifically, we condition the decoder on the cell position in a precomputed single-cell embedding resulting in strong generalization capability. Applied to a hematopoiesis dataset, scooby recapitulates cell-specific expression levels of held-out genes, and identifies regulators and their putative target genes through in silico motif deletion. Moreover, accurate variant effect prediction with scooby allows for breaking down bulk eQTL effects into single-cell effects and delineating their impact on chromatin accessibility and gene expression. We anticipate scooby to aid unraveling the complexities of gene regulation at the resolution of individual cells. Read Abstract
• Hu Y, Horlbeck MA, Zhang R, Ma S, Shrestha R, Kartha VK, Duarte FM, Hock C, Savage RE, Labade A, Kletzien H, Meliki A, Castillo A, Durand NC, Mattei E, Anderson LJ, Tay T, Earl AS, Shoresh N, Epstein CB, Wagers AJ, Buenrostro JD. 2025. Multiscale footprints reveal the organization of cis-regulatory elements. Nature. 638(8051):779-786. Pubmed: 39843737 DOI:10.1038/s41586-024-08443-4 Hu Y, Horlbeck MA, Zhang R, Ma S, Shrestha R, Kartha VK, Duarte FM, Hock C, Savage RE, Labade A, Kletzien H, Meliki A, Castillo A, Durand NC, Mattei E, Anderson LJ, Tay T, Earl AS, Shoresh N, Epstein CB, Wagers AJ, Buenrostro JD. 2025. Multiscale footprints reveal the organization of cis-regulatory elements. Nature. 638(8051):779-786. Pubmed: 39843737 DOI:10.1038/s41586-024-08443-4 Cis-regulatory elements (CREs) control gene expression and are dynamic in their structure and function, reflecting changes in the composition of diverse effector proteins over time. However, methods for measuring the organization of effector proteins at CREs across the genome are limited, hampering efforts to connect CRE structure to their function in cell fate and disease. Here we developed PRINT, a computational method that identifies footprints of DNA-protein interactions from bulk and single-cell chromatin accessibility data across multiple scales of protein size. Using these multiscale footprints, we created the seq2PRINT framework, which uses deep learning to allow precise inference of transcription factor and nucleosome binding and interprets regulatory logic at CREs. Applying seq2PRINT to single-cell chromatin accessibility data from human bone marrow, we observe sequential establishment and widening of CREs centred on pioneer factors across haematopoiesis. We further discover age-associated alterations in the structure of CREs in murine haematopoietic stem cells, including widespread reduction of nucleosome footprints and gain of de novo identified Ets composite motifs. Collectively, we establish a method for obtaining rich insights into DNA-binding protein dynamics from chromatin accessibility data, and reveal the architecture of regulatory elements across differentiation and ageing. © 2025. The Author(s). Read Abstract
• Chandra NA, Hu Y, Buenrostro JD, Mostafavi S, Sasse A. 2025. Refining sequence-to-activity models by increasing model resolution. bioRxiv : the preprint server for biology. Pubmed: 39975126 DOI:10.1101/2025.01.24.634804 Chandra NA, Hu Y, Buenrostro JD, Mostafavi S, Sasse A. 2025. Refining sequence-to-activity models by increasing model resolution. bioRxiv : the preprint server for biology. Pubmed: 39975126 DOI:10.1101/2025.01.24.634804 Decoding the cis-regulatory syntax that controls gene expression is essential for improving our understanding of cell differentiation and disease. To identify regulatory motifs and their regulatory syntax, deep learning based sequence-to-activity (S2A) models learn transcription factor binding motifs and their combinations from DNA sequence by modeling measured chromatin accessibility. Previously, we developed AI-TAC, a S2A model that predicts chromatin accessibility across various immune cell types in multi-task fashion, effectively decoding the regulatory syntax underlying immune cell differentiation. While ATAC-seq is commonly used to measure regional accessibility, it also provides high-resolution profiles, the distribution of Tn5 insertion sites, that offer additional insights into the precise location and strength of TF binding sites. Here we demonstrate that modeling ATAC-seq profiles alongside accessibility consistently improves predictions of differential chromatin accessibility across cell types. Moreover, we also find that multi-task learning across related immune cell types consistently outperforms single-task models. To understand what additional information bpAITAC learns from ATAC-seq profiles, we systematically compare sequence attributions from models trained with and without ATAC-seq profiles. We identify novel motifs with strong effect sizes that emerge only when profile data is included. Our findings suggest that modeling ATAC-seq at base-pair resolution enables the model to learn a more nuanced and sensitive representation of the cis-regulatory syntax driving immune cell-specific chromatin landscapes. Read Abstract
• Moore MM, Wekhande S, Issner R, Collins A, Cruz AJ, Liu YV, Javed N, Casaní-Galdón S, Buenrostro JD, Epstein CB, Mattei E, Doench JG, Bernstein BE, Shoresh N, Najm FJ. 2025. Multi-locus CRISPRi targeting with a single truncated guide RNA. Nature communications. 16(1):1357. Pubmed: 39905017 DOI:10.1038/s41467-025-56144-x Moore MM, Wekhande S, Issner R, Collins A, Cruz AJ, Liu YV, Javed N, Casaní-Galdón S, Buenrostro JD, Epstein CB, Mattei E, Doench JG, Bernstein BE, Shoresh N, Najm FJ. 2025. Multi-locus CRISPRi targeting with a single truncated guide RNA. Nature communications. 16(1):1357. Pubmed: 39905017 DOI:10.1038/s41467-025-56144-x A critical goal in functional genomics is evaluating which non-coding elements contribute to gene expression, cellular function, and disease. Functional characterization remains a challenge due to the abundance and complexity of candidate elements. Here, we develop a CRISPRi-based approach for multi-locus screening of putative transcription factor binding sites with a single truncated guide. A truncated guide with hundreds of sequence match sites can reliably disrupt enhancer activity, which expands the targeting scope of CRISPRi while maintaining repressive efficacy. We screen over 13,000 possible CTCF binding sites with 24 guides at 10 nucleotides in spacer length. These truncated guides direct CRISPRi-mediated deposition of repressive H3K9me3 marks and disrupt transcription factor binding at most sequence match target sites. This approach can be a valuable screening step for testing transcription factor binding motifs or other repeated genomic sequences and is easily implemented with existing tools. © 2025. The Author(s). Read Abstract
• Buenrostro J, Nagaraja S, Ojeda-Miron L, Zhang R, Oreskovic E, Hu Y, Zeve D, Sharma K, Hyman R, Zhang Q, Castillo A, Breault D, Yilmaz O. 2025. Clonal memory of colitis accumulates and promotes tumor growth. Research square. Pubmed: 40196012 DOI:10.21203/rs.3.rs-6081101/v1 Buenrostro J, Nagaraja S, Ojeda-Miron L, Zhang R, Oreskovic E, Hu Y, Zeve D, Sharma K, Hyman R, Zhang Q, Castillo A, Breault D, Yilmaz O. 2025. Clonal memory of colitis accumulates and promotes tumor growth. Research square. Pubmed: 40196012 DOI:10.21203/rs.3.rs-6081101/v1 Chronic inflammation is a well-established risk factor for cancer, but the underlying molecular mechanisms remain unclear. Using a mouse model of colitis, we demonstrate that colonic stem cells retain an epigenetic memory of inflammation following disease resolution, characterized by a cumulative gain of activator protein 1 (AP-1) transcription factor activity. Further, we develop SHARE-TRACE, a method that enables simultaneous profiling of gene expression, chromatin accessibility and clonal history in single cells, enabling high resolution tracking of epigenomic memory. This reveals that inflammatory memory is propagated cell-intrinsically and inherited through stem cell lineages, with certain clones demonstrating dramatically stronger memory than others. Finally, we show that colitis primes stem cells for amplified expression of regenerative gene programs following oncogenic mutation that accelerate tumor growth. This includes a subpopulation of tumors that have exceptionally high AP-1 activity and the additional upregulation of pro-oncogenic programs. Together, our findings provide a mechanistic link between chronic inflammation and malignancy, revealing how long-lived epigenetic alterations in regenerative tissues may contribute to disease susceptibility and suggesting potential therapeutic strategies to mitigate cancer risk in patients with chronic inflammatory conditions. Read Abstract
• Huang YH, Belk JA, Zhang R, Weiser NE, Chiang Z, Jones MG, Mischel PS, Buenrostro JD, Chang HY. 2025. Unified molecular approach for spatial epigenome, transcriptome, and cell lineages. Proceedings of the National Academy of Sciences of the United States of America. 122(16):e2424070122. Pubmed: 40249782 DOI:10.1073/pnas.2424070122 Huang YH, Belk JA, Zhang R, Weiser NE, Chiang Z, Jones MG, Mischel PS, Buenrostro JD, Chang HY. 2025. Unified molecular approach for spatial epigenome, transcriptome, and cell lineages. Proceedings of the National Academy of Sciences of the United States of America. 122(16):e2424070122. Pubmed: 40249782 DOI:10.1073/pnas.2424070122 Spatial epigenomics and multiomics can provide fine-grained insights into cellular states but their widespread adoption is limited by the requirement for bespoke slides and capture chemistries for each data modality. Here, we present SPatial assay for Accessible chromatin, Cell lineages, and gene Expression with sequencing (SPACE-seq), a method that utilizes polyadenine-tailed epigenomic libraries to enable facile spatial multiomics using standard whole transcriptome reagents. Applying SPACE-seq to a human glioblastoma specimen, we reveal the state of the tumor microenvironment, extrachromosomal DNA copy numbers, and identify putative mitochondrial DNA variants. Read Abstract
• Nagaraja S, Ojeda-Miron L, Zhang R, Oreskovic E, Hu Y, Zeve D, Sharma K, Hyman RR, Zhang Q, Castillo A, Breault DT, Yilmaz ÖH, Buenrostro JD. 2025. Clonal memory of colitis accumulates and promotes tumor growth. bioRxiv : the preprint server for biology. Pubmed: 40027722 DOI:10.1101/2025.02.13.638099 Nagaraja S, Ojeda-Miron L, Zhang R, Oreskovic E, Hu Y, Zeve D, Sharma K, Hyman RR, Zhang Q, Castillo A, Breault DT, Yilmaz ÖH, Buenrostro JD. 2025. Clonal memory of colitis accumulates and promotes tumor growth. bioRxiv : the preprint server for biology. Pubmed: 40027722 DOI:10.1101/2025.02.13.638099 Chronic inflammation is a well-established risk factor for cancer, but the underlying molecular mechanisms remain unclear. Using a mouse model of colitis, we demonstrate that colonic stem cells retain an epigenetic memory of inflammation following disease resolution, characterized by a cumulative gain of activator protein 1 (AP-1) transcription factor activity. Further, we develop SHARE-TRACE, a method that enables simultaneous profiling of gene expression, chromatin accessibility and clonal history in single cells, enabling high resolution tracking of epigenomic memory. This reveals that inflammatory memory is propagated cell-intrinsically and inherited through stem cell lineages, with certain clones demonstrating dramatically stronger memory than others. Finally, we show that colitis primes stem cells for amplified expression of regenerative gene programs following oncogenic mutation that accelerate tumor growth. This includes a subpopulation of tumors that have exceptionally high AP-1 activity and the additional upregulation of pro-oncogenic programs. Together, our findings provide a mechanistic link between chronic inflammation and malignancy, revealing how long-lived epigenetic alterations in regenerative tissues may contribute to disease susceptibility and suggesting potential therapeutic strategies to mitigate cancer risk in patients with chronic inflammatory conditions. Read Abstract
• LaFave LM, Kartha VK, Ma S, Meli K, Del Priore I, Lareau C, Naranjo S, Westcott PMK, Duarte FM, Sankar V, Chiang Z, Brack A, Law T, Hauck H, Okimoto A, Regev A, Buenrostro JD, Jacks T. 2025. Epigenomic State Transitions Characterize Tumor Progression in Mouse Lung Adenocarcinoma. Cancer cell. 43(5):981-984. Pubmed: 40054468 DOI:S1535-6108(25)00077-7 LaFave LM, Kartha VK, Ma S, Meli K, Del Priore I, Lareau C, Naranjo S, Westcott PMK, Duarte FM, Sankar V, Chiang Z, Brack A, Law T, Hauck H, Okimoto A, Regev A, Buenrostro JD, Jacks T. 2025. Epigenomic State Transitions Characterize Tumor Progression in Mouse Lung Adenocarcinoma. Cancer cell. 43(5):981-984. Pubmed: 40054468 DOI:S1535-6108(25)00077-7
• Jacques E, Herzog C, Ying K, Tomusiak A, Kasamoto J, Sehgal R, Paulson S, Reinhard J, Träuble J, Hastings WJ, Tyshkovskiy A, Hägg S, Earls JC, Behrens CE, Lasky-Su J, Zhou G, Morgen E, Tsang JS, Marioni RE, Ma XJ, Stolzing A, Glorioso C, Gootenberg JS, Abudayyeh OO, Argentieri MA, Mak RH, Cox LS, Brack AS, Lauc G, Furman D, Buenrostro JD, Schumacher B, Justice JN, Woods T, Gobel D, Perez VI, Sinclair DA, Maier AB, Barzilai N, Snyder MP, Wyss-Coray T, Horvath S, Ferrucci L, Poganik JR, Moqri M, Gladyshev VN. 2025. Invigorating discovery and clinical translation of aging biomarkers. Nature aging. 5(4):539-543. Pubmed: 40164770 DOI:10.1038/s43587-025-00838-w Jacques E, Herzog C, Ying K, Tomusiak A, Kasamoto J, Sehgal R, Paulson S, Reinhard J, Träuble J, Hastings WJ, Tyshkovskiy A, Hägg S, Earls JC, Behrens CE, Lasky-Su J, Zhou G, Morgen E, Tsang JS, Marioni RE, Ma XJ, Stolzing A, Glorioso C, Gootenberg JS, Abudayyeh OO, Argentieri MA, Mak RH, Cox LS, Brack AS, Lauc G, Furman D, Buenrostro JD, Schumacher B, Justice JN, Woods T, Gobel D, Perez VI, Sinclair DA, Maier AB, Barzilai N, Snyder MP, Wyss-Coray T, Horvath S, Ferrucci L, Poganik JR, Moqri M, Gladyshev VN. 2025. Invigorating discovery and clinical translation of aging biomarkers. Nature aging. 5(4):539-543. Pubmed: 40164770 DOI:10.1038/s43587-025-00838-w

• 2024

• Tay T, Bommakanti G, Jaensch E, Gorthi A, Karapa Reddy I, Hu Y, Zhang R, Doshi AS, Tan SL, Brucklacher-Waldert V, Prickett L, Kurasawa J, Overstreet MG, Criscione S, Buenrostro JD, Mele DA. 2024. Degradation of IKZF1 prevents epigenetic progression of T cell exhaustion in an antigen-specific assay. Cell reports. Medicine. 5(11):101804. Pubmed: 39486420 DOI:10.1016/j.xcrm.2024.101804 Tay T, Bommakanti G, Jaensch E, Gorthi A, Karapa Reddy I, Hu Y, Zhang R, Doshi AS, Tan SL, Brucklacher-Waldert V, Prickett L, Kurasawa J, Overstreet MG, Criscione S, Buenrostro JD, Mele DA. 2024. Degradation of IKZF1 prevents epigenetic progression of T cell exhaustion in an antigen-specific assay. Cell reports. Medicine. 5(11):101804. Pubmed: 39486420 DOI:10.1016/j.xcrm.2024.101804 In cancer, chronic antigen stimulation drives effector T cells to exhaustion, limiting the efficacy of T cell therapies. Recent studies have demonstrated that epigenetic rewiring governs the transition of T cells from effector to exhausted states and makes a subset of exhausted T cells non-responsive to PD1 checkpoint blockade. Here, we describe an antigen-specific assay for T cell exhaustion that generates T cells phenotypically and transcriptionally similar to those found in human tumors. We perform a screen of human epigenetic regulators, identifying IKZF1 as a driver of T cell exhaustion. We determine that the IKZF1 degrader iberdomide prevents exhaustion by blocking chromatin remodeling at T cell effector enhancers and preserving the binding of AP-1, NF-κB, and NFAT. Thus, our study uncovers a role for IKZF1 as a driver of T cell exhaustion through epigenetic modulation, providing a rationale for the use of iberdomide in solid tumors to prevent T cell exhaustion. Copyright © 2024. Published by Elsevier Inc. Read Abstract
• Labade AS, Chiang ZD, Comenho C, Reginato PL, Payne AC, Earl AS, Shrestha R, Duarte FM, Habibi E, Zhang R, Church GM, Boyden ES, Chen F, Buenrostro JD. 2024. Expansion genome sequencing links nuclear abnormalities to hotspots of aberrant euchromatin repression. bioRxiv : the preprint server for biology. Pubmed: 39386718 DOI:10.1101/2024.09.24.614614 Labade AS, Chiang ZD, Comenho C, Reginato PL, Payne AC, Earl AS, Shrestha R, Duarte FM, Habibi E, Zhang R, Church GM, Boyden ES, Chen F, Buenrostro JD. 2024. Expansion genome sequencing links nuclear abnormalities to hotspots of aberrant euchromatin repression. bioRxiv : the preprint server for biology. Pubmed: 39386718 DOI:10.1101/2024.09.24.614614 Microscopy and genomics are both used to characterize cell function, but approaches to connect the two types of information are lacking, particularly at subnuclear resolution. While emerging multiplexed imaging methods can simultaneously localize genomic regions and nuclear proteins, their ability to accurately measure DNA-protein interactions is constrained by the diffraction limit of optical microscopy. Here, we describe expansion in situ genome sequencing (ExIGS), a technology that enables sequencing of genomic DNA and superresolution localization of nuclear proteins in single cells. We applied ExIGS to fibroblast cells derived from an individual with Hutchinson-Gilford progeria syndrome to characterize how variation in nuclear morphology affects spatial chromatin organization. Using this data, we discovered that lamin abnormalities are linked to hotspots of aberrant euchromatin repression that may erode cell identity. Further, we show that lamin abnormalities heterogeneously increase the repressive environment of the nucleus in tissues and aged cells. These results demonstrate that ExIGS may serve as a generalizable platform for connecting nuclear abnormalities to changes in gene regulation across disease contexts. Read Abstract
• Thakore PI, Schnell A, Huang L, Zhao M, Hou Y, Christian E, Zaghouani S, Wang C, Singh V, Singaraju A, Krishnan RK, Kozoriz D, Ma S, Sankar V, Notarbartolo S, Buenrostro JD, Sallusto F, Patsopoulos NA, Rozenblatt-Rosen O, Kuchroo VK, Regev A. 2024. BACH2 regulates diversification of regulatory and proinflammatory chromatin states in T17 cells. Nature immunology. 25(8):1395-1410. Pubmed: 39009838 DOI:10.1038/s41590-024-01901-1 Thakore PI, Schnell A, Huang L, Zhao M, Hou Y, Christian E, Zaghouani S, Wang C, Singh V, Singaraju A, Krishnan RK, Kozoriz D, Ma S, Sankar V, Notarbartolo S, Buenrostro JD, Sallusto F, Patsopoulos NA, Rozenblatt-Rosen O, Kuchroo VK, Regev A. 2024. BACH2 regulates diversification of regulatory and proinflammatory chromatin states in T17 cells. Nature immunology. 25(8):1395-1410. Pubmed: 39009838 DOI:10.1038/s41590-024-01901-1 Interleukin-17 (IL-17)-producing helper T (T17) cells are heterogenous and consist of nonpathogenic T17 (npT17) cells that contribute to tissue homeostasis and pathogenic T17 (pT17) cells that mediate tissue inflammation. Here, we characterize regulatory pathways underlying T17 heterogeneity and discover substantial differences in the chromatin landscape of npT17 and pT17 cells both in vitro and in vivo. Compared to other CD4 T cell subsets, npT17 cells share accessible chromatin configurations with regulatory T cells, whereas pT17 cells exhibit features of both npT17 cells and type 1 helper T (T1) cells. Integrating single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) and single-cell RNA sequencing (scRNA-seq), we infer self-reinforcing and mutually exclusive regulatory networks controlling different cell states and predicted transcription factors regulating T17 cell pathogenicity. We validate that BACH2 promotes immunomodulatory npT17 programs and restrains proinflammatory T1-like programs in T17 cells in vitro and in vivo. Furthermore, human genetics implicate BACH2 in multiple sclerosis. Overall, our work identifies regulators of T17 heterogeneity as potential targets to mitigate autoimmunity. © 2024. The Author(s), under exclusive licence to Springer Nature America, Inc. Read Abstract
• Schiroli G, Kartha V, Duarte FM, Kristiansen TA, Mayerhofer C, Shrestha R, Earl A, Hu Y, Tay T, Rhee C, Buenrostro JD, Scadden DT. 2024. Cell of origin epigenetic priming determines susceptibility to Tet2 mutation. Nature communications. 15(1):4325. Pubmed: 38773071 DOI:10.1038/s41467-024-48508-6 Schiroli G, Kartha V, Duarte FM, Kristiansen TA, Mayerhofer C, Shrestha R, Earl A, Hu Y, Tay T, Rhee C, Buenrostro JD, Scadden DT. 2024. Cell of origin epigenetic priming determines susceptibility to Tet2 mutation. Nature communications. 15(1):4325. Pubmed: 38773071 DOI:10.1038/s41467-024-48508-6 Hematopoietic stem cell (HSC) mutations can result in clonal hematopoiesis (CH) with heterogeneous clinical outcomes. Here, we investigate how the cell state preceding Tet2 mutation impacts the pre-malignant phenotype. Using an inducible system for clonal analysis of myeloid progenitors, we find that the epigenetic features of clones at similar differentiation status are highly heterogeneous and functionally respond differently to Tet2 mutation. Cell differentiation stage also influences Tet2 mutation response indicating that the cell of origin's epigenome modulates clone-specific behaviors in CH. Molecular features associated with higher risk outcomes include Sox4 that sensitizes cells to Tet2 inactivation, inducing dedifferentiation, altered metabolism and increasing the in vivo clonal output of mutant cells, as confirmed in primary GMP and HSC models. Our findings validate the hypothesis that epigenetic features can predispose specific clones for dominance, explaining why identical genetic mutations can result in different phenotypes. © 2024. The Author(s). Read Abstract
• Joung J, Ma S, Tay T, Geiger-Schuller KR, Kirchgatterer PC, Verdine VK, Guo B, Arias-Garcia MA, Allen WE, Singh A, Kuksenko O, Abudayyeh OO, Gootenberg JS, Fu Z, Macrae RK, Buenrostro JD, Regev A, Zhang F. 2024. A transcription factor atlas of directed differentiation. Cell. 187(12):3161. Pubmed: 38697106 DOI:S0092-8674(24)00464-1 Joung J, Ma S, Tay T, Geiger-Schuller KR, Kirchgatterer PC, Verdine VK, Guo B, Arias-Garcia MA, Allen WE, Singh A, Kuksenko O, Abudayyeh OO, Gootenberg JS, Fu Z, Macrae RK, Buenrostro JD, Regev A, Zhang F. 2024. A transcription factor atlas of directed differentiation. Cell. 187(12):3161. Pubmed: 38697106 DOI:S0092-8674(24)00464-1
• De Rop FV, Hulselmans G, Flerin C, Soler-Vila P, Rafels A, Christiaens V, González-Blas CB, Marchese D, Caratù G, Poovathingal S, Rozenblatt-Rosen O, Slyper M, Luo W, Muus C, Duarte F, Shrestha R, Bagdatli ST, Corces MR, Mamanova L, Knights A, Meyer KB, Mulqueen R, Taherinasab A, Maschmeyer P, Pezoldt J, Lambert CLG, Iglesias M, Najle SR, Dossani ZY, Martelotto LG, Burkett Z, Lebofsky R, Martin-Subero JI, Pillai S, Sebé-Pedrós A, Deplancke B, Teichmann SA, Ludwig LS, Braun TP, Adey AC, Greenleaf WJ, Buenrostro JD, Regev A, Aerts S, Heyn H. 2024. Systematic benchmarking of single-cell ATAC-sequencing protocols. Nature biotechnology. 42(6):916-926. Pubmed: 37537502 DOI:10.1038/s41587-023-01881-x De Rop FV, Hulselmans G, Flerin C, Soler-Vila P, Rafels A, Christiaens V, González-Blas CB, Marchese D, Caratù G, Poovathingal S, Rozenblatt-Rosen O, Slyper M, Luo W, Muus C, Duarte F, Shrestha R, Bagdatli ST, Corces MR, Mamanova L, Knights A, Meyer KB, Mulqueen R, Taherinasab A, Maschmeyer P, Pezoldt J, Lambert CLG, Iglesias M, Najle SR, Dossani ZY, Martelotto LG, Burkett Z, Lebofsky R, Martin-Subero JI, Pillai S, Sebé-Pedrós A, Deplancke B, Teichmann SA, Ludwig LS, Braun TP, Adey AC, Greenleaf WJ, Buenrostro JD, Regev A, Aerts S, Heyn H. 2024. Systematic benchmarking of single-cell ATAC-sequencing protocols. Nature biotechnology. 42(6):916-926. Pubmed: 37537502 DOI:10.1038/s41587-023-01881-x Single-cell assay for transposase-accessible chromatin by sequencing (scATAC-seq) has emerged as a powerful tool for dissecting regulatory landscapes and cellular heterogeneity. However, an exploration of systemic biases among scATAC-seq technologies has remained absent. In this study, we benchmark the performance of eight scATAC-seq methods across 47 experiments using human peripheral blood mononuclear cells (PBMCs) as a reference sample and develop PUMATAC, a universal preprocessing pipeline, to handle the various sequencing data formats. Our analyses reveal significant differences in sequencing library complexity and tagmentation specificity, which impact cell-type annotation, genotype demultiplexing, peak calling, differential region accessibility and transcription factor motif enrichment. Our findings underscore the importance of sample extraction, method selection, data processing and total cost of experiments, offering valuable guidance for future research. Finally, our data and analysis pipeline encompasses 169,000 PBMC scATAC-seq profiles and a best practices code repository for scATAC-seq data analysis, which are freely available to extend this benchmarking effort to future protocols. © 2023. The Author(s). Read Abstract

• 2023

• Joung J, Ma S, Tay T, Geiger-Schuller KR, Kirchgatterer PC, Verdine VK, Guo B, Arias-Garcia MA, Allen WE, Singh A, Kuksenko O, Abudayyeh OO, Gootenberg JS, Fu Z, Macrae RK, Buenrostro JD, Regev A, Zhang F. 2023. A transcription factor atlas of directed differentiation. Cell. 186(1):209-229.e26. Pubmed: 36608654 DOI:S0092-8674(22)01470-2 Joung J, Ma S, Tay T, Geiger-Schuller KR, Kirchgatterer PC, Verdine VK, Guo B, Arias-Garcia MA, Allen WE, Singh A, Kuksenko O, Abudayyeh OO, Gootenberg JS, Fu Z, Macrae RK, Buenrostro JD, Regev A, Zhang F. 2023. A transcription factor atlas of directed differentiation. Cell. 186(1):209-229.e26. Pubmed: 36608654 DOI:S0092-8674(22)01470-2 Transcription factors (TFs) regulate gene programs, thereby controlling diverse cellular processes and cell states. To comprehensively understand TFs and the programs they control, we created a barcoded library of all annotated human TF splice isoforms (>3,500) and applied it to build a TF Atlas charting expression profiles of human embryonic stem cells (hESCs) overexpressing each TF at single-cell resolution. We mapped TF-induced expression profiles to reference cell types and validated candidate TFs for generation of diverse cell types, spanning all three germ layers and trophoblasts. Targeted screens with subsets of the library allowed us to create a tailored cellular disease model and integrate mRNA expression and chromatin accessibility data to identify downstream regulators. Finally, we characterized the effects of combinatorial TF overexpression by developing and validating a strategy for predicting combinations of TFs that produce target expression profiles matching reference cell types to accelerate cellular engineering efforts. Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved. Read Abstract
• Hu Y, Ma S, Kartha VK, Duarte FM, Horlbeck M, Zhang R, Shrestha R, Labade A, Kletzien H, Meliki A, Castillo A, Durand N, Mattei E, Anderson LJ, Tay T, Earl AS, Shoresh N, Epstein CB, Wagers A, Buenrostro JD. 2023. Single-cell multi-scale footprinting reveals the modular organization of DNA regulatory elements. bioRxiv : the preprint server for biology. Pubmed: 37034577 DOI:10.1101/2023.03.28.533945 Hu Y, Ma S, Kartha VK, Duarte FM, Horlbeck M, Zhang R, Shrestha R, Labade A, Kletzien H, Meliki A, Castillo A, Durand N, Mattei E, Anderson LJ, Tay T, Earl AS, Shoresh N, Epstein CB, Wagers A, Buenrostro JD. 2023. Single-cell multi-scale footprinting reveals the modular organization of DNA regulatory elements. bioRxiv : the preprint server for biology. Pubmed: 37034577 DOI:10.1101/2023.03.28.533945 Array Read Abstract
• Papathanasiou S, Mynhier NA, Liu S, Brunette G, Stokasimov E, Jacob E, Li L, Comenho C, van Steensel B, Buenrostro JD, Zhang CZ, Pellman D. 2023. Heritable transcriptional defects from aberrations of nuclear architecture. Nature. 619(7968):184-192. Pubmed: 37286600 DOI:10.1038/s41586-023-06157-7 Papathanasiou S, Mynhier NA, Liu S, Brunette G, Stokasimov E, Jacob E, Li L, Comenho C, van Steensel B, Buenrostro JD, Zhang CZ, Pellman D. 2023. Heritable transcriptional defects from aberrations of nuclear architecture. Nature. 619(7968):184-192. Pubmed: 37286600 DOI:10.1038/s41586-023-06157-7 Transcriptional heterogeneity due to plasticity of the epigenetic state of chromatin contributes to tumour evolution, metastasis and drug resistance. However, the mechanisms that cause this epigenetic variation are incompletely understood. Here we identify micronuclei and chromosome bridges, aberrations in the nucleus common in cancer, as sources of heritable transcriptional suppression. Using a combination of approaches, including long-term live-cell imaging and same-cell single-cell RNA sequencing (Look-Seq2), we identified reductions in gene expression in chromosomes from micronuclei. With heterogeneous penetrance, these changes in gene expression can be heritable even after the chromosome from the micronucleus has been re-incorporated into a normal daughter cell nucleus. Concomitantly, micronuclear chromosomes acquire aberrant epigenetic chromatin marks. These defects may persist as variably reduced chromatin accessibility and reduced gene expression after clonal expansion from single cells. Persistent transcriptional repression is strongly associated with, and may be explained by, markedly long-lived DNA damage. Epigenetic alterations in transcription may therefore be inherently coupled to chromosomal instability and aberrations in nuclear architecture. © 2023. The Author(s). Read Abstract
• Mangiameli SM, Chen H, Earl AS, Dobkin JA, Lesman D, Buenrostro JD, Chen F. 2023. Photoselective sequencing: microscopically guided genomic measurements with subcellular resolution. Nature methods. 20(5):686-694. Pubmed: 37106232 DOI:10.1038/s41592-023-01845-8 Mangiameli SM, Chen H, Earl AS, Dobkin JA, Lesman D, Buenrostro JD, Chen F. 2023. Photoselective sequencing: microscopically guided genomic measurements with subcellular resolution. Nature methods. 20(5):686-694. Pubmed: 37106232 DOI:10.1038/s41592-023-01845-8 In biological systems, spatial organization and function are interconnected. Here we present photoselective sequencing, a new method for genomic and epigenomic profiling within morphologically distinct regions. Starting with an intact biological specimen, photoselective sequencing uses targeted illumination to selectively unblock a photocaged fragment library, restricting the sequencing-based readout to microscopically identified spatial regions. We validate photoselective sequencing by measuring the chromatin accessibility profiles of fluorescently labeled cell types within the mouse brain and comparing with published data. Furthermore, by combining photoselective sequencing with a computational strategy for decomposing bulk accessibility profiles, we find that the oligodendrocyte-lineage-cell population is relatively enriched for oligodendrocyte-progenitor cells in the cortex versus the corpus callosum. Finally, we leverage photoselective sequencing at the subcellular scale to identify features of chromatin that are correlated with positioning at the nuclear periphery. These results collectively demonstrate that photoselective sequencing is a flexible and generalizable platform for exploring the interplay of spatial structures with genomic and epigenomic properties. © 2023. The Author(s), under exclusive licence to Springer Nature America, Inc. Read Abstract
• Otto JE, Ursu O, Wu AP, Winter EB, Cuoco MS, Ma S, Qian K, Michel BC, Buenrostro JD, Berger B, Regev A, Kadoch C. 2023. Structural and functional properties of mSWI/SNF chromatin remodeling complexes revealed through single-cell perturbation screens. Molecular cell. 83(8):1350-1367.e7. Pubmed: 37028419 DOI:S1097-2765(23)00203-4 Otto JE, Ursu O, Wu AP, Winter EB, Cuoco MS, Ma S, Qian K, Michel BC, Buenrostro JD, Berger B, Regev A, Kadoch C. 2023. Structural and functional properties of mSWI/SNF chromatin remodeling complexes revealed through single-cell perturbation screens. Molecular cell. 83(8):1350-1367.e7. Pubmed: 37028419 DOI:S1097-2765(23)00203-4 The mammalian SWI/SNF (mSWI/SNF or BAF) family of chromatin remodeling complexes play critical roles in regulating DNA accessibility and gene expression. The three final-form subcomplexes-cBAF, PBAF, and ncBAF-are distinct in biochemical componentry, chromatin targeting, and roles in disease; however, the contributions of their constituent subunits to gene expression remain incompletely defined. Here, we performed Perturb-seq-based CRISPR-Cas9 knockout screens targeting mSWI/SNF subunits individually and in select combinations, followed by single-cell RNA-seq and SHARE-seq. We uncovered complex-, module-, and subunit-specific contributions to distinct regulatory networks and defined paralog subunit relationships and shifted subcomplex functions upon perturbations. Synergistic, intra-complex genetic interactions between subunits reveal functional redundancy and modularity. Importantly, single-cell subunit perturbation signatures mapped across bulk primary human tumor expression profiles both mirror and predict cBAF loss-of-function status in cancer. Our findings highlight the utility of Perturb-seq to dissect disease-relevant gene regulatory impacts of heterogeneous, multi-component master regulatory complexes. Copyright © 2023 The Author(s). Published by Elsevier Inc. All rights reserved. Read Abstract
• Cheong JG, Ravishankar A, Sharma S, Parkhurst CN, Grassmann SA, Wingert CK, Laurent P, Ma S, Paddock L, Miranda IC, Karakaslar EO, Nehar-Belaid D, Thibodeau A, Bale MJ, Kartha VK, Yee JK, Mays MY, Jiang C, Daman AW, Martinez de Paz A, Ahimovic D, Ramos V, Lercher A, Nielsen E, Alvarez-Mulett S, Zheng L, Earl A, Yallowitz A, Robbins L, LaFond E, Weidman KL, Racine-Brzostek S, Yang HS, Price DR, Leyre L, Rendeiro AF, Ravichandran H, Kim J, Borczuk AC, Rice CM, Jones RB, Schenck EJ, Kaner RJ, Chadburn A, Zhao Z, Pascual V, Elemento O, Schwartz RE, Buenrostro JD, Niec RE, Barrat FJ, Lief L, Sun JC, Ucar D, Josefowicz SZ. 2023. Epigenetic memory of coronavirus infection in innate immune cells and their progenitors. Cell. 186(18):3882-3902.e24. Pubmed: 37597510 DOI:S0092-8674(23)00796-1 Cheong JG, Ravishankar A, Sharma S, Parkhurst CN, Grassmann SA, Wingert CK, Laurent P, Ma S, Paddock L, Miranda IC, Karakaslar EO, Nehar-Belaid D, Thibodeau A, Bale MJ, Kartha VK, Yee JK, Mays MY, Jiang C, Daman AW, Martinez de Paz A, Ahimovic D, Ramos V, Lercher A, Nielsen E, Alvarez-Mulett S, Zheng L, Earl A, Yallowitz A, Robbins L, LaFond E, Weidman KL, Racine-Brzostek S, Yang HS, Price DR, Leyre L, Rendeiro AF, Ravichandran H, Kim J, Borczuk AC, Rice CM, Jones RB, Schenck EJ, Kaner RJ, Chadburn A, Zhao Z, Pascual V, Elemento O, Schwartz RE, Buenrostro JD, Niec RE, Barrat FJ, Lief L, Sun JC, Ucar D, Josefowicz SZ. 2023. Epigenetic memory of coronavirus infection in innate immune cells and their progenitors. Cell. 186(18):3882-3902.e24. Pubmed: 37597510 DOI:S0092-8674(23)00796-1 Inflammation can trigger lasting phenotypes in immune and non-immune cells. Whether and how human infections and associated inflammation can form innate immune memory in hematopoietic stem and progenitor cells (HSPC) has remained unclear. We found that circulating HSPC, enriched from peripheral blood, captured the diversity of bone marrow HSPC, enabling investigation of their epigenomic reprogramming following coronavirus disease 2019 (COVID-19). Alterations in innate immune phenotypes and epigenetic programs of HSPC persisted for months to 1 year following severe COVID-19 and were associated with distinct transcription factor (TF) activities, altered regulation of inflammatory programs, and durable increases in myelopoiesis. HSPC epigenomic alterations were conveyed, through differentiation, to progeny innate immune cells. Early activity of IL-6 contributed to these persistent phenotypes in human COVID-19 and a mouse coronavirus infection model. Epigenetic reprogramming of HSPC may underlie altered immune function following infection and be broadly relevant, especially for millions of COVID-19 survivors. Copyright © 2023 Elsevier Inc. All rights reserved. Read Abstract
• Lareau CA, Ludwig LS, Muus C, Gohil SH, Zhao T, Chiang Z, Pelka K, Verboon JM, Luo W, Christian E, Rosebrock D, Getz G, Boland GM, Chen F, Buenrostro JD, Hacohen N, Wu CJ, Aryee MJ, Regev A, Sankaran VG. 2023. Author Correction: Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling. Nature biotechnology. 41(9):1345. Pubmed: 37653227 DOI:10.1038/s41587-023-01942-1 Lareau CA, Ludwig LS, Muus C, Gohil SH, Zhao T, Chiang Z, Pelka K, Verboon JM, Luo W, Christian E, Rosebrock D, Getz G, Boland GM, Chen F, Buenrostro JD, Hacohen N, Wu CJ, Aryee MJ, Regev A, Sankaran VG. 2023. Author Correction: Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling. Nature biotechnology. 41(9):1345. Pubmed: 37653227 DOI:10.1038/s41587-023-01942-1
• Morse DB, Michalowski AM, Ceribelli M, De Jonghe J, Vias M, Riley D, Davies-Hill T, Voss T, Pittaluga S, Muus C, Liu J, Boyle S, Weitz DA, Brenton JD, Buenrostro JD, Knowles TPJ, Thomas CJ. 2023. Positional influence on cellular transcriptional identity revealed through spatially segmented single-cell transcriptomics. Cell systems. 14(6):464-481.e7. Pubmed: 37348462 DOI:S2405-4712(23)00147-3 Morse DB, Michalowski AM, Ceribelli M, De Jonghe J, Vias M, Riley D, Davies-Hill T, Voss T, Pittaluga S, Muus C, Liu J, Boyle S, Weitz DA, Brenton JD, Buenrostro JD, Knowles TPJ, Thomas CJ. 2023. Positional influence on cellular transcriptional identity revealed through spatially segmented single-cell transcriptomics. Cell systems. 14(6):464-481.e7. Pubmed: 37348462 DOI:S2405-4712(23)00147-3 Single-cell RNA sequencing (scRNA-seq) is a powerful technique for describing cell states. Identifying the spatial arrangement of these states in tissues remains challenging, with the existing methods requiring niche methodologies and expertise. Here, we describe segmentation by exogenous perfusion (SEEP), a rapid and integrated method to link surface proximity and environment accessibility to transcriptional identity within three-dimensional (3D) disease models. The method utilizes the steady-state diffusion kinetics of a fluorescent dye to establish a gradient along the radial axis of disease models. Classification of sample layers based on dye accessibility enables dissociated and sorted cells to be characterized by transcriptomic and regional identities. Using SEEP, we analyze spheroid, organoid, and in vivo tumor models of high-grade serous ovarian cancer (HGSOC). The results validate long-standing beliefs about the relationship between cell state and position while revealing new concepts regarding how spatially unique microenvironments influence the identity of individual cells within tumors. Published by Elsevier Inc. Read Abstract

• 2022

• Yuan W, Ma S, Brown JR, Kim K, Murek V, Trastulla L, Meissner A, Lodato S, Shetty AS, Levin JZ, Buenrostro JD, Ziller MJ, Arlotta P. 2022. Temporally divergent regulatory mechanisms govern neuronal diversification and maturation in the mouse and marmoset neocortex. Nature neuroscience. 25(8):1049-1058. Pubmed: 35915179 DOI:10.1038/s41593-022-01123-4 Yuan W, Ma S, Brown JR, Kim K, Murek V, Trastulla L, Meissner A, Lodato S, Shetty AS, Levin JZ, Buenrostro JD, Ziller MJ, Arlotta P. 2022. Temporally divergent regulatory mechanisms govern neuronal diversification and maturation in the mouse and marmoset neocortex. Nature neuroscience. 25(8):1049-1058. Pubmed: 35915179 DOI:10.1038/s41593-022-01123-4 Mammalian neocortical neurons span one of the most diverse cell type spectra of any tissue. Cortical neurons are born during embryonic development, and their maturation extends into postnatal life. The regulatory strategies underlying progressive neuronal development and maturation remain unclear. Here we present an integrated single-cell epigenomic and transcriptional analysis of individual mouse and marmoset cortical neuron classes, spanning both early postmitotic stages of identity acquisition and later stages of neuronal plasticity and circuit integration. We found that, in both species, the regulatory strategies controlling early and late stages of pan-neuronal development diverge. Early postmitotic neurons use more widely shared and evolutionarily conserved molecular regulatory programs. In contrast, programs active during later neuronal maturation are more brain- and neuron-specific and more evolutionarily divergent. Our work uncovers a temporal shift in regulatory choices during neuronal diversification and maturation in both mice and marmosets, which likely reflects unique evolutionary constraints on distinct events of neuronal development in the neocortex. © 2022. The Author(s). Read Abstract
• Uzquiano A, Kedaigle AJ, Pigoni M, Paulsen B, Adiconis X, Kim K, Faits T, Nagaraja S, Antón-Bolaños N, Gerhardinger C, Tucewicz A, Murray E, Jin X, Buenrostro J, Chen F, Velasco S, Regev A, Levin JZ, Arlotta P. 2022. Proper acquisition of cell class identity in organoids allows definition of fate specification programs of the human cerebral cortex. Cell. 185(20):3770-3788.e27. Pubmed: 36179669 DOI:S0092-8674(22)01168-0 Uzquiano A, Kedaigle AJ, Pigoni M, Paulsen B, Adiconis X, Kim K, Faits T, Nagaraja S, Antón-Bolaños N, Gerhardinger C, Tucewicz A, Murray E, Jin X, Buenrostro J, Chen F, Velasco S, Regev A, Levin JZ, Arlotta P. 2022. Proper acquisition of cell class identity in organoids allows definition of fate specification programs of the human cerebral cortex. Cell. 185(20):3770-3788.e27. Pubmed: 36179669 DOI:S0092-8674(22)01168-0 Realizing the full utility of brain organoids to study human development requires understanding whether organoids precisely replicate endogenous cellular and molecular events, particularly since acquisition of cell identity in organoids can be impaired by abnormal metabolic states. We present a comprehensive single-cell transcriptomic, epigenetic, and spatial atlas of human cortical organoid development, comprising over 610,000 cells, from generation of neural progenitors through production of differentiated neuronal and glial subtypes. We show that processes of cellular diversification correlate closely to endogenous ones, irrespective of metabolic state, empowering the use of this atlas to study human fate specification. We define longitudinal molecular trajectories of cortical cell types during organoid development, identify genes with predicted human-specific roles in lineage establishment, and uncover early transcriptional diversity of human callosal neurons. The findings validate this comprehensive atlas of human corticogenesis in vitro as a resource to prime investigation into the mechanisms of human cortical development. Copyright © 2022 Elsevier Inc. All rights reserved. Read Abstract
• Kartha VK, Duarte FM, Hu Y, Ma S, Chew JG, Lareau CA, Earl A, Burkett ZD, Kohlway AS, Lebofsky R, Buenrostro JD. 2022. Functional inference of gene regulation using single-cell multi-omics. Cell genomics. 2(9). Pubmed: 36204155 DOI:10.1016/j.xgen.2022.100166 Kartha VK, Duarte FM, Hu Y, Ma S, Chew JG, Lareau CA, Earl A, Burkett ZD, Kohlway AS, Lebofsky R, Buenrostro JD. 2022. Functional inference of gene regulation using single-cell multi-omics. Cell genomics. 2(9). Pubmed: 36204155 DOI:10.1016/j.xgen.2022.100166 Cells require coordinated control over gene expression when responding to environmental stimuli. Here we apply scATAC-seq and single-cell RNA sequencing (scRNA-seq) in resting and stimulated human blood cells. Collectively, we generate ~91,000 single-cell profiles, allowing us to probe the cis-regulatory landscape of the immunological response across cell types, stimuli, and time. Advancing tools to integrate multi-omics data, we develop functional inference of gene regulation (FigR), a framework to computationally pair scA-TAC-seq with scRNA-seq cells, connect distal cis-regulatory elements to genes, and infer gene-regulatory networks (GRNs) to identify candidate transcription factor (TF) regulators. Utilizing these paired multi-omics data, we define domains of regulatory chromatin (DORCs) of immune stimulation and find that cells alter chromatin accessibility and gene expression at timescales of minutes. Construction of the stimulation GRN elucidates TF activity at disease-associated DORCs. Overall, FigR enables elucidation of regulatory interactions across single-cell data, providing new opportunities to understand the function of cells within tissues. Read Abstract
• Zhao T, Chiang ZD, Morriss JW, LaFave LM, Murray EM, Del Priore I, Meli K, Lareau CA, Nadaf NM, Li J, Earl AS, Macosko EZ, Jacks T, Buenrostro JD, Chen F. 2022. Spatial genomics enables multi-modal study of clonal heterogeneity in tissues. Nature. 601(7891):85-91. Pubmed: 34912115 DOI:10.1038/s41586-021-04217-4 Zhao T, Chiang ZD, Morriss JW, LaFave LM, Murray EM, Del Priore I, Meli K, Lareau CA, Nadaf NM, Li J, Earl AS, Macosko EZ, Jacks T, Buenrostro JD, Chen F. 2022. Spatial genomics enables multi-modal study of clonal heterogeneity in tissues. Nature. 601(7891):85-91. Pubmed: 34912115 DOI:10.1038/s41586-021-04217-4 The state and behaviour of a cell can be influenced by both genetic and environmental factors. In particular, tumour progression is determined by underlying genetic aberrations as well as the makeup of the tumour microenvironment. Quantifying the contributions of these factors requires new technologies that can accurately measure the spatial location of genomic sequence together with phenotypic readouts. Here we developed slide-DNA-seq, a method for capturing spatially resolved DNA sequences from intact tissue sections. We demonstrate that this method accurately preserves local tumour architecture and enables the de novo discovery of distinct tumour clones and their copy number alterations. We then apply slide-DNA-seq to a mouse model of metastasis and a primary human cancer, revealing that clonal populations are confined to distinct spatial regions. Moreover, through integration with spatial transcriptomics, we uncover distinct sets of genes that are associated with clone-specific genetic aberrations, the local tumour microenvironment, or both. Together, this multi-modal spatial genomics approach provides a versatile platform for quantifying how cell-intrinsic and cell-extrinsic factors contribute to gene expression, protein abundance and other cellular phenotypes. © 2021. The Author(s), under exclusive licence to Springer Nature Limited. Read Abstract

• 2021

• Payne AC, Chiang ZD, Reginato PL, Mangiameli SM, Murray EM, Yao CC, Markoulaki S, Earl AS, Labade AS, Jaenisch R, Church GM, Boyden ES, Buenrostro JD, Chen F. 2021. In situ genome sequencing resolves DNA sequence and structure in intact biological samples. Science (New York, N.Y.). 371(6532). Pubmed: 33384301 DOI:10.1126/science.aay3446 Payne AC, Chiang ZD, Reginato PL, Mangiameli SM, Murray EM, Yao CC, Markoulaki S, Earl AS, Labade AS, Jaenisch R, Church GM, Boyden ES, Buenrostro JD, Chen F. 2021. In situ genome sequencing resolves DNA sequence and structure in intact biological samples. Science (New York, N.Y.). 371(6532). Pubmed: 33384301 DOI:10.1126/science.aay3446 Understanding genome organization requires integration of DNA sequence and three-dimensional spatial context; however, existing genome-wide methods lack either base pair sequence resolution or direct spatial localization. Here, we describe in situ genome sequencing (IGS), a method for simultaneously sequencing and imaging genomes within intact biological samples. We applied IGS to human fibroblasts and early mouse embryos, spatially localizing thousands of genomic loci in individual nuclei. Using these data, we characterized parent-specific changes in genome structure across embryonic stages, revealed single-cell chromatin domains in zygotes, and uncovered epigenetic memory of global chromosome positioning within individual embryos. These results demonstrate how IGS can directly connect sequence and structure across length scales from single base pairs to whole organisms. Copyright © 2021 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Read Abstract
• Li Q, Meissner TB, Wang F, Du Z, Ma S, Kshirsagar S, Tilburgs T, Buenrostro JD, Uesugi M, Strominger JL. 2021. ELF3 activated by a superenhancer and an autoregulatory feedback loop is required for high-level HLA-C expression on extravillous trophoblasts. Proceedings of the National Academy of Sciences of the United States of America. 118(9). Pubmed: 33622787 DOI:10.1073/pnas.2025512118 Li Q, Meissner TB, Wang F, Du Z, Ma S, Kshirsagar S, Tilburgs T, Buenrostro JD, Uesugi M, Strominger JL. 2021. ELF3 activated by a superenhancer and an autoregulatory feedback loop is required for high-level HLA-C expression on extravillous trophoblasts. Proceedings of the National Academy of Sciences of the United States of America. 118(9). Pubmed: 33622787 DOI:10.1073/pnas.2025512118 HLA-C arose during evolution of pregnancy in the great apes 10 to 15 million years ago. It has a dual function on placental extravillous trophoblasts (EVTs) as it contributes to both tolerance and immunity at the maternal-fetal interface. The mode of its regulation is of considerable interest in connection with the biology of pregnancy and pregnancy abnormalities. First-trimester primary EVTs in which HLA-C is highly expressed, as well as JEG3, an EVT model cell line, were employed. Single-cell RNA-seq data and quantitative PCR identified high expression of the transcription factor ELF3 in those cells. Chromatin immunoprecipitation (ChIP)-PCR confirmed that both ELF3 and MED1 bound to the proximal HLA-C promoter region. However, binding of RFX5 to this region was absent or severely reduced, and the adjacent HLA-B locus remained closed. Expression of HLA-C was inhibited by ELF3 small interfering RNAs (siRNAs) and by wrenchnolol treatment. Wrenchnolol is a cell-permeable synthetic organic molecule that mimics ELF3 and is relatively specific for binding to ELF3's coactivator, MED23, as our data also showed in JEG3. Moreover, the ELF3 gene is regulated by a superenhancer that spans more than 5 Mb, identified by assay for transposase-accessible chromatin using sequencing (ATAC-seq), as well as by its sensitivity to (+)-JQ1 (inhibitor of BRD4). ELF3 bound to its own promoter, thus creating an autoregulatory feedback loop that establishes expression of ELF3 and HLA-C in trophoblasts. Wrenchnolol blocked binding of MED23 to ELF3, thus disrupting the positive-feedback loop that drives ELF3 expression, with down-regulation of HLA-C expression as a consequence. Copyright © 2021 the Author(s). Published by PNAS. Read Abstract
• Lal A, Chiang ZD, Yakovenko N, Duarte FM, Israeli J, Buenrostro JD. 2021. Deep learning-based enhancement of epigenomics data with AtacWorks. Nature communications. 12(1):1507. Pubmed: 33686069 DOI:10.1038/s41467-021-21765-5 Lal A, Chiang ZD, Yakovenko N, Duarte FM, Israeli J, Buenrostro JD. 2021. Deep learning-based enhancement of epigenomics data with AtacWorks. Nature communications. 12(1):1507. Pubmed: 33686069 DOI:10.1038/s41467-021-21765-5 ATAC-seq is a widely-applied assay used to measure genome-wide chromatin accessibility; however, its ability to detect active regulatory regions can depend on the depth of sequencing coverage and the signal-to-noise ratio. Here we introduce AtacWorks, a deep learning toolkit to denoise sequencing coverage and identify regulatory peaks at base-pair resolution from low cell count, low-coverage, or low-quality ATAC-seq data. Models trained by AtacWorks can detect peaks from cell types not seen in the training data, and are generalizable across diverse sample preparations and experimental platforms. We demonstrate that AtacWorks enhances the sensitivity of single-cell experiments by producing results on par with those of conventional methods using ~10 times as many cells, and further show that this framework can be adapted to enable cross-modality inference of protein-DNA interactions. Finally, we establish that AtacWorks can enable new biological discoveries by identifying active regulatory regions associated with lineage priming in rare subpopulations of hematopoietic stem cells. Read Abstract
• Choi S, Zhang B, Ma S, Gonzalez-Celeiro M, Stein D, Jin X, Kim ST, Kang YL, Besnard A, Rezza A, Grisanti L, Buenrostro JD, Rendl M, Nahrendorf M, Sahay A, Hsu YC. 2021. Corticosterone inhibits GAS6 to govern hair follicle stem-cell quiescence. Nature. 592(7854):428-432. Pubmed: 33790465 DOI:10.1038/s41586-021-03417-2 Choi S, Zhang B, Ma S, Gonzalez-Celeiro M, Stein D, Jin X, Kim ST, Kang YL, Besnard A, Rezza A, Grisanti L, Buenrostro JD, Rendl M, Nahrendorf M, Sahay A, Hsu YC. 2021. Corticosterone inhibits GAS6 to govern hair follicle stem-cell quiescence. Nature. 592(7854):428-432. Pubmed: 33790465 DOI:10.1038/s41586-021-03417-2 Chronic, sustained exposure to stressors can profoundly affect tissue homeostasis, although the mechanisms by which these changes occur are largely unknown. Here we report that the stress hormone corticosterone-which is derived from the adrenal gland and is the rodent equivalent of cortisol in humans-regulates hair follicle stem cell (HFSC) quiescence and hair growth in mice. In the absence of systemic corticosterone, HFSCs enter substantially more rounds of the regeneration cycle throughout life. Conversely, under chronic stress, increased levels of corticosterone prolong HFSC quiescence and maintain hair follicles in an extended resting phase. Mechanistically, corticosterone acts on the dermal papillae to suppress the expression of Gas6, a gene that encodes the secreted factor growth arrest specific 6. Restoring Gas6 expression overcomes the stress-induced inhibition of HFSC activation and hair growth. Our work identifies corticosterone as a systemic inhibitor of HFSC activity through its effect on the niche, and demonstrates that the removal of such inhibition drives HFSCs into frequent regeneration cycles, with no observable defects in the long-term. Read Abstract
• Avagyan S, Weber MC, Ma S, Prasad M, Mannherz WP, Yang S, Buenrostro JD, Zon LI. 2021. Single-cell ATAC-seq reveals GATA2-dependent priming defect in myeloid and a maturation bottleneck in lymphoid lineages. Blood advances. 5(13):2673-2686. Pubmed: 34170284 DOI:10.1182/bloodadvances.2020002992 Avagyan S, Weber MC, Ma S, Prasad M, Mannherz WP, Yang S, Buenrostro JD, Zon LI. 2021. Single-cell ATAC-seq reveals GATA2-dependent priming defect in myeloid and a maturation bottleneck in lymphoid lineages. Blood advances. 5(13):2673-2686. Pubmed: 34170284 DOI:10.1182/bloodadvances.2020002992 Germline heterozygous mutations in GATA2 are associated with a syndrome characterized by cytopenias, atypical infections, and increased risk of hematologic malignancies. Here, we generated a zebrafish mutant of gata2b that recapitulated the myelomonocytopenia and B-cell lymphopenia of GATA2 deficiency syndrome. Using single-cell assay for transposase accessible chromatin with sequencing of marrow cells, we showed that loss of gata2b led to contrasting alterations in chromosome accessibility in early myeloid and lymphoid progenitors, associated with defects in gene expression. Within the myeloid lineage in gata2b mutant zebrafish, we identified an attenuated myeloid differentiation with reduced transcriptional priming and skewing away from the monocytic program. In contrast, in early lymphoid progenitors, gata2b loss led to accumulation of B-lymphoid transcription factor accessibility coupled with increased expression of the B-cell lineage-specification program. However, gata2b mutant zebrafish had incomplete B-cell lymphopoiesis with loss of lineage-specific transcription factor accessibility in differentiating B cells, in the context of aberrantly reduced oxidative metabolic pathways. Our results establish that transcriptional events in early progenitors driven by Gata2 are required to complete normal differentiation. © 2021 by The American Society of Hematology. Read Abstract
• Rose SA, Wroblewska A, Dhainaut M, Yoshida H, Shaffer JM, Bektesevic A, Ben-Zvi B, Rhoads A, Kim EY, Yu B, Lavin Y, Merad M, Buenrostro JD, Brown BD. 2021. A microRNA expression and regulatory element activity atlas of the mouse immune system. Nature immunology. 22(7):914-927. Pubmed: 34099919 DOI:10.1038/s41590-021-00944-y Rose SA, Wroblewska A, Dhainaut M, Yoshida H, Shaffer JM, Bektesevic A, Ben-Zvi B, Rhoads A, Kim EY, Yu B, Lavin Y, Merad M, Buenrostro JD, Brown BD. 2021. A microRNA expression and regulatory element activity atlas of the mouse immune system. Nature immunology. 22(7):914-927. Pubmed: 34099919 DOI:10.1038/s41590-021-00944-y To better define the control of immune system regulation, we generated an atlas of microRNA (miRNA) expression from 63 mouse immune cell populations and connected these signatures with assay for transposase-accessible chromatin using sequencing (ATAC-seq), chromatin immunoprecipitation followed by sequencing (ChIP-seq) and nascent RNA profiles to establish a map of miRNA promoter and enhancer usage in immune cells. miRNA complexity was relatively low, with >90% of the miRNA compartment of each population comprising 87% of the captured sequence originated from the intended target region with sequencing coverage falling within a tenfold range for a majority of all targets. Single nucleotide variants (SNVs) called from OS-Seq data agreed with >95% of variants obtained from whole-genome sequencing of the same individual. We also demonstrate mutation discovery from a colorectal cancer tumor sample matched with normal tissue. Overall, we show the robust performance and utility of OS-Seq for the resequencing analysis of human germline and cancer genomes. Read Abstract

• 2010

• Whittall JB, Syring J, Parks M, Buenrostro J, Dick C, Liston A, Cronn R. 2010. Finding a (pine) needle in a haystack: chloroplast genome sequence divergence in rare and widespread pines. Molecular ecology. 19 Suppl 1:100-14. Pubmed: 20331774 DOI:10.1111/j.1365-294X.2009.04474.x Whittall JB, Syring J, Parks M, Buenrostro J, Dick C, Liston A, Cronn R. 2010. Finding a (pine) needle in a haystack: chloroplast genome sequence divergence in rare and widespread pines. Molecular ecology. 19 Suppl 1:100-14. Pubmed: 20331774 DOI:10.1111/j.1365-294X.2009.04474.x Critical to conservation efforts and other investigations at low taxonomic levels, DNA sequence data offer important insights into the distinctiveness, biogeographic partitioning and evolutionary histories of species. The resolving power of DNA sequences is often limited by insufficient variability at the intraspecific level. This is particularly true of studies involving plant organelles, as the conservative mutation rate of chloroplasts and mitochondria makes it difficult to detect polymorphisms necessary to track genealogical relationships among individuals, populations and closely related taxa, through space and time. Massively parallel sequencing (MPS) makes it possible to acquire entire organelle genome sequences to identify cryptic variation that would be difficult to detect otherwise. We are using MPS to evaluate intraspecific chloroplast-level divergence across biogeographic boundaries in narrowly endemic and widespread species of Pinus. We focus on one of the world's rarest pines - Torrey pine (Pinus torreyana) - due to its conservation interest and because it provides a marked contrast to more widespread pine species. Detailed analysis of nearly 90% ( approximately 105 000 bp each) of these chloroplast genomes shows that mainland and island populations of Torrey pine differ at five sites in their plastome, with the differences fixed between populations. This is an exceptionally low level of divergence (1 polymorphism/ approximately 21 kb), yet it is comparable to intraspecific divergence present in widespread pine species and species complexes. Population-level organelle genome sequencing offers new vistas into the timing and magnitude of divergence within species, and is certain to provide greater insight into pollen dispersal, migration patterns and evolutionary dynamics in plants. Read Abstract

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