1
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Hong CKY, Ramu A, Zhao S, Cohen BA. Effect of genomic and cellular environments on gene expression noise. Genome Biol 2024; 25:137. [PMID: 38790076 PMCID: PMC11127367 DOI: 10.1186/s13059-024-03277-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
BACKGROUND Individual cells from isogenic populations often display large cell-to-cell differences in gene expression. This "noise" in expression derives from several sources, including the genomic and cellular environment in which a gene resides. Large-scale maps of genomic environments have revealed the effects of epigenetic modifications and transcription factor occupancy on mean expression levels, but leveraging such maps to explain expression noise will require new methods to assay how expression noise changes at locations across the genome. RESULTS To address this gap, we present Single-cell Analysis of Reporter Gene Expression Noise and Transcriptome (SARGENT), a method that simultaneously measures the noisiness of reporter genes integrated throughout the genome and the global mRNA profiles of individual reporter-gene-containing cells. Using SARGENT, we perform the first comprehensive genome-wide survey of how genomic locations impact gene expression noise. We find that the mean and noise of expression correlate with different histone modifications. We quantify the intrinsic and extrinsic components of reporter gene noise and, using the associated mRNA profiles, assign the extrinsic component to differences between the CD24+ "stem-like" substate and the more "differentiated" substate. SARGENT also reveals the effects of transgene integrations on endogenous gene expression, which will help guide the search for "safe-harbor" loci. CONCLUSIONS Taken together, we show that SARGENT is a powerful tool to measure both the mean and noise of gene expression at locations across the genome and that the data generatd by SARGENT reveals important insights into the regulation of gene expression noise genome-wide.
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Affiliation(s)
- Clarice K Y Hong
- The Edison Family Center for Genome Sciences and Systems Biology, School of Medicine, Washington University in St. Louis, Saint Louis, MO, 63110, USA
- Department of Genetics, School of Medicine, Washington University in St. Louis, Saint Louis, MO, 63110, USA
| | - Avinash Ramu
- The Edison Family Center for Genome Sciences and Systems Biology, School of Medicine, Washington University in St. Louis, Saint Louis, MO, 63110, USA
- Department of Genetics, School of Medicine, Washington University in St. Louis, Saint Louis, MO, 63110, USA
| | - Siqi Zhao
- The Edison Family Center for Genome Sciences and Systems Biology, School of Medicine, Washington University in St. Louis, Saint Louis, MO, 63110, USA
- Department of Genetics, School of Medicine, Washington University in St. Louis, Saint Louis, MO, 63110, USA
| | - Barak A Cohen
- The Edison Family Center for Genome Sciences and Systems Biology, School of Medicine, Washington University in St. Louis, Saint Louis, MO, 63110, USA.
- Department of Genetics, School of Medicine, Washington University in St. Louis, Saint Louis, MO, 63110, USA.
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2
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Tian H, Luan P, Liu Y, Li G. Tet-mediated DNA methylation dynamics affect chromosome organization. Nucleic Acids Res 2024; 52:3654-3666. [PMID: 38300758 DOI: 10.1093/nar/gkae054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 02/03/2024] Open
Abstract
DNA Methylation is a significant epigenetic modification that can modulate chromosome states, but its role in orchestrating chromosome organization has not been well elucidated. Here we systematically assessed the effects of DNA Methylation on chromosome organization with a multi-omics strategy to capture DNA Methylation and high-order chromosome interaction simultaneously on mouse embryonic stem cells with DNA methylation dioxygenase Tet triple knock-out (Tet-TKO). Globally, upon Tet-TKO, we observed weakened compartmentalization, corresponding to decreased methylation differences between CpG island (CGI) rich and poor domains. Tet-TKO could also induce hypermethylation for the CTCF binding peaks in TAD boundaries and chromatin loop anchors. Accordingly, CTCF peak generally weakened upon Tet-TKO, which results in weakened TAD structure and depletion of long-range chromatin loops. Genes that lost enhancer-promoter looping upon Tet-TKO showed DNA hypermethylation in their gene bodies, which may compensate for the disruption of gene expression. We also observed distinct effects of Tet1 and Tet2 on chromatin organization and increased DNA methylation correlation on spatially interacted fragments upon Tet inactivation. Our work showed the broad effects of Tet inactivation and DNA methylation dynamics on chromosome organization.
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Affiliation(s)
- Hao Tian
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics, Peking University, Beijing 100871, China
| | - Pengfei Luan
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing 100020, China
| | - Yaping Liu
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Guoqiang Li
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics, Peking University, Beijing 100871, China
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3
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Lack N, Altintas UB, Seo JH, Giambartolomei C, Ozturan D, Fortunato B, Nelson G, Goldman S, Adelman K, Hach F, Freedman M. Decoding the Epigenetics and Chromatin Loop Dynamics of Androgen Receptor-Mediated Transcription. RESEARCH SQUARE 2024:rs.3.rs-3854707. [PMID: 38352568 PMCID: PMC10862967 DOI: 10.21203/rs.3.rs-3854707/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
Androgen receptor (AR)-mediated transcription plays a critical role in normal prostate development and prostate cancer growth. AR drives gene expression by binding to thousands of cis-regulatory elements (CRE) that loop to hundreds of target promoters. With multiple CREs interacting with a single promoter, it remains unclear how individual AR bound CREs contribute to gene expression. To characterize the involvement of these CREs, we investigated the AR-driven epigenetic and chromosomal chromatin looping changes. We collected a kinetic multi-omic dataset comprised of steady-state mRNA, chromatin accessibility, transcription factor binding, histone modifications, chromatin looping, and nascent RNA. Using an integrated regulatory network, we found that AR binding induces sequential changes in the epigenetic features at CREs, independent of gene expression. Further, we showed that binding of AR does not result in a substantial rewiring of chromatin loops, but instead increases the contact frequency of pre-existing loops to target promoters. Our results show that gene expression strongly correlates to the changes in contact frequency. We then proposed and experimentally validated an unbalanced multi-enhancer model where the impact on gene expression of AR-bound enhancers is heterogeneous, and is proportional to their contact frequency with target gene promoters. Overall, these findings provide new insight into AR-mediated gene expression upon acute androgen simulation and develop a mechanistic framework to investigate nuclear receptor mediated perturbations.
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4
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Xie B, Dean A. Noncoding function of super enhancer derived mRNA in modulating neighboring gene expression and TAD interaction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.05.570115. [PMID: 38105946 PMCID: PMC10723268 DOI: 10.1101/2023.12.05.570115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Super enhancers are important regulators of gene expression that often overlap with protein-coding genes. However, it is unclear whether the overlapping protein-coding genes and the mRNA derived from them contribute to enhancer activity. Using an erythroid-specific super enhancer that overlaps the Cpox gene as a model, we found that Cpox mRNA has a non-coding function in regulating neighboring protein-coding genes, eRNA expression and TAD interactions. Depletion of Cpox mRNA leads to accumulation of H3K27me3 and release of p300 from the Cpox locus, activating an intra-TAD enhancer and gene expression. Additionally, we identified a head-to-tail interaction between the TAD boundary genes Cpox and Dcbld2 that is facilitated by a novel type of repressive loop anchored by p300 and PRC2/H3K27me3. Our results uncover a regulatory role for mRNA transcribed within a super enhancer context and provide insight into head-to-tail inter-gene interaction in the regulation of gene expression and oncogene activation.
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Affiliation(s)
- Bingning Xie
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Ann Dean
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892, USA
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5
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Yan Y, Tian Y, Wu Z, Zhang K, Yang R. Interchromosomal Colocalization with Parental Genes Is Linked to the Function and Evolution of Mammalian Retrocopies. Mol Biol Evol 2023; 40:msad265. [PMID: 38060983 PMCID: PMC10733166 DOI: 10.1093/molbev/msad265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 10/25/2023] [Accepted: 11/29/2023] [Indexed: 12/22/2023] Open
Abstract
Retrocopies are gene duplicates arising from reverse transcription of mature mRNA transcripts and their insertion back into the genome. While long being regarded as processed pseudogenes, more and more functional retrocopies have been discovered. How the stripped-down retrocopies recover expression capability and become functional paralogs continually intrigues evolutionary biologists. Here, we investigated the function and evolution of retrocopies in the context of 3D genome organization. By mapping retrocopy-parent pairs onto sequencing-based and imaging-based chromatin contact maps in human and mouse cell lines and onto Hi-C interaction maps in 5 other mammals, we found that retrocopies and their parental genes show a higher-than-expected interchromosomal colocalization frequency. The spatial interactions between retrocopies and parental genes occur frequently at loci in active subcompartments and near nuclear speckles. Accordingly, colocalized retrocopies are more actively transcribed and translated and are more evolutionarily conserved than noncolocalized ones. The active transcription of colocalized retrocopies may result from their permissive epigenetic environment and shared regulatory elements with parental genes. Population genetic analysis of retroposed gene copy number variants in human populations revealed that retrocopy insertions are not entirely random in regard to interchromosomal interactions and that colocalized retroposed gene copy number variants are more likely to reach high frequencies, suggesting that both insertion bias and natural selection contribute to the colocalization of retrocopy-parent pairs. Further dissection implies that reduced selection efficacy, rather than positive selection, contributes to the elevated allele frequency of colocalized retroposed gene copy number variants. Overall, our results hint a role of interchromosomal colocalization in the "resurrection" of initially neutral retrocopies.
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Affiliation(s)
- Yubin Yan
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Yuhan Tian
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Zefeng Wu
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Kunling Zhang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Ruolin Yang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
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6
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Tav C, Fournier É, Fournier M, Khadangi F, Baguette A, Côté MC, Silveira MAD, Bérubé-Simard FA, Bourque G, Droit A, Bilodeau S. Glucocorticoid stimulation induces regionalized gene responses within topologically associating domains. Front Genet 2023; 14:1237092. [PMID: 37576549 PMCID: PMC10413275 DOI: 10.3389/fgene.2023.1237092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 07/07/2023] [Indexed: 08/15/2023] Open
Abstract
Transcription-factor binding to cis-regulatory regions regulates the gene expression program of a cell, but occupancy is often a poor predictor of the gene response. Here, we show that glucocorticoid stimulation led to the reorganization of transcriptional coregulators MED1 and BRD4 within topologically associating domains (TADs), resulting in active or repressive gene environments. Indeed, we observed a bias toward the activation or repression of a TAD when their activities were defined by the number of regions gaining and losing MED1 and BRD4 following dexamethasone (Dex) stimulation. Variations in Dex-responsive genes at the RNA levels were consistent with the redistribution of MED1 and BRD4 at the associated cis-regulatory regions. Interestingly, Dex-responsive genes without the differential recruitment of MED1 and BRD4 or binding by the glucocorticoid receptor were found within TADs, which gained or lost MED1 and BRD4, suggesting a role of the surrounding environment in gene regulation. However, the amplitude of the response of Dex-regulated genes was higher when the differential recruitment of the glucocorticoid receptor and transcriptional coregulators was observed, reaffirming the role of transcription factor-driven gene regulation and attributing a lesser role to the TAD environment. These results support a model where a signal-induced transcription factor induces a regionalized effect throughout the TAD, redefining the notion of direct and indirect effects of transcription factors on target genes.
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Affiliation(s)
- Christophe Tav
- Centre de Recherche du CHU de Québec—Université Laval, Axe Oncologie, Québec, QC, Canada
- Centre de Recherche sur le Cancer de l’Université Laval, Québec, QC, Canada
- Centre de Recherche en Données Massives de l’Université Laval, Québec, QC, Canada
| | - Éric Fournier
- Centre de Recherche du CHU de Québec—Université Laval, Axe Oncologie, Québec, QC, Canada
- Centre de Recherche sur le Cancer de l’Université Laval, Québec, QC, Canada
- Centre de Recherche en Données Massives de l’Université Laval, Québec, QC, Canada
| | - Michèle Fournier
- Centre de Recherche du CHU de Québec—Université Laval, Axe Oncologie, Québec, QC, Canada
- Centre de Recherche sur le Cancer de l’Université Laval, Québec, QC, Canada
| | - Fatemeh Khadangi
- Centre de Recherche du CHU de Québec—Université Laval, Axe Oncologie, Québec, QC, Canada
- Centre de Recherche sur le Cancer de l’Université Laval, Québec, QC, Canada
| | - Audrey Baguette
- Department of Human Genetics, Faculty of Medicine, McGill University, Montréal, QC, Canada
| | - Maxime C. Côté
- Centre de Recherche du CHU de Québec—Université Laval, Axe Oncologie, Québec, QC, Canada
- Centre de Recherche sur le Cancer de l’Université Laval, Québec, QC, Canada
| | - Maruhen A. D. Silveira
- Centre de Recherche du CHU de Québec—Université Laval, Axe Oncologie, Québec, QC, Canada
- Centre de Recherche sur le Cancer de l’Université Laval, Québec, QC, Canada
| | - Félix-Antoine Bérubé-Simard
- Centre de Recherche du CHU de Québec—Université Laval, Axe Oncologie, Québec, QC, Canada
- Centre de Recherche sur le Cancer de l’Université Laval, Québec, QC, Canada
| | - Guillaume Bourque
- Department of Human Genetics, Faculty of Medicine, McGill University, Montréal, QC, Canada
- Canadian Center for Computational Genomics, McGill University, Montréal, QC, Canada
| | - Arnaud Droit
- Centre de Recherche sur le Cancer de l’Université Laval, Québec, QC, Canada
- Centre de Recherche en Données Massives de l’Université Laval, Québec, QC, Canada
- Centre de Recherche du CHU de Québec—Université Laval, Axe Endocrinologie et Néphrologie, Québec, QC, Canada
- Département de Médecine Moléculaire, Faculté de Médecine, Université Laval, Québec, QC, Canada
| | - Steve Bilodeau
- Centre de Recherche du CHU de Québec—Université Laval, Axe Oncologie, Québec, QC, Canada
- Centre de Recherche sur le Cancer de l’Université Laval, Québec, QC, Canada
- Centre de Recherche en Données Massives de l’Université Laval, Québec, QC, Canada
- Département de Biologie Moléculaire, Biochimie Médicale et Pathologie, Faculté de Médecine, Université Laval, Québec, QC, Canada
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7
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Li D, Zhao XY, Zhou S, Hu Q, Wu F, Lee HY. Multidimensional profiling reveals GATA1-modulated stage-specific chromatin states and functional associations during human erythropoiesis. Nucleic Acids Res 2023; 51:6634-6653. [PMID: 37254808 PMCID: PMC10359633 DOI: 10.1093/nar/gkad468] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 04/18/2023] [Accepted: 05/13/2023] [Indexed: 06/01/2023] Open
Abstract
Mammalian erythroid development can be divided into three stages: hematopoietic stem and progenitor cell (HSPC), erythroid progenitor (Ery-Pro), and erythroid precursor (Ery-Pre). However, the mechanisms by which the 3D genome changes to establish the stage-specific transcription programs that are critical for erythropoiesis remain unclear. Here, we analyze the chromatin landscape at multiple levels in defined populations from primary human erythroid culture. While compartments and topologically associating domains remain largely unchanged, ∼50% of H3K27Ac-marked enhancers are dynamic in HSPC versus Ery-Pre. The enhancer anchors of enhancer-promoter loops are enriched for occupancy of respective stage-specific transcription factors (TFs), indicating these TFs orchestrate the enhancer connectome rewiring. The master TF of erythropoiesis, GATA1, is found to occupy most erythroid gene promoters at the Ery-Pro stage, and mediate conspicuous local rewiring through acquiring binding at the distal regions in Ery-Pre, promoting productive erythroid transcription output. Knocking out GATA1 binding sites precisely abrogates local rewiring and corresponding gene expression. Interestingly, knocking down GATA1 can transiently revert the cell state to an earlier stage and prolong the window of progenitor state. This study reveals mechanistic insights underlying chromatin rearrangements during development by integrating multidimensional chromatin landscape analyses to associate with transcription output and cellular states.
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Affiliation(s)
- Dong Li
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Xin-Ying Zhao
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Shuo Zhou
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Qi Hu
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Fan Wu
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Hsiang-Ying Lee
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing 100871, China
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8
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Brown AC, Cohen CJ, Mielczarek O, Migliorini G, Costantino F, Allcock A, Davidson C, Elliott KS, Fang H, Lledó Lara A, Martin AC, Osgood JA, Sanniti A, Scozzafava G, Vecellio M, Zhang P, Black MH, Li S, Truong D, Molineros J, Howe T, Wordsworth BP, Bowness P, Knight JC. Comprehensive epigenomic profiling reveals the extent of disease-specific chromatin states and informs target discovery in ankylosing spondylitis. CELL GENOMICS 2023; 3:100306. [PMID: 37388915 PMCID: PMC10300554 DOI: 10.1016/j.xgen.2023.100306] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 01/30/2023] [Accepted: 03/27/2023] [Indexed: 07/01/2023]
Abstract
Ankylosing spondylitis (AS) is a common, highly heritable inflammatory arthritis characterized by enthesitis of the spine and sacroiliac joints. Genome-wide association studies (GWASs) have revealed more than 100 genetic associations whose functional effects remain largely unresolved. Here, we present a comprehensive transcriptomic and epigenomic map of disease-relevant blood immune cell subsets from AS patients and healthy controls. We find that, while CD14+ monocytes and CD4+ and CD8+ T cells show disease-specific differences at the RNA level, epigenomic differences are only apparent upon multi-omics integration. The latter reveals enrichment at disease-associated loci in monocytes. We link putative functional SNPs to genes using high-resolution Capture-C at 10 loci, including PTGER4 and ETS1, and show how disease-specific functional genomic data can be integrated with GWASs to enhance therapeutic target discovery. This study combines epigenetic and transcriptional analysis with GWASs to identify disease-relevant cell types and gene regulation of likely pathogenic relevance and prioritize drug targets.
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Affiliation(s)
- Andrew C. Brown
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Carla J. Cohen
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
- Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7LD, UK
| | - Olga Mielczarek
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Horizon Discovery (PerkinElmer) Cambridge Research Park, 8100 Beach Dr., Waterbeach, Cambridge CB25 9TL, UK
| | - Gabriele Migliorini
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Félicie Costantino
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- UVSQ, INSERM UMR1173, Infection et Inflammation, Laboratory of Excellence INFLAMEX, Université Paris-Saclay, Paris, France
- Rheumatology Department, AP-HP, Ambroise Paré Hospital, Paris, France
| | - Alice Allcock
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Connor Davidson
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7LD, UK
| | | | - Hai Fang
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine at Shanghai, Ruijin Hospital affiliated with Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Alicia Lledó Lara
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Alice C. Martin
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Julie A. Osgood
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Anna Sanniti
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Giuseppe Scozzafava
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Matteo Vecellio
- Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7LD, UK
- Centro Ricerche Fondazione Italiana Ricerca sull’Artrite (FIRA), Fondazione Pisana per la Scienza ONLUS, Via Ferruccio Giovannini 13, 56017 San Giuliano Terme (Pisa), Italy
| | - Ping Zhang
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Chinese Academy of Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Mary Helen Black
- Data Science, Population Analytics, Janssen R&D, Spring House, PA 19002, USA
| | - Shuwei Li
- Data Science, Population Analytics, Janssen R&D, Spring House, PA 19002, USA
| | - Dongnhu Truong
- Data Science, Population Analytics, Janssen R&D, Spring House, PA 19002, USA
| | - Julio Molineros
- Data Science, Population Analytics, Janssen R&D, Spring House, PA 19002, USA
| | - Trevor Howe
- Data Science, External Innovation, Janssen R&D, London W1G 0BG, UK
| | - B. Paul Wordsworth
- Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7LD, UK
- National Institute for Health Research, Comprehensive Biomedical Research Centre, Oxford OX4 2PG, UK
| | - Paul Bowness
- Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7LD, UK
- National Institute for Health Research, Comprehensive Biomedical Research Centre, Oxford OX4 2PG, UK
| | - Julian C. Knight
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Chinese Academy of Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
- National Institute for Health Research, Comprehensive Biomedical Research Centre, Oxford OX4 2PG, UK
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9
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Wright GM, Menzel J, Tatman PD, Black JC. Transition from Transient DNA Rereplication to Inherited Gene Amplification Following Prolonged Environmental Stress. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.08.539886. [PMID: 37214911 PMCID: PMC10197558 DOI: 10.1101/2023.05.08.539886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Cells require the ability to adapt to changing environmental conditions, however, it is unclear how these changes elicit stable permanent changes in genomes. We demonstrate that, in response to environmental metal exposure, the metallothionein (MT) locus undergoes DNA rereplication generating transient site-specific gene amplifications (TSSGs). Chronic metal exposure allows transition from MT TSSG to inherited MT gene amplification through homologous recombination within and outside of the MT locus. DNA rereplication of the MT locus is suppressed by H3K27me3 and EZH2. Long-term ablation of EZH2 activity eventually leads to integration and inheritance of MT gene amplifications without the selective pressure of metal exposure. The rereplication and inheritance of MT gene amplification is an evolutionarily conserved response to environmental metal from yeast to human. Our results describe a new paradigm for adaptation to environmental stress where targeted, transient DNA rereplication precedes stable inherited gene amplification.
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Dozmorov MG, Marshall MA, Rashid NS, Grible JM, Valentine A, Olex AL, Murthy K, Chakraborty A, Reyna J, Figueroa DS, Hinojosa-Gonzalez L, Da-Inn Lee E, Baur BA, Roy S, Ay F, Harrell JC. Rewiring of the 3D genome during acquisition of carboplatin resistance in a triple-negative breast cancer patient-derived xenograft. Sci Rep 2023; 13:5420. [PMID: 37012431 PMCID: PMC10070455 DOI: 10.1038/s41598-023-32568-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 03/29/2023] [Indexed: 04/05/2023] Open
Abstract
Changes in the three-dimensional (3D) structure of the genome are an emerging hallmark of cancer. Cancer-associated copy number variants and single nucleotide polymorphisms promote rewiring of chromatin loops, disruption of topologically associating domains (TADs), active/inactive chromatin state switching, leading to oncogene expression and silencing of tumor suppressors. However, little is known about 3D changes during cancer progression to a chemotherapy-resistant state. We integrated chromatin conformation capture (Hi-C), RNA-seq, and whole-genome sequencing obtained from triple-negative breast cancer patient-derived xenograft primary tumors (UCD52) and carboplatin-resistant samples and found increased short-range (< 2 Mb) interactions, chromatin looping, formation of TAD, chromatin state switching into a more active state, and amplification of ATP-binding cassette transporters. Transcriptome changes suggested the role of long-noncoding RNAs in carboplatin resistance. Rewiring of the 3D genome was associated with TP53, TP63, BATF, FOS-JUN family of transcription factors and led to activation of aggressiveness-, metastasis- and other cancer-related pathways. Integrative analysis highlighted increased ribosome biogenesis and oxidative phosphorylation, suggesting the role of mitochondrial energy metabolism. Our results suggest that 3D genome remodeling may be a key mechanism underlying carboplatin resistance.
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Affiliation(s)
- Mikhail G Dozmorov
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, 23298, USA.
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23284, USA.
| | - Maggie A Marshall
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Narmeen S Rashid
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23284, USA
- Department of Biology, University of Richmond, Richmond, VA, 23173, USA
| | - Jacqueline M Grible
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - Aaron Valentine
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23284, USA
- Department of Biochemistry, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - Amy L Olex
- C. Kenneth and Dianne Wright Center for Clinical and Translational Research, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Kavita Murthy
- Center for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Abhijit Chakraborty
- Center for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Joaquin Reyna
- Center for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Daniela Salgado Figueroa
- Center for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Laura Hinojosa-Gonzalez
- Center for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Erika Da-Inn Lee
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53792, USA
| | - Brittany A Baur
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53792, USA
| | - Sushmita Roy
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53792, USA
| | - Ferhat Ay
- Center for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
- Department of Pediatrics, UC San Diego-School of Medicine, La Jolla, CA, 92093, USA
| | - J Chuck Harrell
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23284, USA.
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11
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Zhang B, Zhang Z, Koeken VA, Kumar S, Aillaud M, Tsay HC, Liu Z, Kraft AR, Soon CF, Odak I, Bošnjak B, Vlot A, Swertz MA, Ohler U, Geffers R, Illig T, Huehn J, Saliba AE, Sander LE, Förster R, Xu CJ, Cornberg M, Schulte LN, Li Y. Altered and allele-specific open chromatin landscape reveals epigenetic and genetic regulators of innate immunity in COVID-19. CELL GENOMICS 2023; 3:100232. [PMID: 36474914 PMCID: PMC9715265 DOI: 10.1016/j.xgen.2022.100232] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 10/21/2022] [Accepted: 11/17/2022] [Indexed: 12/05/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection causes severe COVID-19 in some patients and mild COVID-19 in others. Dysfunctional innate immune responses have been identified to contribute to COVID-19 severity, but the key regulators are still unknown. Here, we present an integrative single-cell multi-omics analysis of peripheral blood mononuclear cells from hospitalized and convalescent COVID-19 patients. In classical monocytes, we identified genes that were potentially regulated by differential chromatin accessibility. Then, sub-clustering and motif-enrichment analyses revealed disease condition-specific regulation by transcription factors and their targets, including an interaction between C/EBPs and a long-noncoding RNA LUCAT1, which we validated through loss-of-function experiments. Finally, we investigated genetic risk variants that exhibit allele-specific open chromatin (ASoC) in COVID-19 patients and identified a SNP rs6800484-C, which is associated with lower expression of CCR2 and may contribute to higher viral loads and higher risk of COVID-19 hospitalization. Altogether, our study highlights the diverse genetic and epigenetic regulators that contribute to COVID-19.
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Affiliation(s)
- Bowen Zhang
- Department of Computational Biology for Individualised Infection Medicine, Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
- TWINCORE, a joint venture between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
- Beijing Normal University, College of Life Sciences, Beijing, China
| | - Zhenhua Zhang
- Department of Computational Biology for Individualised Infection Medicine, Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
- TWINCORE, a joint venture between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
- Genomics Coordination Center, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Valerie A.C.M. Koeken
- Department of Computational Biology for Individualised Infection Medicine, Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
- TWINCORE, a joint venture between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Saumya Kumar
- Department of Computational Biology for Individualised Infection Medicine, Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
- TWINCORE, a joint venture between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
| | - Michelle Aillaud
- Institute for Lung Research, Philipps University, Marburg, Germany
| | - Hsin-Chieh Tsay
- Department of Computational Biology for Individualised Infection Medicine, Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
- TWINCORE, a joint venture between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
| | - Zhaoli Liu
- Department of Computational Biology for Individualised Infection Medicine, Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
- TWINCORE, a joint venture between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
| | - Anke R.M. Kraft
- Department of Computational Biology for Individualised Infection Medicine, Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
- TWINCORE, a joint venture between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
- German Centre for Infection Research (Deutsches Zentrum für Infektionsforschung [DZIF]), Partner Site Hannover-Braunschweig, Hannover, Germany
- Cluster of Excellence Resolving Infection Susceptibility (RESIST; EXC 2155), Hannover Medical School, Hannover, Germany
| | - Chai Fen Soon
- TWINCORE, a joint venture between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Ivan Odak
- Institute of Immunology, Hannover Medical School, Hannover, Germany
| | - Berislav Bošnjak
- Institute of Immunology, Hannover Medical School, Hannover, Germany
| | - Anna Vlot
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Deutsche COVID-19 OMICS Initiative (DeCOI)
- Department of Computational Biology for Individualised Infection Medicine, Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
- TWINCORE, a joint venture between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
- Beijing Normal University, College of Life Sciences, Beijing, China
- Genomics Coordination Center, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, the Netherlands
- Institute for Lung Research, Philipps University, Marburg, Germany
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
- German Centre for Infection Research (Deutsches Zentrum für Infektionsforschung [DZIF]), Partner Site Hannover-Braunschweig, Hannover, Germany
- Cluster of Excellence Resolving Infection Susceptibility (RESIST; EXC 2155), Hannover Medical School, Hannover, Germany
- Institute of Immunology, Hannover Medical School, Hannover, Germany
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Genome Analytics, Helmholtz-Center for Infection Research (HZI), Braunschweig, Germany
- German Center for Lung Research (DZL), Giessen, Germany
- Hannover Unified Biobank, Hannover Medical School, Hannover, Germany
- Department of Experimental Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), Wurzburg, Germany
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Morris A. Swertz
- Genomics Coordination Center, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Uwe Ohler
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Robert Geffers
- Genome Analytics, Helmholtz-Center for Infection Research (HZI), Braunschweig, Germany
| | - Thomas Illig
- German Center for Lung Research (DZL), Giessen, Germany
- Hannover Unified Biobank, Hannover Medical School, Hannover, Germany
| | - Jochen Huehn
- Cluster of Excellence Resolving Infection Susceptibility (RESIST; EXC 2155), Hannover Medical School, Hannover, Germany
- Department of Experimental Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Antoine-Emmanuel Saliba
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), Wurzburg, Germany
| | - Leif Erik Sander
- German Center for Lung Research (DZL), Giessen, Germany
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Reinhold Förster
- German Centre for Infection Research (Deutsches Zentrum für Infektionsforschung [DZIF]), Partner Site Hannover-Braunschweig, Hannover, Germany
- Cluster of Excellence Resolving Infection Susceptibility (RESIST; EXC 2155), Hannover Medical School, Hannover, Germany
- Institute of Immunology, Hannover Medical School, Hannover, Germany
| | - Cheng-Jian Xu
- Department of Computational Biology for Individualised Infection Medicine, Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
- TWINCORE, a joint venture between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Markus Cornberg
- Department of Computational Biology for Individualised Infection Medicine, Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
- TWINCORE, a joint venture between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
- German Centre for Infection Research (Deutsches Zentrum für Infektionsforschung [DZIF]), Partner Site Hannover-Braunschweig, Hannover, Germany
- Cluster of Excellence Resolving Infection Susceptibility (RESIST; EXC 2155), Hannover Medical School, Hannover, Germany
| | - Leon N. Schulte
- Institute for Lung Research, Philipps University, Marburg, Germany
- German Center for Lung Research (DZL), Giessen, Germany
| | - Yang Li
- Department of Computational Biology for Individualised Infection Medicine, Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
- TWINCORE, a joint venture between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, the Netherlands
- Cluster of Excellence Resolving Infection Susceptibility (RESIST; EXC 2155), Hannover Medical School, Hannover, Germany
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12
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Yang BA, Larouche JA, Sabin KM, Fraczek PM, Parker SCJ, Aguilar CA. Three-dimensional chromatin re-organization during muscle stem cell aging. Aging Cell 2023; 22:e13789. [PMID: 36727578 PMCID: PMC10086523 DOI: 10.1111/acel.13789] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/29/2022] [Accepted: 01/11/2023] [Indexed: 02/03/2023] Open
Abstract
Age-related skeletal muscle atrophy or sarcopenia is a significant societal problem that is becoming amplified as the world's population continues to increase. The regeneration of damaged skeletal muscle is mediated by muscle stem cells, but in old age muscle stem cells become functionally attenuated. The molecular mechanisms that govern muscle stem cell aging encompass changes across multiple regulatory layers and are integrated by the three-dimensional organization of the genome. To quantitatively understand how hierarchical chromatin architecture changes during muscle stem cell aging, we generated 3D chromatin conformation maps (Hi-C) and integrated these datasets with multi-omic (chromatin accessibility and transcriptome) profiles from bulk populations and single cells. We observed that muscle stem cells display static behavior at global scales of chromatin organization during aging and extensive rewiring of local contacts at finer scales that were associated with variations in transcription factor binding and aberrant gene expression. These data provide insights into genome topology as a regulator of molecular function in stem cell aging.
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Affiliation(s)
- Benjamin A Yang
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, USA.,Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - Jacqueline A Larouche
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, USA.,Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - Kaitlyn M Sabin
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, USA.,Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - Paula M Fraczek
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, USA.,Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - Stephen C J Parker
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, Michigan, USA.,Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.,Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - Carlos A Aguilar
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, USA.,Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan, USA.,Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, Michigan, USA
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13
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Arce AL, Mencia R, Cambiagno DA, Lang PL, Liu C, Burbano HA, Weigel D, Manavella PA. Polymorphic inverted repeats near coding genes impact chromatin topology and phenotypic traits in Arabidopsis thaliana. Cell Rep 2023; 42:112029. [PMID: 36689329 DOI: 10.1016/j.celrep.2023.112029] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 11/03/2022] [Accepted: 01/10/2023] [Indexed: 01/23/2023] Open
Abstract
Transposons are mobile elements that are commonly silenced to protect eukaryotic genome integrity. In plants, transposable element (TE)-derived inverted repeats (IRs) are commonly found near genes, where they affect host gene expression. However, the molecular mechanisms of such regulation are unclear in most cases. Expression of these IRs is associated with production of 24-nt small RNAs, methylation of the IRs, and drastic changes in local 3D chromatin organization. Notably, many of these IRs differ between Arabidopsis thaliana accessions, causing variation in short-range chromatin interactions and gene expression. CRISPR-Cas9-mediated disruption of two IRs leads to a switch in genome topology and gene expression with phenotypic consequences. Our data show that insertion of an IR near a gene provides an anchor point for chromatin interactions that profoundly impact the activity of neighboring loci. This turns IRs into powerful evolutionary agents that can contribute to rapid adaptation.
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Affiliation(s)
- Agustín L Arce
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Regina Mencia
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Damian A Cambiagno
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Patricia L Lang
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, 72076 Tübingen, Germany
| | - Chang Liu
- Department of Epigenetics, Institute of Biology, University of Hohenheim, Garbenstraße 30, 70599 Stuttgart, Germany
| | - Hernán A Burbano
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, 72076 Tübingen, Germany; Centre for Life's Origins and Evolution, University College London, London, UK
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, 72076 Tübingen, Germany
| | - Pablo A Manavella
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina.
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14
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Three-dimensional chromatin architecture datasets for aging and Alzheimer's disease. Sci Data 2023; 10:51. [PMID: 36693875 PMCID: PMC9873630 DOI: 10.1038/s41597-023-01948-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 01/10/2023] [Indexed: 01/25/2023] Open
Abstract
Recently, increasing studies are indicating a close association between dysregulated enhancers and neurodegenerative diseases, such as Alzheimer's disease (AD). However, their contributions were poorly defined for lacking direct links to disease genes. To bridge this gap, we presented the Hi-C datasets of 4 AD patients, 4 dementia-free aged and 3 young subjects, including 30 billion reads. As applications, we utilized them to link the AD risk SNPs and dysregulated epigenetic marks to the target genes. Combining with epigenetic data, we observed more detailed interactions among regulatory regions and found that many known AD risk genes were under long-distance promoter-enhancer interactions. For future AD and aging studies, our datasets provide a reference landscape to better interpret findings of association and epigenetic studies for AD and aging process.
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15
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Liu N, Sadlon T, Wong YY, Pederson S, Breen J, Barry SC. 3DFAACTS-SNP: using regulatory T cell-specific epigenomics data to uncover candidate mechanisms of type 1 diabetes (T1D) risk. Epigenetics Chromatin 2022; 15:24. [PMID: 35773720 PMCID: PMC9244893 DOI: 10.1186/s13072-022-00456-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 06/06/2022] [Indexed: 11/26/2022] Open
Abstract
Background Genome-wide association studies (GWAS) have enabled the discovery of single nucleotide polymorphisms (SNPs) that are significantly associated with many autoimmune diseases including type 1 diabetes (T1D). However, many of the identified variants lie in non-coding regions, limiting the identification of mechanisms that contribute to autoimmune disease progression. To address this problem, we developed a variant filtering workflow called 3DFAACTS-SNP to link genetic variants to target genes in a cell-specific manner. Here, we use 3DFAACTS-SNP to identify candidate SNPs and target genes associated with the loss of immune tolerance in regulatory T cells (Treg) in T1D. Results Using 3DFAACTS-SNP, we identified from a list of 1228 previously fine-mapped variants, 36 SNPs with plausible Treg-specific mechanisms of action. The integration of cell type-specific chromosome conformation capture data in 3DFAACTS-SNP identified 266 regulatory regions and 47 candidate target genes that interact with these variant-containing regions in Treg cells. We further demonstrated the utility of the workflow by applying it to three other SNP autoimmune datasets, identifying 16 Treg-centric candidate variants and 60 interacting genes. Finally, we demonstrate the broad utility of 3DFAACTS-SNP for functional annotation of all known common (> 10% allele frequency) variants from the Genome Aggregation Database (gnomAD). We identified 9376 candidate variants and 4968 candidate target genes, generating a list of potential sites for future T1D or other autoimmune disease research. Conclusions We demonstrate that it is possible to further prioritise variants that contribute to T1D based on regulatory function, and illustrate the power of using cell type-specific multi-omics datasets to determine disease mechanisms. Our workflow can be customised to any cell type for which the individual datasets for functional annotation have been generated, giving broad applicability and utility. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-022-00456-5.
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Affiliation(s)
- Ning Liu
- South Australian Health and Medical Research Institute, Adelaide, Australia.,Robinson Research Institute, University of Adelaide, Adelaide, Australia.,Bioinformatics Hub, School of Biological Sciences, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, Australia
| | - Timothy Sadlon
- Robinson Research Institute, University of Adelaide, Adelaide, Australia.,Women's and Children's Health Network, Women's and Children's Hospital, Adelaide, Australia
| | - Ying Y Wong
- Robinson Research Institute, University of Adelaide, Adelaide, Australia.,Women's and Children's Health Network, Women's and Children's Hospital, Adelaide, Australia
| | - Stephen Pederson
- Bioinformatics Hub, School of Biological Sciences, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, Australia
| | - James Breen
- South Australian Health and Medical Research Institute, Adelaide, Australia. .,Robinson Research Institute, University of Adelaide, Adelaide, Australia. .,Bioinformatics Hub, School of Biological Sciences, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, Australia. .,Black Ochre Data Labs, Indigenous Genomics, Telethon Kids Institute, Adelaide, Australia. .,John Curtin School of Medical Research, Australian National University, Canberra, Australia.
| | - Simon C Barry
- Robinson Research Institute, University of Adelaide, Adelaide, Australia.,Women's and Children's Health Network, Women's and Children's Hospital, Adelaide, Australia
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16
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Llimos G, Gardeux V, Koch U, Kribelbauer JF, Hafner A, Alpern D, Pezoldt J, Litovchenko M, Russeil J, Dainese R, Moia R, Mahmoud AM, Rossi D, Gaidano G, Plass C, Lutsik P, Gerhauser C, Waszak SM, Boettiger A, Radtke F, Deplancke B. A leukemia-protective germline variant mediates chromatin module formation via transcription factor nucleation. Nat Commun 2022; 13:2042. [PMID: 35440565 PMCID: PMC9018852 DOI: 10.1038/s41467-022-29625-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 03/24/2022] [Indexed: 12/13/2022] Open
Abstract
Non-coding variants coordinate transcription factor (TF) binding and chromatin mark enrichment changes over regions spanning >100 kb. These molecularly coordinated regions are named “variable chromatin modules” (VCMs), providing a conceptual framework of how regulatory variation might shape complex traits. To better understand the molecular mechanisms underlying VCM formation, here, we mechanistically dissect a VCM-modulating noncoding variant that is associated with reduced chronic lymphocytic leukemia (CLL) predisposition and disease progression. This common, germline variant constitutes a 5-bp indel that controls the activity of an AXIN2 gene-linked VCM by creating a MEF2 binding site, which, upon binding, activates a super-enhancer-like regulatory element. This triggers a large change in TF binding activity and chromatin state at an enhancer cluster spanning >150 kb, coinciding with subtle, long-range chromatin compaction and robust AXIN2 up-regulation. Our results support a model in which the indel acts as an AXIN2 VCM-activating TF nucleation event, which modulates CLL pathology. Non-coding variants can regulate transcription factor binding and gene expression at variable chromatin modules. Here, the authors show that a germline variant induces transcription factor nucleation through chromatin compaction leading to AXIN2 up-regulation and is associated to better prognosis in chronic lymphocytic leukaemia.
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Affiliation(s)
- Gerard Llimos
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Vincent Gardeux
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Ute Koch
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Judith F Kribelbauer
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Antonina Hafner
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
| | - Daniel Alpern
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Joern Pezoldt
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Maria Litovchenko
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Cancer Research UK Lung Cancer Centre of Excellence, University College London (UCL) Cancer Institute, Cancer Genome Evolution Research Group, London, UK
| | - Julie Russeil
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Riccardo Dainese
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Riccardo Moia
- Division of Hematology, Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - Abdurraouf Mokhtar Mahmoud
- Division of Hematology, Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - Davide Rossi
- Oncology Institute of Southern Switzerland, Università della Svizzera italiana, Bellinzona, Switzerland.,Institute of Oncology Research, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Gianluca Gaidano
- Division of Hematology, Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - Christoph Plass
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Pavlo Lutsik
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Clarissa Gerhauser
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sebastian M Waszak
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, Oslo, Norway.,Department of Pediatric Research, Division of Paediatric and Adolescent Medicine, Rikshospitalet, Oslo University Hospital, Oslo, Norway
| | - Alistair Boettiger
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
| | - Freddy Radtke
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Bart Deplancke
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland. .,Swiss Institute of Bioinformatics, Lausanne, Switzerland.
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17
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Chua EHZ, Yasar S, Harmston N. The importance of considering regulatory domains in genome-wide analyses - the nearest gene is often wrong! Biol Open 2022; 11:274931. [PMID: 35377406 PMCID: PMC9002814 DOI: 10.1242/bio.059091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The expression of a large number of genes is regulated by regulatory elements that are located far away from their promoters. Identifying which gene is the target of a specific regulatory element or is affected by a non-coding mutation is often accomplished by assigning these regions to the nearest gene in the genome. However, this heuristic ignores key features of genome organisation and gene regulation; in that the genome is partitioned into regulatory domains, which at some loci directly coincide with the span of topologically associated domains (TADs), and that genes are regulated by enhancers located throughout these regions, even across intervening genes. In this review, we examine the results from genome-wide studies using chromosome conformation capture technologies and from those dissecting individual gene regulatory domains, to highlight that the phenomenon of enhancer skipping is pervasive and affects multiple types of genes. We discuss how simply assigning a genomic region of interest to its nearest gene is problematic and often leads to incorrect predictions and highlight that where possible information on both the conservation and topological organisation of the genome should be used to generate better hypotheses. The article has an associated Future Leader to Watch interview. Summary: Identifying which gene is the target of an enhancer is often accomplished by assigning it to the nearest gene, here we discuss how this heuristic can lead to incorrect predictions.
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Affiliation(s)
| | - Samen Yasar
- Science Division, Yale-NUS College, Singapore 138527, Singapore
| | - Nathan Harmston
- Science Division, Yale-NUS College, Singapore 138527, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore
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18
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Ankill J, Aure MR, Bjørklund S, Langberg S, Kristensen VN, Vitelli V, Tekpli X, Fleischer T. Epigenetic alterations at distal enhancers are linked to proliferation in human breast cancer. NAR Cancer 2022; 4:zcac008. [PMID: 35350772 PMCID: PMC8947789 DOI: 10.1093/narcan/zcac008] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 02/23/2022] [Accepted: 03/14/2022] [Indexed: 11/26/2022] Open
Abstract
Aberrant DNA methylation is an early event in breast carcinogenesis and plays a critical role in regulating gene expression. Here, we perform genome-wide expression-methylation Quantitative Trait Loci (emQTL) analysis through the integration of DNA methylation and gene expression to identify disease-driving pathways under epigenetic control. By grouping the emQTLs using biclustering we identify associations representing important biological processes associated with breast cancer pathogenesis including regulation of proliferation and tumor-infiltrating fibroblasts. We report genome-wide loss of enhancer methylation at binding sites of proliferation-driving transcription factors including CEBP-β, FOSL1, and FOSL2 with concomitant high expression of proliferation-related genes in aggressive breast tumors as we confirm with scRNA-seq. The identified emQTL-CpGs and genes were found connected through chromatin loops, indicating that proliferation in breast tumors is under epigenetic regulation by DNA methylation. Interestingly, the associations between enhancer methylation and proliferation-related gene expression were also observed within known subtypes of breast cancer, suggesting a common role of epigenetic regulation of proliferation. Taken together, we show that proliferation in breast cancer is linked to loss of methylation at specific enhancers and transcription factor binding and gene activation through chromatin looping.
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Affiliation(s)
- Jørgen Ankill
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Miriam Ragle Aure
- Department of Medical Genetics, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Sunniva Bjørklund
- Department of Medical Genetics, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | | | | | - Vessela N Kristensen
- Department of Medical Genetics, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Valeria Vitelli
- Oslo Centre for Biostatistics and Epidemiology, Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Xavier Tekpli
- Department of Medical Genetics, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Thomas Fleischer
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
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19
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Hait TA, Elkon R, Shamir R. CT-FOCS: a novel method for inferring cell type-specific enhancer–promoter maps. Nucleic Acids Res 2022; 50:e55. [PMID: 35100425 PMCID: PMC9178001 DOI: 10.1093/nar/gkac048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 01/09/2022] [Accepted: 01/15/2022] [Indexed: 11/13/2022] Open
Abstract
Spatiotemporal gene expression patterns are governed to a large extent by the activity of enhancer elements, which engage in physical contacts with their target genes. Identification of enhancer–promoter (EP) links that are functional only in a specific subset of cell types is a key challenge in understanding gene regulation. We introduce CT-FOCS (cell type FOCS), a statistical inference method that uses linear mixed effect models to infer EP links that show marked activity only in a single or a small subset of cell types out of a large panel of probed cell types. Analyzing 808 samples from FANTOM5, covering 472 cell lines, primary cells and tissues, CT-FOCS inferred such EP links more accurately than recent state-of-the-art methods. Furthermore, we show that strictly cell type-specific EP links are very uncommon in the human genome.
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Affiliation(s)
- Tom Aharon Hait
- The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ron Shamir
- The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
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20
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Warwick T, Schulz MH, Gilsbach R, Brandes RP, Seuter S. OUP accepted manuscript. Nucleic Acids Res 2022; 50:3745-3763. [PMID: 35325193 PMCID: PMC9023275 DOI: 10.1093/nar/gkac178] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 02/23/2022] [Accepted: 03/07/2022] [Indexed: 12/02/2022] Open
Abstract
Spatial genome organization is tightly controlled by several regulatory mechanisms and is essential for gene expression control. Nuclear receptors are ligand-activated transcription factors that modulate physiological and pathophysiological processes and are primary pharmacological targets. DNA binding of the important loop-forming insulator protein CCCTC-binding factor (CTCF) was modulated by 1α,25-dihydroxyvitamin D3 (1,25(OH)2D3). We performed CTCF HiChIP assays to produce the first genome-wide dataset of CTCF long-range interactions in 1,25(OH)2D3-treated cells, and to determine whether dynamic changes of spatial chromatin interactions are essential for fine-tuning of nuclear receptor signaling. We detected changes in 3D chromatin organization upon vitamin D receptor (VDR) activation at 3.1% of all observed CTCF interactions. VDR binding was enriched at both differential loop anchors and within differential loops. Differential loops were observed in several putative functional roles including TAD border formation, promoter-enhancer looping, and establishment of VDR-responsive insulated neighborhoods. Vitamin D target genes were enriched in differential loops and at their anchors. Secondary vitamin D effects related to dynamic chromatin domain changes were linked to location of downstream transcription factors in differential loops. CRISPR interference and loop anchor deletion experiments confirmed the functional relevance of nuclear receptor ligand-induced adjustments of the chromatin 3D structure for gene expression regulation.
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Affiliation(s)
- Timothy Warwick
- Institute for Cardiovascular Physiology, Goethe University, Frankfurt/Main, Germany
- German Center for Cardiovascular Research (DZHK), Partner site Rhein-Main 60590, Frankfurt am Main, Germany
| | - Marcel H Schulz
- Institute for Cardiovascular Regeneration, Goethe University, Frankfurt/Main, Germany
- German Center for Cardiovascular Research (DZHK), Partner site Rhein-Main 60590, Frankfurt am Main, Germany
| | - Ralf Gilsbach
- Institute for Cardiovascular Physiology, Goethe University, Frankfurt/Main, Germany
- German Center for Cardiovascular Research (DZHK), Partner site Rhein-Main 60590, Frankfurt am Main, Germany
| | - Ralf P Brandes
- Institute for Cardiovascular Physiology, Goethe University, Frankfurt/Main, Germany
- German Center for Cardiovascular Research (DZHK), Partner site Rhein-Main 60590, Frankfurt am Main, Germany
| | - Sabine Seuter
- To whom correspondence should be addressed. Tel: +49 69 6301 6996,
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21
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Huang CCF, Lingadahalli S, Morova T, Ozturan D, Hu E, Yu IPL, Linder S, Hoogstraat M, Stelloo S, Sar F, van der Poel H, Altintas UB, Saffarzadeh M, Le Bihan S, McConeghy B, Gokbayrak B, Feng FY, Gleave ME, Bergman AM, Collins C, Hach F, Zwart W, Emberly E, Lack NA. Functional mapping of androgen receptor enhancer activity. Genome Biol 2021; 22:149. [PMID: 33975627 PMCID: PMC8112059 DOI: 10.1186/s13059-021-02339-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 04/02/2021] [Indexed: 01/22/2023] Open
Abstract
Background Androgen receptor (AR) is critical to the initiation, growth, and progression of prostate cancer. Once activated, the AR binds to cis-regulatory enhancer elements on DNA that drive gene expression. Yet, there are 10–100× more binding sites than differentially expressed genes. It is unclear how or if these excess binding sites impact gene transcription. Results To characterize the regulatory logic of AR-mediated transcription, we generated a locus-specific map of enhancer activity by functionally testing all common clinical AR binding sites with Self-Transcribing Active Regulatory Regions sequencing (STARRseq). Only 7% of AR binding sites displayed androgen-dependent enhancer activity. Instead, the vast majority of AR binding sites were either inactive or constitutively active enhancers. These annotations strongly correlated with enhancer-associated features of both in vitro cell lines and clinical prostate cancer samples. Evaluating the effect of each enhancer class on transcription, we found that AR-regulated enhancers frequently interact with promoters and form central chromosomal loops that are required for transcription. Somatic mutations of these critical AR-regulated enhancers often impact enhancer activity. Conclusions Using a functional map of AR enhancer activity, we demonstrated that AR-regulated enhancers act as a regulatory hub that increases interactions with other AR binding sites and gene promoters.
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Affiliation(s)
- Chia-Chi Flora Huang
- Vancouver Prostate Centre, Department of Urologic Science, University of British Columbia, Vancouver, Canada
| | - Shreyas Lingadahalli
- Vancouver Prostate Centre, Department of Urologic Science, University of British Columbia, Vancouver, Canada
| | - Tunc Morova
- Vancouver Prostate Centre, Department of Urologic Science, University of British Columbia, Vancouver, Canada
| | - Dogancan Ozturan
- School of Medicine, Koç University, Istanbul, Turkey.,Koç University Research Centre for Translational Medicine (KUTTAM), Koç University, Istanbul, Turkey
| | - Eugene Hu
- Department of Physics, Simon Fraser University, Burnaby, Canada
| | - Ivan Pak Lok Yu
- Vancouver Prostate Centre, Department of Urologic Science, University of British Columbia, Vancouver, Canada
| | - Simon Linder
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Marlous Hoogstraat
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Suzan Stelloo
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Funda Sar
- Vancouver Prostate Centre, Department of Urologic Science, University of British Columbia, Vancouver, Canada
| | - Henk van der Poel
- Division of Urology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Umut Berkay Altintas
- School of Medicine, Koç University, Istanbul, Turkey.,Koç University Research Centre for Translational Medicine (KUTTAM), Koç University, Istanbul, Turkey
| | - Mohammadali Saffarzadeh
- Vancouver Prostate Centre, Department of Urologic Science, University of British Columbia, Vancouver, Canada
| | - Stephane Le Bihan
- Vancouver Prostate Centre, Department of Urologic Science, University of British Columbia, Vancouver, Canada
| | - Brian McConeghy
- Vancouver Prostate Centre, Department of Urologic Science, University of British Columbia, Vancouver, Canada
| | - Bengul Gokbayrak
- School of Medicine, Koç University, Istanbul, Turkey.,Koç University Research Centre for Translational Medicine (KUTTAM), Koç University, Istanbul, Turkey
| | - Felix Y Feng
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, USA
| | - Martin E Gleave
- Vancouver Prostate Centre, Department of Urologic Science, University of British Columbia, Vancouver, Canada
| | - Andries M Bergman
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Division of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Colin Collins
- Vancouver Prostate Centre, Department of Urologic Science, University of British Columbia, Vancouver, Canada
| | - Faraz Hach
- Vancouver Prostate Centre, Department of Urologic Science, University of British Columbia, Vancouver, Canada
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Department of Biomedical Engineering, Eindhoven University of Technology, Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven, The Netherlands
| | - Eldon Emberly
- Department of Physics, Simon Fraser University, Burnaby, Canada
| | - Nathan A Lack
- Vancouver Prostate Centre, Department of Urologic Science, University of British Columbia, Vancouver, Canada. .,School of Medicine, Koç University, Istanbul, Turkey. .,Koç University Research Centre for Translational Medicine (KUTTAM), Koç University, Istanbul, Turkey.
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22
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Tsybulskyi V, Mounir M, Meyer IM. R-chie: a web server and R package for visualizing cis and trans RNA-RNA, RNA-DNA and DNA-DNA interactions. Nucleic Acids Res 2020; 48:e105. [PMID: 32976561 PMCID: PMC7544209 DOI: 10.1093/nar/gkaa708] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 06/25/2020] [Accepted: 09/22/2020] [Indexed: 12/15/2022] Open
Abstract
Interactions between biological entities are key to understanding their potential functional roles. Three fields of research have recently made particular progress: the investigation of transRNA-RNA and RNA-DNA transcriptome interactions and of trans DNA-DNA genome interactions. We now have both experimental and computational methods for examining these interactions in vivo and on a transcriptome- and genome-wide scale, respectively. Often, key insights can be gained by visually inspecting figures that manage to combine different sources of evidence and quantitative information. We here present R-chie, a web server and R package for visualizing cis and transRNA-RNA, RNA-DNA and DNA-DNA interactions. For this, we have completely revised and significantly extended an earlier version of R-chie (1) which was initially introduced for visualizing RNA secondary structure features. The new R-chie offers a range of unique features for visualizing cis and transRNA-RNA, RNA-DNA and DNA-DNA interactions. Particularly note-worthy features include the ability to incorporate evolutionary information, e.g. multiple-sequence alignments, to compare two alternative sets of information and to incorporate detailed, quantitative information. R-chie is readily available via a web server as well as a corresponding R package called R4RNA which can be used to run the software locally.
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Affiliation(s)
- Volodymyr Tsybulskyi
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str. 28, 10115 Berlin, Germany.,Freie Universität Berlin, Department of Mathematics and Computer Science, Bioinformatics Division, Takustr. 9, 14195 Berlin, Germany
| | - Mohamed Mounir
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str. 28, 10115 Berlin, Germany
| | - Irmtraud M Meyer
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str. 28, 10115 Berlin, Germany.,Freie Universität Berlin, Department of Biology, Chemistry and Pharmacy, Institute of Chemistry and Biochemistry, Thielallee 63, 14195 Berlin, Germany
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23
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Hu G, Dong X, Gong S, Song Y, Hutchins AP, Yao H. Systematic screening of CTCF binding partners identifies that BHLHE40 regulates CTCF genome-wide distribution and long-range chromatin interactions. Nucleic Acids Res 2020; 48:9606-9620. [PMID: 32885250 PMCID: PMC7515718 DOI: 10.1093/nar/gkaa705] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 07/27/2020] [Accepted: 08/14/2020] [Indexed: 11/14/2022] Open
Abstract
CTCF plays a pivotal role in mediating chromatin interactions, but it does not do so alone. A number of factors have been reported to co-localize with CTCF and regulate CTCF loops, but no comprehensive analysis of binding partners has been performed. This prompted us to identify CTCF loop participants and regulators by co-localization analysis with CTCF. We screened all factors that had ChIP-seq data in humans by co-localization analysis with human super conserved CTCF (hscCTCF) binding sites, and identified many new factors that overlapped with hscCTCF binding sites. Combined with CTCF loop information, we observed that clustered factors could promote CTCF loops. After in-depth mining of each factor, we found that many factors might have the potential to promote CTCF loops. Our data further demonstrated that BHLHE40 affected CTCF loops by regulating CTCF binding. Together, this study revealed that many factors have the potential to participate in or regulate CTCF loops, and discovered a new role for BHLHE40 in modulating CTCF loop formation.
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Affiliation(s)
- Gongcheng Hu
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou 510005, China.,Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaotao Dong
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou 510005, China.,Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shixin Gong
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou 510005, China.,Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yawei Song
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou 510005, China.,Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Andrew P Hutchins
- Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
| | - Hongjie Yao
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou 510005, China.,Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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24
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Fernandez LR, Gilgenast TG, Phillips-Cremins JE. 3DeFDR: statistical methods for identifying cell type-specific looping interactions in 5C and Hi-C data. Genome Biol 2020; 21:219. [PMID: 32859248 PMCID: PMC7496221 DOI: 10.1186/s13059-020-02061-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 05/27/2020] [Indexed: 11/18/2022] Open
Abstract
An important unanswered question in chromatin biology is the extent to which long-range looping interactions change across developmental models, genetic perturbations, drug treatments, and disease states. Computational tools for rigorous assessment of cell type-specific loops across multiple biological conditions are needed. We present 3DeFDR, a simple and effective statistical tool for classifying dynamic loops across biological conditions from Chromosome-Conformation-Capture-Carbon-Copy (5C) and Hi-C data. Our work provides a statistical framework and open-source coding libraries for sensitive detection of cell type-specific loops in high-resolution 5C and Hi-C data from multiple cellular conditions.
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Affiliation(s)
- Lindsey R Fernandez
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Thomas G Gilgenast
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jennifer E Phillips-Cremins
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA. .,Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA. .,Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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25
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de Anda-Jáuregui G, Hernández-Lemus E. Computational Oncology in the Multi-Omics Era: State of the Art. Front Oncol 2020; 10:423. [PMID: 32318338 PMCID: PMC7154096 DOI: 10.3389/fonc.2020.00423] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 03/10/2020] [Indexed: 12/24/2022] Open
Abstract
Cancer is the quintessential complex disease. As technologies evolve faster each day, we are able to quantify the different layers of biological elements that contribute to the emergence and development of malignancies. In this multi-omics context, the use of integrative approaches is mandatory in order to gain further insights on oncological phenomena, and to move forward toward the precision medicine paradigm. In this review, we will focus on computational oncology as an integrative discipline that incorporates knowledge from the mathematical, physical, and computational fields to further the biomedical understanding of cancer. We will discuss the current roles of computation in oncology in the context of multi-omic technologies, which include: data acquisition and processing; data management in the clinical and research settings; classification, diagnosis, and prognosis; and the development of models in the research setting, including their use for therapeutic target identification. We will discuss the machine learning and network approaches as two of the most promising emerging paradigms, in computational oncology. These approaches provide a foundation on how to integrate different layers of biological description into coherent frameworks that allow advances both in the basic and clinical settings.
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Affiliation(s)
- Guillermo de Anda-Jáuregui
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico
- Cátedras Conacyt Para Jóvenes Investigadores, National Council on Science and Technology, Mexico City, Mexico
| | - Enrique Hernández-Lemus
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico
- Center for Complexity Sciences, Universidad Nacional Autónoma de México, Mexico City, Mexico
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26
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Ibn-Salem J, Andrade-Navarro MA. 7C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs. BMC Genomics 2019; 20:777. [PMID: 31653198 PMCID: PMC6814980 DOI: 10.1186/s12864-019-6088-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 09/09/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Knowledge of the three-dimensional structure of the genome is necessary to understand how gene expression is regulated. Recent experimental techniques such as Hi-C or ChIA-PET measure long-range chromatin interactions genome-wide but are experimentally elaborate, have limited resolution and such data is only available for a limited number of cell types and tissues. RESULTS While ChIP-seq was not designed to detect chromatin interactions, the formaldehyde treatment in the ChIP-seq protocol cross-links proteins with each other and with DNA. Consequently, also regions that are not directly bound by the targeted TF but interact with the binding site via chromatin looping are co-immunoprecipitated and sequenced. This produces minor ChIP-seq signals at loop anchor regions close to the directly bound site. We use the position and shape of ChIP-seq signals around CTCF motif pairs to predict whether they interact or not. We implemented this approach in a prediction method, termed Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs (7C). We applied 7C to all CTCF motif pairs within 1 Mb in the human genome and validated predicted interactions with high-resolution Hi-C and ChIA-PET. A single ChIP-seq experiment from known architectural proteins (CTCF, Rad21, Znf143) but also from other TFs (like TRIM22 or RUNX3) predicts loops accurately. Importantly, 7C predicts loops in cell types and for TF ChIP-seq datasets not used in training. CONCLUSION 7C predicts chromatin loops which can help to associate TF binding sites to regulated genes. Furthermore, profiling of hundreds of ChIP-seq datasets results in novel candidate factors functionally involved in chromatin looping. Our method is available as an R/Bioconductor package: http://bioconductor.org/packages/sevenC .
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Affiliation(s)
- Jonas Ibn-Salem
- Faculty of Biology, Johannes Gutenberg University of Mainz, 55128, Mainz, Germany.
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27
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Ing-Simmons E, Vaquerizas JM. Visualising three-dimensional genome organisation in two dimensions. Development 2019; 146:146/19/dev177162. [PMID: 31558569 DOI: 10.1242/dev.177162] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The three-dimensional organisation of the genome plays a crucial role in developmental gene regulation. In recent years, techniques to investigate this organisation have become more accessible to labs worldwide due to improvements in protocols and decreases in the cost of high-throughput sequencing. However, the resulting datasets are complex and can be challenging to analyse and interpret. Here, we provide a guide to visualisation approaches that can aid the interpretation of such datasets and the communication of biological results.
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Affiliation(s)
- Elizabeth Ing-Simmons
- Max Planck Institute for Molecular Biomedicine, Roentgenstrasse 20, DE-48149 Muenster, Germany
| | - Juan M Vaquerizas
- Max Planck Institute for Molecular Biomedicine, Roentgenstrasse 20, DE-48149 Muenster, Germany
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28
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Ling SC, Dastidar SG, Tokunaga S, Ho WY, Lim K, Ilieva H, Parone PA, Tyan SH, Tse TM, Chang JC, Platoshyn O, Bui NB, Bui A, Vetto A, Sun S, McAlonis-Downes M, Han JS, Swing D, Kapeli K, Yeo GW, Tessarollo L, Marsala M, Shaw CE, Tucker-Kellogg G, La Spada AR, Lagier-Tourenne C, Da Cruz S, Cleveland DW. Overriding FUS autoregulation in mice triggers gain-of-toxic dysfunctions in RNA metabolism and autophagy-lysosome axis. eLife 2019; 8:40811. [PMID: 30747709 PMCID: PMC6389288 DOI: 10.7554/elife.40811] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Accepted: 02/11/2019] [Indexed: 12/12/2022] Open
Abstract
Mutations in coding and non-coding regions of FUS cause amyotrophic lateral sclerosis (ALS). The latter mutations may exert toxicity by increasing FUS accumulation. We show here that broad expression within the nervous system of wild-type or either of two ALS-linked mutants of human FUS in mice produces progressive motor phenotypes accompanied by characteristic ALS-like pathology. FUS levels are autoregulated by a mechanism in which human FUS downregulates endogenous FUS at mRNA and protein levels. Increasing wild-type human FUS expression achieved by saturating this autoregulatory mechanism produces a rapidly progressive phenotype and dose-dependent lethality. Transcriptome analysis reveals mis-regulation of genes that are largely not observed upon FUS reduction. Likely mechanisms for FUS neurotoxicity include autophagy inhibition and defective RNA metabolism. Thus, our results reveal that overriding FUS autoregulation will trigger gain-of-function toxicity via altered autophagy-lysosome pathway and RNA metabolism function, highlighting a role for protein and RNA dyshomeostasis in FUS-mediated toxicity.
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Affiliation(s)
- Shuo-Chien Ling
- Ludwig Institute for Cancer Research, University of California, San Diego, San Diego, United States.,Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, United States.,Department of Neurosciences, University of California, San Diego, San Diego, United States.,Department of Physiology, National University of Singapore, Singapore, Singapore.,Neurobiology/Ageing Programme, National University of Singapore, Singapore, Singapore.,Program in Neuroscience and Behavior Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Somasish Ghosh Dastidar
- Sanford Consortium for Regenerative Medicine, University of California, San Diego, San Diego, United States
| | - Seiya Tokunaga
- Ludwig Institute for Cancer Research, University of California, San Diego, San Diego, United States
| | - Wan Yun Ho
- Department of Physiology, National University of Singapore, Singapore, Singapore
| | - Kenneth Lim
- Department of Physiology, National University of Singapore, Singapore, Singapore
| | - Hristelina Ilieva
- Ludwig Institute for Cancer Research, University of California, San Diego, San Diego, United States.,Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, United States
| | - Philippe A Parone
- Ludwig Institute for Cancer Research, University of California, San Diego, San Diego, United States.,Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, United States
| | - Sheue-Houy Tyan
- Department of Neurosciences, University of California, San Diego, San Diego, United States.,Department of Medicine, National University of Singapore, Singapore, Singapore
| | - Tsemay M Tse
- Department of Physiology, National University of Singapore, Singapore, Singapore
| | - Jer-Cherng Chang
- Ludwig Institute for Cancer Research, University of California, San Diego, San Diego, United States
| | - Oleksandr Platoshyn
- Department of Anesthesiology, University of California, San Diego, San Diego, United States
| | - Ngoc B Bui
- Ludwig Institute for Cancer Research, University of California, San Diego, San Diego, United States
| | - Anh Bui
- Ludwig Institute for Cancer Research, University of California, San Diego, San Diego, United States
| | - Anne Vetto
- Ludwig Institute for Cancer Research, University of California, San Diego, San Diego, United States
| | - Shuying Sun
- Ludwig Institute for Cancer Research, University of California, San Diego, San Diego, United States.,Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, United States
| | - Melissa McAlonis-Downes
- Ludwig Institute for Cancer Research, University of California, San Diego, San Diego, United States.,Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, United States
| | - Joo Seok Han
- Ludwig Institute for Cancer Research, University of California, San Diego, San Diego, United States.,Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, United States
| | - Debbie Swing
- Mouse Cancer Genetics Program, National Cancer Institute, Frederick, United States
| | - Katannya Kapeli
- Department of Physiology, National University of Singapore, Singapore, Singapore
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, United States.,Department of Physiology, National University of Singapore, Singapore, Singapore.,Sanford Consortium for Regenerative Medicine, University of California, San Diego, San Diego, United States
| | - Lino Tessarollo
- Mouse Cancer Genetics Program, National Cancer Institute, Frederick, United States
| | - Martin Marsala
- Department of Anesthesiology, University of California, San Diego, San Diego, United States
| | - Christopher E Shaw
- Dementia Research Institute Centre, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom.,Centre for Brain Research, University of Auckland, Auckland, New Zealand
| | - Greg Tucker-Kellogg
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Albert R La Spada
- Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, United States.,Department of Neurosciences, University of California, San Diego, San Diego, United States.,Sanford Consortium for Regenerative Medicine, University of California, San Diego, San Diego, United States
| | - Clotilde Lagier-Tourenne
- Ludwig Institute for Cancer Research, University of California, San Diego, San Diego, United States.,Department of Neurosciences, University of California, San Diego, San Diego, United States
| | - Sandrine Da Cruz
- Ludwig Institute for Cancer Research, University of California, San Diego, San Diego, United States
| | - Don W Cleveland
- Ludwig Institute for Cancer Research, University of California, San Diego, San Diego, United States.,Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, United States.,Department of Neurosciences, University of California, San Diego, San Diego, United States
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29
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Gongol B, Sari I, Bryant T, Rosete G, Marin T. AMPK: An Epigenetic Landscape Modulator. Int J Mol Sci 2018; 19:ijms19103238. [PMID: 30347687 PMCID: PMC6214086 DOI: 10.3390/ijms19103238] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 10/14/2018] [Accepted: 10/17/2018] [Indexed: 12/22/2022] Open
Abstract
Activated by AMP-dependent and -independent mechanisms, AMP-activated protein kinase (AMPK) plays a central role in the regulation of cellular bioenergetics and cellular survival. AMPK regulates a diverse set of signaling networks that converge to epigenetically mediate transcriptional events. Reversible histone and DNA modifications, such as acetylation and methylation, result in structural chromatin alterations that influence transcriptional machinery access to genomic regulatory elements. The orchestration of these epigenetic events differentiates physiological from pathophysiological phenotypes. AMPK phosphorylation of histones, DNA methyltransferases and histone post-translational modifiers establish AMPK as a key player in epigenetic regulation. This review focuses on the role of AMPK as a mediator of cellular survival through its regulation of chromatin remodeling and the implications this has for health and disease.
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Affiliation(s)
- Brendan Gongol
- Department of Medicine, University of California, San Diego, CA 92093, USA.
- Department of Cardiopulmonary Sciences, School of Allied Health Professions, Loma Linda University, Loma Linda, CA 92350, USA.
| | - Indah Sari
- Department of Cardiopulmonary Sciences, School of Allied Health Professions, Loma Linda University, Loma Linda, CA 92350, USA.
| | - Tiffany Bryant
- Department of Cardiopulmonary Sciences, School of Allied Health Professions, Loma Linda University, Loma Linda, CA 92350, USA.
| | - Geraldine Rosete
- Department of Cardiopulmonary Sciences, School of Allied Health Professions, Loma Linda University, Loma Linda, CA 92350, USA.
| | - Traci Marin
- Department of Medicine, University of California, San Diego, CA 92093, USA.
- Department of Health Sciences, Victor Valley College, Victorville, CA 92395, USA.
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30
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Cuartero S, Weiss FD, Dharmalingam G, Guo Y, Ing-Simmons E, Masella S, Robles-Rebollo I, Xiao X, Wang YF, Barozzi I, Djeghloul D, Amano MT, Niskanen H, Petretto E, Dowell RD, Tachibana K, Kaikkonen MU, Nasmyth KA, Lenhard B, Natoli G, Fisher AG, Merkenschlager M. Control of inducible gene expression links cohesin to hematopoietic progenitor self-renewal and differentiation. Nat Immunol 2018; 19:932-941. [PMID: 30127433 PMCID: PMC6195188 DOI: 10.1038/s41590-018-0184-1] [Citation(s) in RCA: 145] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 07/17/2018] [Indexed: 02/07/2023]
Abstract
Cohesin is important for 3D genome organization. Nevertheless, even the complete removal of cohesin has surprisingly little impact on steady-state gene transcription and enhancer activity. Here we show that cohesin is required for the core transcriptional response of primary macrophages to microbial signals, and for inducible enhancer activity that underpins inflammatory gene expression. Consistent with a role for inflammatory signals in promoting myeloid differentiation of hematopoietic stem and progenitor cells (HPSCs), cohesin mutations in HSPCs led to reduced inflammatory gene expression and increased resistance to differentiation-inducing inflammatory stimuli. These findings uncover an unexpected dependence of inducible gene expression on cohesin, link cohesin with myeloid differentiation, and may help explain the prevalence of cohesin mutations in human acute myeloid leukemia.
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Affiliation(s)
- Sergi Cuartero
- Lymphocyte Development Group, Epigenetics Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Felix D Weiss
- Lymphocyte Development Group, Epigenetics Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Gopuraja Dharmalingam
- MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Ya Guo
- Lymphocyte Development Group, Epigenetics Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Elizabeth Ing-Simmons
- Lymphocyte Development Group, Epigenetics Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
- Computational Regulatory Genomics Group, Integrative Biology Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
- Max Planck Institute for Molecular Biomedicine, Muenster, Germany
| | - Silvia Masella
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
| | - Irene Robles-Rebollo
- Lymphocyte Development Group, Epigenetics Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Xiaolin Xiao
- MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Yi-Fang Wang
- MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Iros Barozzi
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
- Department of Surgery and Cancer, Department of Medicine, Imperial College London, London, UK
| | - Dounia Djeghloul
- Lymphocyte Development Group, Epigenetics Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Mariane T Amano
- Lymphocyte Development Group, Epigenetics Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
- Hospital Sírio-Libanês, Sao Paulo, Brazil
| | - Henri Niskanen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Enrico Petretto
- MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
- Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Robin D Dowell
- BioFrontiers Institute and Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Kikuë Tachibana
- Department of Biochemistry, University of Oxford, Oxford, UK
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Minna U Kaikkonen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Kim A Nasmyth
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Boris Lenhard
- Computational Regulatory Genomics Group, Integrative Biology Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Gioacchino Natoli
- Humanitas Clinical and Research Center, Milan, Italy
- Humanitas University, Milan, Italy
| | - Amanda G Fisher
- Lymphocyte Development Group, Epigenetics Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Matthias Merkenschlager
- Lymphocyte Development Group, Epigenetics Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK.
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31
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Ferrero E. Using regulatory genomics data to interpret the function of disease variants and prioritise genes from expression studies. F1000Res 2018; 7:121. [PMID: 29568492 PMCID: PMC5850119 DOI: 10.12688/f1000research.13577.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/16/2018] [Indexed: 12/15/2022] Open
Abstract
The identification of therapeutic targets is a critical step in the research and developement of new drugs, with several drug discovery programmes failing because of a weak linkage between target and disease. Genome-wide association studies and large-scale gene expression experiments are providing insights into the biology of several common diseases, but the complexity of transcriptional regulation mechanisms often limits our understanding of how genetic variation can influence changes in gene expression. Several initiatives in the field of regulatory genomics are aiming to close this gap by systematically identifying and cataloguing regulatory elements such as promoters and enhacers across different tissues and cell types. In this Bioconductor workflow, we will explore how different types of regulatory genomic data can be used for the functional interpretation of disease-associated variants and for the prioritisation of gene lists from gene expression experiments.
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Affiliation(s)
- Enrico Ferrero
- Computational Biology, GSK, Medicines Research Centre, Stevenage, SG1 2NY, UK
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32
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Kustatscher G, Grabowski P, Rappsilber J. Pervasive coexpression of spatially proximal genes is buffered at the protein level. Mol Syst Biol 2017; 13:937. [PMID: 28835372 PMCID: PMC5572396 DOI: 10.15252/msb.20177548] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Genes are not randomly distributed in the genome. In humans, 10% of protein-coding genes are transcribed from bidirectional promoters and many more are organised in larger clusters. Intriguingly, neighbouring genes are frequently coexpressed but rarely functionally related. Here we show that coexpression of bidirectional gene pairs, and closeby genes in general, is buffered at the protein level. Taking into account the 3D architecture of the genome, we find that co-regulation of spatially close, functionally unrelated genes is pervasive at the transcriptome level, but does not extend to the proteome. We present evidence that non-functional mRNA coexpression in human cells arises from stochastic chromatin fluctuations and direct regulatory interference between spatially close genes. Protein-level buffering likely reflects a lack of coordination of post-transcriptional regulation of functionally unrelated genes. Grouping human genes together along the genome sequence, or through long-range chromosome folding, is associated with reduced expression noise. Our results support the hypothesis that the selection for noise reduction is a major driver of the evolution of genome organisation.
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Affiliation(s)
- Georg Kustatscher
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Piotr Grabowski
- Chair of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Juri Rappsilber
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK .,Chair of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
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33
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Pgltools: a genomic arithmetic tool suite for manipulation of Hi-C peak and other chromatin interaction data. BMC Bioinformatics 2017; 18:207. [PMID: 28388874 PMCID: PMC5384132 DOI: 10.1186/s12859-017-1621-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 03/31/2017] [Indexed: 11/21/2022] Open
Abstract
Background Genomic interaction studies use next-generation sequencing (NGS) to examine the interactions between two loci on the genome, with subsequent bioinformatics analyses typically including annotation, intersection, and merging of data from multiple experiments. While many file types and analysis tools exist for storing and manipulating single locus NGS data, there is currently no file standard or analysis tool suite for manipulating and storing paired-genomic-loci: the data type resulting from “genomic interaction” studies. As genomic interaction sequencing data are becoming prevalent, a standard file format and tools for working with these data conveniently and efficiently are needed. Results This article details a file standard and novel software tool suite for working with paired-genomic-loci data. We present the paired-genomic-loci (PGL) file standard for genomic-interactions data, and the accompanying analysis tool suite “pgltools”: a cross platform, pypy compatible python package available both as an easy-to-use UNIX package, and as a python module, for integration into pipelines of paired-genomic-loci analyses. Conclusions Pgltools is a freely available, open source tool suite for manipulating paired-genomic-loci data. Source code, an in-depth manual, and a tutorial are available publicly at www.github.com/billgreenwald/pgltools, and a python module of the operations can be installed from PyPI via the PyGLtools module.
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34
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QuIN: A Web Server for Querying and Visualizing Chromatin Interaction Networks. PLoS Comput Biol 2016; 12:e1004809. [PMID: 27336171 PMCID: PMC4919057 DOI: 10.1371/journal.pcbi.1004809] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 05/12/2016] [Indexed: 01/30/2023] Open
Abstract
Recent studies of the human genome have indicated that regulatory elements (e.g. promoters and enhancers) at distal genomic locations can interact with each other via chromatin folding and affect gene expression levels. Genomic technologies for mapping interactions between DNA regions, e.g., ChIA-PET and HiC, can generate genome-wide maps of interactions between regulatory elements. These interaction datasets are important resources to infer distal gene targets of non-coding regulatory elements and to facilitate prioritization of critical loci for important cellular functions. With the increasing diversity and complexity of genomic information and public ontologies, making sense of these datasets demands integrative and easy-to-use software tools. Moreover, network representation of chromatin interaction maps enables effective data visualization, integration, and mining. Currently, there is no software that can take full advantage of network theory approaches for the analysis of chromatin interaction datasets. To fill this gap, we developed a web-based application, QuIN, which enables: 1) building and visualizing chromatin interaction networks, 2) annotating networks with user-provided private and publicly available functional genomics and interaction datasets, 3) querying network components based on gene name or chromosome location, and 4) utilizing network based measures to identify and prioritize critical regulatory targets and their direct and indirect interactions. AVAILABILITY: QuIN’s web server is available at http://quin.jax.org QuIN is developed in Java and JavaScript, utilizing an Apache Tomcat web server and MySQL database and the source code is available under the GPLV3 license available on GitHub: https://github.com/UcarLab/QuIN/.
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35
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Lun ATL, Perry M, Ing-Simmons E. Infrastructure for genomic interactions: Bioconductor classes for Hi-C, ChIA-PET and related experiments. F1000Res 2016; 5:950. [PMID: 27303634 PMCID: PMC4890298 DOI: 10.12688/f1000research.8759.2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/23/2016] [Indexed: 11/20/2022] Open
Abstract
The study of genomic interactions has been greatly facilitated by techniques such as chromatin conformation capture with high-throughput sequencing (Hi-C). These genome-wide experiments generate large amounts of data that require careful analysis to obtain useful biological conclusions. However, development of the appropriate software tools is hindered by the lack of basic infrastructure to represent and manipulate genomic interaction data. Here, we present the
InteractionSet package that provides classes to represent genomic interactions and store their associated experimental data, along with the methods required for low-level manipulation and processing of those classes. The
InteractionSet package exploits existing infrastructure in the open-source Bioconductor project, while in turn being used by Bioconductor packages designed for higher-level analyses. For new packages, use of the functionality in
InteractionSet will simplify development, allow access to more features and improve interoperability between packages.
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Affiliation(s)
- Aaron T L Lun
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Malcolm Perry
- MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, London, UK
| | - Elizabeth Ing-Simmons
- MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, London, UK
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36
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Lun ATL, Perry M, Ing-Simmons E. Infrastructure for genomic interactions: Bioconductor classes for Hi-C, ChIA-PET and related experiments. F1000Res 2016; 5:950. [PMID: 27303634 DOI: 10.12688/f1000research.8759.1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/16/2016] [Indexed: 11/20/2022] Open
Abstract
The study of genomic interactions has been greatly facilitated by techniques such as chromatin conformation capture with high-throughput sequencing (Hi-C). These genome-wide experiments generate large amounts of data that require careful analysis to obtain useful biological conclusions. However, development of the appropriate software tools is hindered by the lack of basic infrastructure to represent and manipulate genomic interaction data. Here, we present the InteractionSet package that provides classes to represent genomic interactions and store their associated experimental data, along with the methods required for low-level manipulation and processing of those classes. The InteractionSet package exploits existing infrastructure in the open-source Bioconductor project, while in turn being used by Bioconductor packages designed for higher-level analyses. For new packages, use of the functionality in InteractionSet will simplify development, allow access to more features and improve interoperability between packages.
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Affiliation(s)
- Aaron T L Lun
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Malcolm Perry
- MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, London, UK
| | - Elizabeth Ing-Simmons
- MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, London, UK
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