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A Myc enhancer cluster regulates normal and leukaemic haematopoietic stem cell hierarchies. Nature 2018; 553:515-520. [PMID: 29342133 DOI: 10.1038/nature25193] [Citation(s) in RCA: 220] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 12/04/2017] [Indexed: 12/11/2022]
Abstract
The transcription factor Myc is essential for the regulation of haematopoietic stem cells and progenitors and has a critical function in haematopoietic malignancies. Here we show that an evolutionarily conserved region located 1.7 megabases downstream of the Myc gene that has previously been labelled as a 'super-enhancer' is essential for the regulation of Myc expression levels in both normal haematopoietic and leukaemic stem cell hierarchies in mice and humans. Deletion of this region in mice leads to a complete loss of Myc expression in haematopoietic stem cells and progenitors. This caused an accumulation of differentiation-arrested multipotent progenitors and loss of myeloid and B cells, mimicking the phenotype caused by Mx1-Cre-mediated conditional deletion of the Myc gene in haematopoietic stem cells. This super-enhancer comprises multiple enhancer modules with selective activity that recruits a compendium of transcription factors, including GFI1b, RUNX1 and MYB. Analysis of mice carrying deletions of individual enhancer modules suggests that specific Myc expression levels throughout most of the haematopoietic hierarchy are controlled by the combinatorial and additive activity of individual enhancer modules, which collectively function as a 'blood enhancer cluster' (BENC). We show that BENC is also essential for the maintenance of MLL-AF9-driven leukaemia in mice. Furthermore, a BENC module, which controls Myc expression in mouse haematopoietic stem cells and progenitors, shows increased chromatin accessibility in human acute myeloid leukaemia stem cells compared to blasts. This difference correlates with MYC expression and patient outcome. We propose that clusters of enhancers, such as BENC, form highly combinatorial systems that allow precise control of gene expression across normal cellular hierarchies and which also can be hijacked in malignancies.
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Berthelot C, Villar D, Horvath JE, Odom DT, Flicek P. Complexity and conservation of regulatory landscapes underlie evolutionary resilience of mammalian gene expression. Nat Ecol Evol 2018; 2:152-163. [PMID: 29180706 PMCID: PMC5733139 DOI: 10.1038/s41559-017-0377-2] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 10/10/2017] [Indexed: 02/02/2023]
Abstract
To gain insight into how mammalian gene expression is controlled by rapidly evolving regulatory elements, we jointly analysed promoter and enhancer activity with downstream transcription levels in liver samples from 15 species. Genes associated with complex regulatory landscapes generally exhibit high expression levels that remain evolutionarily stable. While the number of regulatory elements is the key driver of transcriptional output and resilience, regulatory conservation matters: elements active across mammals most effectively stabilize gene expression. In contrast, recently evolved enhancers typically contribute weakly, consistent with their high evolutionary plasticity. These effects are observed across the entire mammalian clade and are robust to potential confounders, such as the gene expression level. Using liver as a representative somatic tissue, our results illuminate how the evolutionary stability of gene expression is profoundly entwined with both the number and conservation of surrounding promoters and enhancers.
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Affiliation(s)
- Camille Berthelot
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
- Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique UMR8197, Institut National de la Santé et de la Recherche Médicale U1024, 46 Rue d'Ulm, 75230, Paris, Cedex 05, France
| | - Diego Villar
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
| | - Julie E Horvath
- Biological and Biomedical Sciences, North Carolina Central University, Durham, NC, 27707, USA
- North Carolina Museum of Natural Sciences, Raleigh, NC, 27601, USA
- Evolutionary Anthropology Department, Duke University, Durham, NC, 27707, USA
| | - Duncan T Odom
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK.
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
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103
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Ron G, Globerson Y, Moran D, Kaplan T. Promoter-enhancer interactions identified from Hi-C data using probabilistic models and hierarchical topological domains. Nat Commun 2017; 8:2237. [PMID: 29269730 PMCID: PMC5740158 DOI: 10.1038/s41467-017-02386-3] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 11/24/2017] [Indexed: 01/06/2023] Open
Abstract
Proximity-ligation methods such as Hi-C allow us to map physical DNA–DNA interactions along the genome, and reveal its organization into topologically associating domains (TADs). As the Hi-C data accumulate, computational methods were developed for identifying domain borders in multiple cell types and organisms. Here, we present PSYCHIC, a computational approach for analyzing Hi-C data and identifying promoter–enhancer interactions. We use a unified probabilistic model to segment the genome into domains, which we then merge hierarchically and fit using a local background model, allowing us to identify over-represented DNA–DNA interactions across the genome. By analyzing the published Hi-C data sets in human and mouse, we identify hundreds of thousands of putative enhancers and their target genes, and compile an extensive genome-wide catalog of gene regulation in human and mouse. As we show, our predictions are highly enriched for ChIP-seq and DNA accessibility data, evolutionary conservation, eQTLs and other DNA–DNA interaction data. Proximity-ligation methods like Hi-C map DNA-DNA interactions and reveal its organization into topologically associating domains (TADs). Here the authors describe PSYCHIC, a computational approach for analysing Hi-C data that allows the identification of promoter-enhancer interactions.
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Affiliation(s)
- Gil Ron
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Yuval Globerson
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Dror Moran
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Tommy Kaplan
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel.
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104
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Multiple enhancer regions govern the transcription of CCN2 during embryonic development. J Cell Commun Signal 2017; 12:231-243. [PMID: 29256171 PMCID: PMC5842200 DOI: 10.1007/s12079-017-0440-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 12/05/2017] [Indexed: 01/22/2023] Open
Abstract
CCN2 is a critical matricellular protein that is expressed in several cells with major implications in physiology and different pathologies. However, the transcriptional regulation of this gene remains obscure. We used the Encyclopaedia of DNA Elements browser (ENCODE) to visualise the region spanning from 300 kb upstream to the CCN2 start site in silico in order to identify enhancer regions that regulate transcription of this gene. Selection was based on three criteria associated with enhancer regions: 1) H3K4me1 and H3K27ac histone modifications, 2) DNase I hypersensitivity of chromatin and 3) inter-species conservation. Reporter constructs were created with sequences spanning each of the regions of interest placed upstream of an Hsp68 silent proximal promoter sequence in order to drive the expression of β-galactosidase transgene. Each of these constructs was subsequently used to create transgenic mice in which reporter gene production was assessed at the E15.5 developmental stage. Four functional enhancers were identified, with each driving distinct, tissue-specific patterns of transgene expression. An enhancer located -100 kb from the CCN2 transcription start site facilitated expression within vascular tissue. An enhancer -135 kb upstream of CCN2 drove expression within the articular chondrocytes of synovial joints. The other two enhancers, located at -198 kb and -229 kb, mediated transgene expression within dermal fibroblasts, however the most prevalent activity was found within hypertrophic chondrocytes and periosteal tissue, respectively. These findings suggest that the global expression of CCN2 during development results from the activity of several tissue-specific enhancer regions in addition to proximal regulatory elements that have previously been demonstrated to drive transcription of the gene during development.
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105
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Boya R, Yadavalli AD, Nikhat S, Kurukuti S, Palakodeti D, Pongubala JMR. Developmentally regulated higher-order chromatin interactions orchestrate B cell fate commitment. Nucleic Acids Res 2017; 45:11070-11087. [PMID: 28977418 PMCID: PMC5737614 DOI: 10.1093/nar/gkx722] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 08/09/2017] [Indexed: 12/17/2022] Open
Abstract
Genome organization in 3D nuclear-space is important for regulation of gene expression. However, the alterations of chromatin architecture that impinge on the B cell-fate choice of multi-potent progenitors are still unclear. By integrating in situ Hi-C analyses with epigenetic landscapes and genome-wide expression profiles, we tracked the changes in genome architecture as the cells transit from a progenitor to a committed state. We identified the genomic loci that undergo developmental switch between A and B compartments during B-cell fate determination. Furthermore, although, topologically associating domains (TADs) are stable, a significant number of TADs display structural alterations that are associated with changes in cis-regulatory interaction landscape. Finally, we demonstrate the potential roles for Ebf1 and its downstream factor, Pax5, in chromatin reorganization and transcription regulation. Collectively, our studies provide a general paradigm of the dynamic relationship between chromatin reorganization and lineage-specific gene expression pattern that dictates cell-fate determination.
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Affiliation(s)
- Ravi Boya
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Anurupa Devi Yadavalli
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Sameena Nikhat
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Sreenivasulu Kurukuti
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Dasaradhi Palakodeti
- Institute for Stem Cell Biology and Regenerative Medicine, National Centre for Biological Sciences, Bangalore 560065, India
| | - Jagan M R Pongubala
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
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106
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107
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DNA Replication Origins in Immunoglobulin Switch Regions Regulate Class Switch Recombination in an R-Loop-Dependent Manner. Cell Rep 2017; 17:2927-2942. [PMID: 27974207 DOI: 10.1016/j.celrep.2016.11.041] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 09/07/2016] [Accepted: 11/11/2016] [Indexed: 11/22/2022] Open
Abstract
Class switch recombination (CSR) at the immunoglobulin heavy chain (IgH) locus generates antibody isotypes. CSR depends on double-strand breaks (DSBs) induced by activation-induced cytidine deaminase (AID). Although DSB formation and repair machineries are active in G1 phase, efficient CSR is dependent on cell proliferation and S phase entry; however, the underlying mechanisms are obscure. Here, we show that efficient CSR requires the replicative helicase, the Mcm complex. Mcm proteins are enriched at IgH switch regions during CSR, leading to assembly of facultative replication origins that require Mcm helicase function for productive CSR. Assembly of CSR-associated origins is facilitated by R loops and promotes the physical proximity (synapsis) of recombining switch regions, which is reduced by R loop inhibition or Mcm complex depletion. Thus, R loops contribute to replication origin specification that promotes DSB resolution in CSR. This suggests a mechanism for the dependence of CSR on S phase and cell division.
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108
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Rodríguez-Carballo E, Lopez-Delisle L, Zhan Y, Fabre PJ, Beccari L, El-Idrissi I, Huynh THN, Ozadam H, Dekker J, Duboule D. The HoxD cluster is a dynamic and resilient TAD boundary controlling the segregation of antagonistic regulatory landscapes. Genes Dev 2017; 31:2264-2281. [PMID: 29273679 PMCID: PMC5769770 DOI: 10.1101/gad.307769.117] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 11/21/2017] [Indexed: 12/11/2022]
Abstract
The mammalian HoxD cluster lies between two topologically associating domains (TADs) matching distinct enhancer-rich regulatory landscapes. During limb development, the telomeric TAD controls the early transcription of Hoxd genes in forearm cells, whereas the centromeric TAD subsequently regulates more posterior Hoxd genes in digit cells. Therefore, the TAD boundary prevents the terminal Hoxd13 gene from responding to forearm enhancers, thereby allowing proper limb patterning. To assess the nature and function of this CTCF-rich DNA region in embryos, we compared chromatin interaction profiles between proximal and distal limb bud cells isolated from mutant stocks where various parts of this boundary region were removed. The resulting progressive release in boundary effect triggered inter-TAD contacts, favored by the activity of the newly accessed enhancers. However, the boundary was highly resilient, and only a 400-kb deletion, including the whole-gene cluster, was eventually able to merge the neighboring TADs into a single structure. In this unified TAD, both proximal and distal limb enhancers nevertheless continued to work independently over a targeted transgenic reporter construct. We propose that the whole HoxD cluster is a dynamic TAD border and that the exact boundary position varies depending on both the transcriptional status and the developmental context.
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Affiliation(s)
| | - Lucille Lopez-Delisle
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Ye Zhan
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Pierre J Fabre
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Leonardo Beccari
- Department of Genetics and Evolution, University of Geneva, 1205 Geneva, Switzerland
| | - Imane El-Idrissi
- Department of Genetics and Evolution, University of Geneva, 1205 Geneva, Switzerland
| | - Thi Hanh Nguyen Huynh
- Department of Genetics and Evolution, University of Geneva, 1205 Geneva, Switzerland
| | - Hakan Ozadam
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Job Dekker
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Denis Duboule
- Department of Genetics and Evolution, University of Geneva, 1205 Geneva, Switzerland
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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109
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Decato BE, Lopez-Tello J, Sferruzzi-Perri AN, Smith AD, Dean MD. DNA Methylation Divergence and Tissue Specialization in the Developing Mouse Placenta. Mol Biol Evol 2017; 34:1702-1712. [PMID: 28379409 DOI: 10.1093/molbev/msx112] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The placental epigenome plays a vital role in regulating mammalian growth and development. Aberrations in placental DNA methylation are linked to several disease states, including intrauterine growth restriction and preeclampsia. Studying the evolution and development of the placental epigenome is critical to understanding the origin and progression of such diseases. Although high-resolution studies have found substantial variation between placental methylomes of different species, the nature of methylome variation has yet to be characterized within any individual species. We conducted a study of placental DNA methylation at high resolution in multiple strains and closely related species of house mice (Mus musculus musculus, Mus m. domesticus, and M. spretus), across developmental timepoints (embryonic days 15-18), and between two distinct layers (labyrinthine transport and junctional endocrine). We observed substantial genome-wide methylation heterogeneity in mouse placenta compared with other differentiated tissues. Species-specific methylation profiles were concentrated in retrotransposon subfamilies, specifically RLTR10 and RLTR20 subfamilies. Regulatory regions such as gene promoters and CpG islands displayed cross-species conservation, but showed strong differences between layers and developmental timepoints. Partially methylated domains exist in the mouse placenta and widen during development. Taken together, our results characterize the mouse placental methylome as a highly heterogeneous and deregulated landscape globally, intermixed with actively regulated promoter and retrotransposon sequences.
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Affiliation(s)
- Benjamin E Decato
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA
| | - Jorge Lopez-Tello
- Department of Physiology, Development, and Neuroscience, Centre for Trophoblast Research, University of Cambridge, Cambridge, United Kingdom
| | - Amanda N Sferruzzi-Perri
- Department of Physiology, Development, and Neuroscience, Centre for Trophoblast Research, University of Cambridge, Cambridge, United Kingdom
| | - Andrew D Smith
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA
| | - Matthew D Dean
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA
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110
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Denisenko E, Guler R, Mhlanga MM, Suzuki H, Brombacher F, Schmeier S. Genome-wide profiling of transcribed enhancers during macrophage activation. Epigenetics Chromatin 2017; 10:50. [PMID: 29061167 PMCID: PMC5654053 DOI: 10.1186/s13072-017-0158-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Accepted: 10/13/2017] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Macrophages are sentinel cells essential for tissue homeostasis and host defence. Owing to their plasticity, macrophages acquire a range of functional phenotypes in response to microenvironmental stimuli, of which M(IFN-γ) and M(IL-4/IL-13) are well known for their opposing pro- and anti-inflammatory roles. Enhancers have emerged as regulatory DNA elements crucial for transcriptional activation of gene expression. RESULTS Using cap analysis of gene expression and epigenetic data, we identify on large-scale transcribed enhancers in bone marrow-derived mouse macrophages, their time kinetics, and target protein-coding genes. We observe an increase in target gene expression, concomitant with increasing numbers of associated enhancers, and find that genes associated with many enhancers show a shift towards stronger enrichment for macrophage-specific biological processes. We infer enhancers that drive transcriptional responses of genes upon M(IFN-γ) and M(IL-4/IL-13) macrophage activation and demonstrate stimuli specificity of regulatory associations. Finally, we show that enhancer regions are enriched for binding sites of inflammation-related transcription factors, suggesting a link between stimuli response and enhancer transcriptional control. CONCLUSIONS Our study provides new insights into genome-wide enhancer-mediated transcriptional control of macrophage genes, including those implicated in macrophage activation, and offers a detailed genome-wide catalogue of transcribed enhancers in bone marrow-derived mouse macrophages.
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Affiliation(s)
- Elena Denisenko
- Institute of Natural and Mathematical Sciences, Massey University, Albany, Auckland, 0632 New Zealand
| | - Reto Guler
- Division of Immunology, Institute of Infectious Diseases and Molecular Medicine (IDM), South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925 South Africa
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town Component, Cape Town, 7925 South Africa
| | - Musa M. Mhlanga
- Gene Expression and Biophysics Group, CSIR Synthetic Biology ERA, Pretoria, 0001 South Africa
- Division of Chemical Systems and Synthetic Biology, Institute of Infectious Diseases and Molecular Medicine (IDM), University of Cape Town, Cape Town, 7925 South Africa
- Gene Expression and Biophysics Unit, Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, 1649-028 Lisbon, Portugal
| | - Harukazu Suzuki
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan
| | - Frank Brombacher
- Division of Immunology, Institute of Infectious Diseases and Molecular Medicine (IDM), South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925 South Africa
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town Component, Cape Town, 7925 South Africa
| | - Sebastian Schmeier
- Institute of Natural and Mathematical Sciences, Massey University, Albany, Auckland, 0632 New Zealand
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111
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Huang L, Liu P, Yuan Z, Zhou T, Yu J. The free-energy cost of interaction between DNA loops. Sci Rep 2017; 7:12610. [PMID: 28974770 PMCID: PMC5626758 DOI: 10.1038/s41598-017-12765-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 09/14/2017] [Indexed: 12/03/2022] Open
Abstract
From the viewpoint of thermodynamics, the formation of DNA loops and the interaction between them, which are all non-equilibrium processes, result in the change of free energy, affecting gene expression and further cell-to-cell variability as observed experimentally. However, how these processes dissipate free energy remains largely unclear. Here, by analyzing a mechanic model that maps three fundamental topologies of two interacting DNA loops into a 4-state model of gene transcription, we first show that a longer DNA loop needs more mean free energy consumption. Then, independent of the type of interacting two DNA loops (nested, side-by-side or alternating), the promotion between them always consumes less mean free energy whereas the suppression dissipates more mean free energy. More interestingly, we find that in contrast to the mechanism of direct looping between promoter and enhancer, the facilitated-tracking mechanism dissipates less mean free energy but enhances the mean mRNA expression, justifying the facilitated-tracking hypothesis, a long-standing debate in biology. Based on minimal energy principle, we thus speculate that organisms would utilize the mechanisms of loop-loop promotion and facilitated tracking to survive in complex environments. Our studies provide insights into the understanding of gene expression regulation mechanism from the view of energy consumption.
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Affiliation(s)
- Lifang Huang
- Research Centre of Applied Mathematics, Guangzhou University, Guangzhou, 510006, P.R. China
- School of Statistics and Mathematics, Guangdong University of Finance & Economics, Guangzhou, 510275, P.R. China
| | - Peijiang Liu
- School of Statistics and Mathematics, Guangdong University of Finance & Economics, Guangzhou, 510275, P.R. China
| | - Zhanjiang Yuan
- Guangdong Province Key Laboratory of Computational Science, School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou, 510275, P.R. China
| | - Tianshou Zhou
- Guangdong Province Key Laboratory of Computational Science, School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou, 510275, P.R. China.
| | - Jianshe Yu
- Research Centre of Applied Mathematics, Guangzhou University, Guangzhou, 510006, P.R. China.
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112
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Le Noir S, Laffleur B, Carrion C, Garot A, Lecardeur S, Pinaud E, Denizot Y, Skok J, Cogné M. The IgH locus 3' cis-regulatory super-enhancer co-opts AID for allelic transvection. Oncotarget 2017; 8:12929-12940. [PMID: 28088785 PMCID: PMC5355067 DOI: 10.18632/oncotarget.14585] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 01/01/2017] [Indexed: 11/25/2022] Open
Abstract
Immunoglobulin heavy chain (IgH) alleles have ambivalent relationships: they feature both allelic exclusion, ensuring monoallelic expression of a single immunoglobulin (Ig) allele, and frequent inter-allelic class-switch recombination (CSR) reassembling genes from both alleles. The IgH locus 3' regulatory region (3'RR) includes several transcriptional cis-enhancers promoting activation-induced cytidine deaminase (AID)-dependent somatic hypermutation (SHM) and CSR, and altogether behaves as a strong super-enhancer. It can also promote deregulated expression of translocated oncogenes during lymphomagenesis. Besides these rare, illegitimate and pathogenic interactions, we now show that under physiological conditions, the 3'RR super-enhancer supports not only legitimate cis- , but also trans-recruitment of AID, contributing to IgH inter-allelic proximity and enabling the super-enhancer on one allele to stimulate biallelic SHM and CSR. Such inter-allelic activating interactions define transvection, a phenomenon well-known in drosophila but rarely observed in mammalian cells, now appearing as a unique feature of the IgH 3'RR super-enhancer.
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Affiliation(s)
- Sandrine Le Noir
- UMR 7276 CNRS and Université de Limoges: Contrôle de la Réponse Immune B et Lymphoprolifération, Limoges, France
| | - Brice Laffleur
- UMR 7276 CNRS and Université de Limoges: Contrôle de la Réponse Immune B et Lymphoprolifération, Limoges, France
| | - Claire Carrion
- UMR 7276 CNRS and Université de Limoges: Contrôle de la Réponse Immune B et Lymphoprolifération, Limoges, France
| | - Armand Garot
- UMR 7276 CNRS and Université de Limoges: Contrôle de la Réponse Immune B et Lymphoprolifération, Limoges, France
| | - Sandrine Lecardeur
- UMR 7276 CNRS and Université de Limoges: Contrôle de la Réponse Immune B et Lymphoprolifération, Limoges, France
| | - Eric Pinaud
- UMR 7276 CNRS and Université de Limoges: Contrôle de la Réponse Immune B et Lymphoprolifération, Limoges, France
| | - Yves Denizot
- UMR 7276 CNRS and Université de Limoges: Contrôle de la Réponse Immune B et Lymphoprolifération, Limoges, France
| | - Jane Skok
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Michel Cogné
- UMR 7276 CNRS and Université de Limoges: Contrôle de la Réponse Immune B et Lymphoprolifération, Limoges, France
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113
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Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage Development. Mol Cell 2017; 67:1037-1048.e6. [PMID: 28890333 DOI: 10.1016/j.molcel.2017.08.006] [Citation(s) in RCA: 187] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 07/21/2017] [Accepted: 08/11/2017] [Indexed: 01/25/2023]
Abstract
The three-dimensional arrangement of the human genome comprises a complex network of structural and regulatory chromatin loops important for coordinating changes in transcription during human development. To better understand the mechanisms underlying context-specific 3D chromatin structure and transcription during cellular differentiation, we generated comprehensive in situ Hi-C maps of DNA loops in human monocytes and differentiated macrophages. We demonstrate that dynamic looping events are regulatory rather than structural in nature and uncover widespread coordination of dynamic enhancer activity at preformed and acquired DNA loops. Enhancer-bound loop formation and enhancer activation of preformed loops together form multi-loop activation hubs at key macrophage genes. Activation hubs connect 3.4 enhancers per promoter and exhibit a strong enrichment for activator protein 1 (AP-1)-binding events, suggesting that multi-loop activation hubs involving cell-type-specific transcription factors represent an important class of regulatory chromatin structures for the spatiotemporal control of transcription.
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114
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Abstract
How eukaryotic chromosomes fold inside the nucleus is an age-old question that remains unanswered today. Early biochemical and microscopic studies revealed the existence of chromatin domains and loops as a pervasive feature of interphase chromosomes, but the biological implications of such organizational features were obscure. Genome-wide analysis of pair-wise chromatin interactions using chromatin conformation capture (3C)-based techniques has shed new light on the organization of chromosomes in interphase nuclei. Particularly, the finding of cell-type invariant, evolutionarily conserved topologically associating domains (TADs) in a broad spectrum of cell types has provided a new molecular framework for the study of animal development and human diseases. Here, we review recent progress in characterization of such chromatin domains and delineation of mechanisms of their formation in animal cells.
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Affiliation(s)
- Jesse R Dixon
- Peptide Biology Lab and the Helmsley Center for Genomic Medicine, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.
| | - David U Gorkin
- Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, CA 92093-0653, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, CA 92093-0653, USA; University of California, San Diego School of Medicine, Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, and Moores Cancer Center, 9500 Gilman Drive, La Jolla, CA 92093-0653, USA.
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115
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Myc Regulates Chromatin Decompaction and Nuclear Architecture during B Cell Activation. Mol Cell 2017; 67:566-578.e10. [PMID: 28803781 DOI: 10.1016/j.molcel.2017.07.013] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 04/25/2017] [Accepted: 07/10/2017] [Indexed: 11/23/2022]
Abstract
50 years ago, Vincent Allfrey and colleagues discovered that lymphocyte activation triggers massive acetylation of chromatin. However, the molecular mechanisms driving epigenetic accessibility are still unknown. We here show that stimulated lymphocytes decondense chromatin by three differentially regulated steps. First, chromatin is repositioned away from the nuclear periphery in response to global acetylation. Second, histone nanodomain clusters decompact into mononucleosome fibers through a mechanism that requires Myc and continual energy input. Single-molecule imaging shows that this step lowers transcription factor residence time and non-specific collisions during sampling for DNA targets. Third, chromatin interactions shift from long range to predominantly short range, and CTCF-mediated loops and contact domains double in numbers. This architectural change facilitates cognate promoter-enhancer contacts and also requires Myc and continual ATP production. Our results thus define the nature and transcriptional impact of chromatin decondensation and reveal an unexpected role for Myc in the establishment of nuclear topology in mammalian cells.
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116
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Initial high-resolution microscopic mapping of active and inactive regulatory sequences proves non-random 3D arrangements in chromatin domain clusters. Epigenetics Chromatin 2017; 10:39. [PMID: 28784182 PMCID: PMC5547466 DOI: 10.1186/s13072-017-0146-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 07/31/2017] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The association of active transcription regulatory elements (TREs) with DNAse I hypersensitivity (DHS[+]) and an 'open' local chromatin configuration has long been known. However, the 3D topography of TREs within the nuclear landscape of individual cells in relation to their active or inactive status has remained elusive. Here, we explored the 3D nuclear topography of active and inactive TREs in the context of a recently proposed model for a functionally defined nuclear architecture, where an active and an inactive nuclear compartment (ANC-INC) form two spatially co-aligned and functionally interacting networks. RESULTS Using 3D structured illumination microscopy, we performed 3D FISH with differently labeled DNA probe sets targeting either sites with DHS[+], apparently active TREs, or DHS[-] sites harboring inactive TREs. Using an in-house image analysis tool, DNA targets were quantitatively mapped on chromatin compaction shaped 3D nuclear landscapes. Our analyses present evidence for a radial 3D organization of chromatin domain clusters (CDCs) with layers of increasing chromatin compaction from the periphery to the CDC core. Segments harboring active TREs are significantly enriched at the decondensed periphery of CDCs with loops penetrating into interchromatin compartment channels, constituting the ANC. In contrast, segments lacking active TREs (DHS[-]) are enriched toward the compacted interior of CDCs (INC). CONCLUSIONS Our results add further evidence in support of the ANC-INC network model. The different 3D topographies of DHS[+] and DHS[-] sites suggest positional changes of TREs between the ANC and INC depending on their functional state, which might provide additional protection against an inappropriate activation. Our finding of a structural organization of CDCs based on radially arranged layers of different chromatin compaction levels indicates a complex higher-order chromatin organization beyond a dichotomic classification of chromatin into an 'open,' active and 'closed,' inactive state.
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117
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Dorri F, Mendelowitz L, Corrada Bravo H. methylFlow: cell-specific methylation pattern reconstruction from high-throughput bisulfite-converted DNA sequencing. Bioinformatics 2017; 32:1618-24. [PMID: 27246923 DOI: 10.1093/bioinformatics/btw287] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 04/17/2016] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION DNA methylation aberrations are now known to, almost universally, accompany the initiation and progression of cancers. In particular, the colon cancer epigenome contains specific genomic regions that, along with differences in methylation levels with respect to normal colon tissue, also show increased epigenetic and gene expression heterogeneity at the population level, i.e. across tumor samples, in comparison with other regions in the genome. Tumors are highly heterogeneous at the clonal level as well, and the relationship between clonal and population heterogeneity is poorly understood. RESULTS We present an approach that uses sequencing reads from high-throughput sequencing of bisulfite-converted DNA to reconstruct heterogeneous cell populations by assembling cell-specific methylation patterns. Our methodology is based on the solution of a specific class of minimum cost network flow problems. We use our methods to analyze the relationship between clonal heterogeneity and population heterogeneity in high-coverage data from multiple samples of colon tumor and matched normal tissues. AVAILABILITY AND IMPLEMENTATION http://github.com/hcorrada/methylFlow CONTACT hcorrada@umiacs.umd.edu SUPPLEMENTARY INFORMATION SUPPLEMENTARY INFORMATION is available at Bioinformatics online.
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Affiliation(s)
- Faezeh Dorri
- Center for Bioinformatics and Computational Biology Department of Computer Science
| | - Lee Mendelowitz
- Center for Bioinformatics and Computational Biology Applied Mathematics, Statistics and Scientific Compoutation Program, University of Maryland, College Park, MD 20745, USA
| | - Héctor Corrada Bravo
- Center for Bioinformatics and Computational Biology Department of Computer Science
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118
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Elkon R, Agami R. Characterization of noncoding regulatory DNA in the human genome. Nat Biotechnol 2017; 35:732-746. [DOI: 10.1038/nbt.3863] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 03/31/2017] [Indexed: 12/22/2022]
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119
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Canela A, Maman Y, Jung S, Wong N, Callen E, Day A, Kieffer-Kwon KR, Pekowska A, Zhang H, Rao SSP, Huang SC, Mckinnon PJ, Aplan PD, Pommier Y, Aiden EL, Casellas R, Nussenzweig A. Genome Organization Drives Chromosome Fragility. Cell 2017; 170:507-521.e18. [PMID: 28735753 PMCID: PMC6133249 DOI: 10.1016/j.cell.2017.06.034] [Citation(s) in RCA: 255] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Revised: 05/22/2017] [Accepted: 06/21/2017] [Indexed: 01/06/2023]
Abstract
In this study, we show that evolutionarily conserved chromosome loop anchors bound by CCCTC-binding factor (CTCF) and cohesin are vulnerable to DNA double strand breaks (DSBs) mediated by topoisomerase 2B (TOP2B). Polymorphisms in the genome that redistribute CTCF/cohesin occupancy rewire DNA cleavage sites to novel loop anchors. While transcription- and replication-coupled genomic rearrangements have been well documented, we demonstrate that DSBs formed at loop anchors are largely transcription-, replication-, and cell-type-independent. DSBs are continuously formed throughout interphase, are enriched on both sides of strong topological domain borders, and frequently occur at breakpoint clusters commonly translocated in cancer. Thus, loop anchors serve as fragile sites that generate DSBs and chromosomal rearrangements. VIDEO ABSTRACT.
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Affiliation(s)
- Andres Canela
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Yaakov Maman
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Seolkyoung Jung
- Genomics and Immunity, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD, USA
| | - Nancy Wong
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Elsa Callen
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Amanda Day
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Kyong-Rim Kieffer-Kwon
- Genomics and Immunity, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD, USA
| | - Aleksandra Pekowska
- Genomics and Immunity, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD, USA
| | - Hongliang Zhang
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, NIH, Bethesda, MD, USA
| | - Suhas S P Rao
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Su-Chen Huang
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA
| | - Peter J Mckinnon
- Department of Genetics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Peter D Aplan
- Genetics Branch, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, NIH, Bethesda, MD, USA
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA
| | - Rafael Casellas
- Genomics and Immunity, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD, USA
| | - André Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA.
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120
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Park SM, Choi EY, Bae M, Choi JK, Kim YJ. A long-range interactive DNA methylation marker panel for the promoters of HOXA9 and HOXA10 predicts survival in breast cancer patients. Clin Epigenetics 2017; 9:73. [PMID: 28748001 PMCID: PMC5525292 DOI: 10.1186/s13148-017-0373-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 07/17/2017] [Indexed: 01/30/2023] Open
Abstract
Background Most DNA cancer methylation markers are based on the transcriptional regulation of the promoter-gene relationship. Recently, the importance of long-range interactions between distal CpGs and target genes has been revealed. Here, we attempted to identify methylation markers for breast cancer that interact with distant genes. Results We performed integrated analysis using chromatin interactome data, methylome data, transcriptome data, and clinical information for breast cancer from public databases. Using the chromatin interactome and methylome data, we defined CpG-distant target gene relationships. After determining the differences in methylation between tumor and paired normal samples, the survival association, and the correlation between CpG methylation and distant target gene expression, we selected CpG methylation marker candidates. Using Cox proportional hazards models, we combined the selected markers and evaluated the prognostic model. We identified six methylation markers in HOXA9 and HOXA10 promoter regions and their long-range target genes. We experimentally validated the chromatin interactions, methylation status, and transcriptional regulation. A prognostic model showed that the combination of six methylation markers was highly associated with poor survival in independent datasets. According to our multivariate analysis, the prognostic model showed significantly better prognostic ability than other histological and molecular markers. Conclusions The combination of long-range interacting HOXA9 and HOXA10 promoter CpGs predicted the survival of breast cancer patients, providing a comprehensive and novel approach for discovering new methylation markers. Electronic supplementary material The online version of this article (doi:10.1186/s13148-017-0373-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Seong-Min Park
- Translational Research Branch, Research Institute, National Cancer Center, Goyang, Gyeonggi 10408 Republic of Korea.,Personalized Genomic Medicine Research Center, KRIBB, Daejeon, 34141 Republic of Korea
| | - Eun-Young Choi
- Translational Research Branch, Research Institute, National Cancer Center, Goyang, Gyeonggi 10408 Republic of Korea
| | - Mingyun Bae
- Department of Bio and Brain Engineering, KAIST, Daejeon, 34141 Republic of Korea
| | - Jung Kyoon Choi
- Department of Bio and Brain Engineering, KAIST, Daejeon, 34141 Republic of Korea
| | - Youn-Jae Kim
- Translational Research Branch, Research Institute, National Cancer Center, Goyang, Gyeonggi 10408 Republic of Korea
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121
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Connected Gene Communities Underlie Transcriptional Changes in Cornelia de Lange Syndrome. Genetics 2017; 207:139-151. [PMID: 28679547 DOI: 10.1534/genetics.117.202291] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 06/28/2017] [Indexed: 12/25/2022] Open
Abstract
Cornelia de Lange syndrome (CdLS) is a complex multisystem developmental disorder caused by mutations in cohesin subunits and regulators. While its precise molecular mechanisms are not well defined, they point toward a global deregulation of the transcriptional gene expression program. Cohesin is associated with the boundaries of chromosome domains and with enhancer and promoter regions connecting the three-dimensional genome organization with transcriptional regulation. Here, we show that connected gene communities, structures emerging from the interactions of noncoding regulatory elements and genes in the three-dimensional chromosomal space, provide a molecular explanation for the pathoetiology of CdLS associated with mutations in the cohesin-loading factor NIPBL and the cohesin subunit SMC1A NIPBL and cohesin are important constituents of connected gene communities that are centrally positioned at noncoding regulatory elements. Accordingly, genes deregulated in CdLS are positioned within reach of NIPBL- and cohesin-occupied regions through promoter-promoter interactions. Our findings suggest a dynamic model where NIPBL loads cohesin to connect genes in communities, offering an explanation for the gene expression deregulation in the CdLS.
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122
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Abstract
Epigenetic regulation in myeloid cells is crucial for cell differentiation and activation in response to developmental and environmental cues. Epigenetic control involves posttranslational modification of DNA or chromatin, and is also coupled to upstream signaling pathways and transcription factors. In this review, we summarize key epigenetic events and how dynamics in the epigenetic landscape of myeloid cells shape the development, immune activation, and innate immune memory.
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123
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Wang Y, Hao DP, Li JJ, Wang L, Di LJ. Genome-wide methylome and chromatin interactome identify abnormal enhancer to be risk factor of breast cancer. Oncotarget 2017; 8:44705-44719. [PMID: 28621677 PMCID: PMC5546512 DOI: 10.18632/oncotarget.18348] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Accepted: 05/15/2017] [Indexed: 11/25/2022] Open
Abstract
Enhancer is critical cis regulatory elements in gene expression. To understand whether and how the aberrant enhancer activation may contribute to cancer risk, the differentially methylated enhancers (eDMRs) in normal and malignant breast tissues were identified and analyzed. By incorporating genome-wide chromatin interaction, integrated analysis of eDMRs and target gene expression identified 1,272 enhancer-promoter pairs. Surprisingly, two functionally distinct groups of genes were identified in these pairs, one showing better correlation to enhancer methylation (eRGs) and the other showing better correlation to promoter methylation (pRGs), and the former group is functionally enriched with cancer related genes. Moreover, enhancer methylation based clustering of breast cancer samples is capable of discriminating basal breast cancer from other subtypes. By correlating enhancer methylation status to patient survival, 345 enhancers show the impact on the disease outcome and the majority of their target genes are important regulators of cell survival pathways including known cancer related genes. Together, these results suggest reactivation of enhancers in cancer cells has the add-on effect and contributes to cancer risk in combination.
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Affiliation(s)
- Yuan Wang
- Cancer Center, Faculty of Health Sciences, University of Macau, Macau, China
| | - Da-Peng Hao
- Cancer Center, Faculty of Health Sciences, University of Macau, Macau, China
| | - Jing-Jing Li
- Cancer Center, Faculty of Health Sciences, University of Macau, Macau, China
| | - Li Wang
- Metabolomics Core, Faculty of Health Sciences, University of Macau, Macau, China
| | - Li-Jun Di
- Cancer Center, Faculty of Health Sciences, University of Macau, Macau, China
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124
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Hnisz D, Shrinivas K, Young RA, Chakraborty AK, Sharp PA. A Phase Separation Model for Transcriptional Control. Cell 2017; 169:13-23. [PMID: 28340338 DOI: 10.1016/j.cell.2017.02.007] [Citation(s) in RCA: 1073] [Impact Index Per Article: 153.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 12/15/2016] [Accepted: 02/02/2017] [Indexed: 12/13/2022]
Abstract
Phase-separated multi-molecular assemblies provide a general regulatory mechanism to compartmentalize biochemical reactions within cells. We propose that a phase separation model explains established and recently described features of transcriptional control. These features include the formation of super-enhancers, the sensitivity of super-enhancers to perturbation, the transcriptional bursting patterns of enhancers, and the ability of an enhancer to produce simultaneous activation at multiple genes. This model provides a conceptual framework to further explore principles of gene control in mammals.
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Affiliation(s)
- Denes Hnisz
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - Krishna Shrinivas
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA
| | - Richard A Young
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Arup K Chakraborty
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA.
| | - Phillip A Sharp
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
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125
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Bradner JE, Hnisz D, Young RA. Transcriptional Addiction in Cancer. Cell 2017; 168:629-643. [PMID: 28187285 DOI: 10.1016/j.cell.2016.12.013] [Citation(s) in RCA: 750] [Impact Index Per Article: 107.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 12/05/2016] [Accepted: 12/08/2016] [Indexed: 12/22/2022]
Abstract
Cancer arises from genetic alterations that invariably lead to dysregulated transcriptional programs. These dysregulated programs can cause cancer cells to become highly dependent on certain regulators of gene expression. Here, we discuss how transcriptional control is disrupted by genetic alterations in cancer cells, why transcriptional dependencies can develop as a consequence of dysregulated programs, and how these dependencies provide opportunities for novel therapeutic interventions in cancer.
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Affiliation(s)
- James E Bradner
- Novartis Institutes for Biomedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Denes Hnisz
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - Richard A Young
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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126
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Wang F, Han J, Wang L, Jing Y, Zhu Z, Hui D, Wang Z, Wang Y, Dong Y, Tan T. CCCTC-Binding Factor Transcriptionally Targets Wdr5 to Mediate Somatic Cell Reprogramming. Stem Cells Dev 2017; 26:743-750. [DOI: 10.1089/scd.2016.0309] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Feng Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
| | - Jinghua Han
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
| | - Li Wang
- Huanghe College of Science and Technology, Zhengzhou City, China
| | - Ying Jing
- Department of Oncology, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Zhu Zhu
- Department of Oncology, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Dawei Hui
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Zhaohui Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Yangzi Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Yang Dong
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Tao Tan
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
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127
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A tiling-deletion-based genetic screen for cis-regulatory element identification in mammalian cells. Nat Methods 2017; 14:629-635. [PMID: 28417999 PMCID: PMC5490986 DOI: 10.1038/nmeth.4264] [Citation(s) in RCA: 179] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 03/15/2017] [Indexed: 12/20/2022]
Abstract
Millions of cis-regulatory elements are predicted in the human genome, but direct evidence for their biological function is still scarce. Here we report a high-throughput method, Cis-Regulatory Element Scan by Tiling-deletion and sequencing (CREST-seq), for unbiased discovery and functional assessment of cis regulatory sequences in the genome. We use it to interrogate the 2Mbp POU5F1 locus in the human embryonic stem cells and identify 45 cis-regulatory elements of POU5F1. A majority of these elements display active chromatin marks, DNase hypersensitivity and occupancy by multiple transcription factors, confirming the utility of chromatin signatures in cis elements mapping. Notably, 17 of them are previously annotated promoters of functionally unrelated genes, and like typical enhancers, they form extensive spatial contacts with the POU5F1 promoter. Taken together, these results support the utility of CREST-seq for large-scale cis regulatory element discovery and point to commonality of enhancer-like promoters in the human genome.
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128
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Budzyńska PM, Kyläniemi MK, Kallonen T, Soikkeli AI, Nera KP, Lassila O, Alinikula J. Bach2 regulates AID-mediated immunoglobulin gene conversion and somatic hypermutation in DT40 B cells. Eur J Immunol 2017; 47:993-1001. [DOI: 10.1002/eji.201646895] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 02/09/2017] [Accepted: 03/13/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Paulina M Budzyńska
- Department of Medical Microbiology and Immunology; University of Turku; Turku Finland
- Turku Doctoral Programme of Biomedical Sciences and Turku Doctoral Programme of Molecular Medicine; University of Turku; Turku Finland
| | - Minna K Kyläniemi
- Department of Medical Microbiology and Immunology; University of Turku; Turku Finland
| | - Teemu Kallonen
- Department of Medical Microbiology and Immunology; University of Turku; Turku Finland
| | - Anni I Soikkeli
- Department of Medical Microbiology and Immunology; University of Turku; Turku Finland
| | - Kalle-Pekka Nera
- Department of Medical Microbiology and Immunology; University of Turku; Turku Finland
| | - Olli Lassila
- Department of Medical Microbiology and Immunology; University of Turku; Turku Finland
- Departament of Medical Microbiology and Immunology; Turku University Hospital; Turku Finland
| | - Jukka Alinikula
- Department of Medical Microbiology and Immunology; University of Turku; Turku Finland
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129
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Long-read ChIA-PET for base-pair-resolution mapping of haplotype-specific chromatin interactions. Nat Protoc 2017; 12:899-915. [PMID: 28358394 DOI: 10.1038/nprot.2017.012] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) is a robust method for capturing genome-wide chromatin interactions. Unlike other 3C-based methods, it includes a chromatin immunoprecipitation (ChIP) step that enriches for interactions mediated by specific target proteins. This unique feature allows ChIA-PET to provide the functional specificity and higher resolution needed to detect chromatin interactions, which chromosome conformation capture (3C)/Hi-C approaches have not achieved. The original ChIA-PET protocol generates short paired-end tags (2 × 20 base pairs (bp)) to detect two genomic loci that are far apart on linear chromosomes but are in spatial proximity in the folded genome. We have improved the original approach by developing long-read ChIA-PET, in which the length of the paired-end tags is increased (up to 2 × 250 bp). The longer PET reads not only improve the tag-mapping efficiency but also increase the probability of covering phased single-nucleotide polymorphisms (SNPs), which allows haplotype-specific chromatin interactions to be identified. Here, we provide the detailed protocol for long-read ChIA-PET that includes cell fixation and lysis, chromatin fragmentation by sonication, ChIP, proximity ligation with a bridge linker, Tn5 tagmentation, PCR amplification and high-throughput sequencing. For a well-trained molecular biologist, it typically takes 6 d from cell harvesting to the completion of library construction, up to a further 36 h for DNA sequencing and <20 h for processing of raw sequencing reads.
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130
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Freire-Pritchett P, Schoenfelder S, Várnai C, Wingett SW, Cairns J, Collier AJ, García-Vílchez R, Furlan-Magaril M, Osborne CS, Fraser P, Rugg-Gunn PJ, Spivakov M. Global reorganisation of cis-regulatory units upon lineage commitment of human embryonic stem cells. eLife 2017; 6:e21926. [PMID: 28332981 PMCID: PMC5407860 DOI: 10.7554/elife.21926] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 03/22/2017] [Indexed: 12/19/2022] Open
Abstract
Long-range cis-regulatory elements such as enhancers coordinate cell-specific transcriptional programmes by engaging in DNA looping interactions with target promoters. Deciphering the interplay between the promoter connectivity and activity of cis-regulatory elements during lineage commitment is crucial for understanding developmental transcriptional control. Here, we use Promoter Capture Hi-C to generate a high-resolution atlas of chromosomal interactions involving ~22,000 gene promoters in human pluripotent and lineage-committed cells, identifying putative target genes for known and predicted enhancer elements. We reveal extensive dynamics of cis-regulatory contacts upon lineage commitment, including the acquisition and loss of promoter interactions. This spatial rewiring occurs preferentially with predicted changes in the activity of cis-regulatory elements and is associated with changes in target gene expression. Our results provide a global and integrated view of promoter interactome dynamics during lineage commitment of human pluripotent cells.
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Affiliation(s)
| | | | - Csilla Várnai
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, United Kingdom
| | - Steven W Wingett
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, United Kingdom
| | - Jonathan Cairns
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, United Kingdom
| | - Amanda J Collier
- Epigenetics Programme, Babraham Institute, Cambridge, United Kingdom
- Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | | | | | - Cameron S Osborne
- Department of Genetics and Molecular Medicine, King's College London School of Medicine, London, United Kingdom
| | - Peter Fraser
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, United Kingdom
| | - Peter J Rugg-Gunn
- Epigenetics Programme, Babraham Institute, Cambridge, United Kingdom
- Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Mikhail Spivakov
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, United Kingdom
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131
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Huang D, Ovcharenko I. Epigenetic and genetic alterations and their influence on gene regulation in chronic lymphocytic leukemia. BMC Genomics 2017; 18:236. [PMID: 28302063 PMCID: PMC5353786 DOI: 10.1186/s12864-017-3617-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 03/10/2017] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND To understand the changes of gene regulation in carcinogenesis, we explored signals of DNA methylation - a stable epigenetic mark of gene regulatory elements - and designed a computational model to profile loss and gain of regulatory elements (REs) during carcinogenesis. We also utilized sequencing data to analyze the allele frequency of single nucleotide polymorphisms (SNPs) and detected the cancer-associated SNPs, i.e., the SNPs displaying the significant allele frequency difference between cancer and normal samples. RESULTS After applying this model to chronic lymphocytic leukemia (CLL) data, we identified REs differentially activated (dREs) between normal and CLL cells, consisting of 6,802 dREs gained and 4,606 dREs lost in CLL. The identified regulatory perturbations coincide with changes in the expression of target genes. In particular, the genes encoding DNA methyltransferases harbor multiple lost-in-cancer dREs and zero gained-in-cancer dREs, indicating that the damaged regulation of these genes might be one of the key causes of tumor formation. dREs display a significantly elevated density of the genome-wide association study (GWAS) SNPs associated with CLL and CLL-related traits. We observed that most of dRE GWAS SNPs associated with CLL and CLL-related traits (83%) display a significant haplotype association among the identified cancer-associated alleles and the risk alleles that have been reported in GWAS. Also dREs are enriched for the binding sites of the well-established B-cell and CLL transcription factors (TFs) NF-kB, AP2, P53, E2F1, PAX5, and SP1. We also identified CLL-associated SNPs and demonstrated that the mutations at these SNPs change the binding sites of key TFs much more frequently than expected. CONCLUSIONS Through exploring sequencing data measuring DNA methylation, we identified the epigenetic alterations (more specifically, DNA methylation) and genetic mutations along non-coding genomic regions CLL, and demonstrated that these changes play a critical role in carcinogenesis through damaging the regulation of key genes and alternating the binding of key TFs in B and CLL cells.
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Affiliation(s)
- Di Huang
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ivan Ovcharenko
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20892, USA.
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132
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Crebbp loss cooperates with Bcl2 overexpression to promote lymphoma in mice. Blood 2017; 129:2645-2656. [PMID: 28288979 DOI: 10.1182/blood-2016-08-733469] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 03/05/2017] [Indexed: 12/16/2022] Open
Abstract
CREBBP is targeted by inactivating mutations in follicular lymphoma (FL) and diffuse large B-cell lymphoma (DLBCL). Here, we provide evidence from transgenic mouse models that Crebbp deletion results in deficits in B-cell development and can cooperate with Bcl2 overexpression to promote B-cell lymphoma. Through transcriptional and epigenetic profiling of these B cells, we found that Crebbp inactivation was associated with broad transcriptional alterations, but no changes in the patterns of histone acetylation at the proximal regulatory regions of these genes. However, B cells with Crebbp inactivation showed high expression of Myc and patterns of altered histone acetylation that were localized to intragenic regions, enriched for Myc DNA binding motifs, and showed Myc binding. Through the analysis of CREBBP mutations from a large cohort of primary human FL and DLBCL, we show a significant difference in the spectrum of CREBBP mutations in these 2 diseases, with higher frequencies of nonsense/frameshift mutations in DLBCL compared with FL. Together, our data therefore provide important links between Crebbp inactivation and Bcl2 dependence and show a role for Crebbp inactivation in the induction of Myc expression. We suggest this may parallel the role of CREBBP frameshift/nonsense mutations in DLBCL that result in loss of the protein, but may contrast the role of missense mutations in the lysine acetyltransferase domain that are more frequently observed in FL and yield an inactive protein.
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133
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Baskin E, Farouni R, Mathé EA. ALTRE: workflow for defining ALTered Regulatory Elements using chromatin accessibility data. Bioinformatics 2017; 33:740-742. [PMID: 28011773 PMCID: PMC5408819 DOI: 10.1093/bioinformatics/btw688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 10/26/2016] [Indexed: 11/13/2022] Open
Abstract
Summary Regulatory elements regulate gene transcription, and their location and accessibility is cell-type specific, particularly for enhancers. Mapping and comparing chromatin accessibility between different cell types may identify mechanisms involved in cellular development and disease progression. To streamline and simplify differential analysis of regulatory elements genome-wide using chromatin accessibility data, such as DNase-seq, ATAC-seq, we developed ALTRE ( ALT ered R egulatory E lements), an R package and associated R Shiny web app. ALTRE makes such analysis accessible to a wide range of users-from novice to practiced computational biologists. Availability and Implementation https://github.com/Mathelab/ALTRE. Contact ewy.mathe@osumc.edu. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Elizabeth Baskin
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Rick Farouni
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Ewy A Mathé
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, USA
- To whom correspondence should be addressed.
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134
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Davies JOJ, Oudelaar AM, Higgs DR, Hughes JR. How best to identify chromosomal interactions: a comparison of approaches. Nat Methods 2017; 14:125-134. [PMID: 28139673 DOI: 10.1038/nmeth.4146] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 12/20/2016] [Indexed: 12/28/2022]
Abstract
Chromosome conformation capture (3C) methods are central to understanding the link between nuclear structure and function, and the physical interactions between distal regulatory elements and promoters. However, no one method is appropriate to address all biological questions, as each variant differs markedly in resolution, reproducibility, throughput and biases. A thorough appreciation of the strengths and weaknesses of each technique is critical when choosing the correct method for a specific application or for gauging how best to interpret different sources of data. In addition, the analysis method must be carefully considered, as this choice can profoundly affect the output. In this Review, we describe and compare the different available 3C-based approaches, with a focus on the analysis of mammalian genomes.
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Affiliation(s)
- James O J Davies
- Medical Research Council (MRC) Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, United Kingdom
| | - A Marieke Oudelaar
- Medical Research Council (MRC) Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, United Kingdom
| | - Douglas R Higgs
- Medical Research Council (MRC) Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, United Kingdom
| | - Jim R Hughes
- Medical Research Council (MRC) Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, United Kingdom
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135
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Galupa R, Heard E. Topologically Associating Domains in Chromosome Architecture and Gene Regulatory Landscapes during Development, Disease, and Evolution. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2017; 82:267-278. [DOI: 10.1101/sqb.2017.82.035030] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
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136
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Pérez-Rico YA, Boeva V, Mallory AC, Bitetti A, Majello S, Barillot E, Shkumatava A. Comparative analyses of super-enhancers reveal conserved elements in vertebrate genomes. Genome Res 2016; 27:259-268. [PMID: 27965291 PMCID: PMC5287231 DOI: 10.1101/gr.203679.115] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 12/09/2016] [Indexed: 12/11/2022]
Abstract
Super-enhancers (SEs) are key transcriptional drivers of cellular, developmental, and disease states in mammals, yet the conservational and regulatory features of these enhancer elements in nonmammalian vertebrates are unknown. To define SEs in zebrafish and enable sequence and functional comparisons to mouse and human SEs, we used genome-wide histone H3 lysine 27 acetylation (H3K27ac) occupancy as a primary SE delineator. Our study determined the set of SEs in pluripotent state cells and adult zebrafish tissues and revealed both similarities and differences between zebrafish and mammalian SEs. Although the total number of SEs was proportional to the genome size, the genomic distribution of zebrafish SEs differed from that of the mammalian SEs. Despite the evolutionary distance separating zebrafish and mammals and the low overall SE sequence conservation, ∼42% of zebrafish SEs were located in close proximity to orthologs that also were associated with SEs in mouse and human. Compared to their nonassociated counterparts, higher sequence conservation was revealed for those SEs that have maintained orthologous gene associations. Functional dissection of two of these SEs identified conserved sequence elements and tissue-specific expression patterns, while chromatin accessibility analyses predicted transcription factors governing the function of pluripotent state zebrafish SEs. Our zebrafish annotations and comparative studies show the extent of SE usage and their conservation across vertebrates, permitting future gene regulatory studies in several tissues.
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Affiliation(s)
- Yuvia A Pérez-Rico
- Institut Curie, PSL Research University, INSERM U934, CNRS UMR 3215, F-75005, Paris, France.,INSERM, U900, F-75005, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, F-75005, Paris, France
| | - Valentina Boeva
- INSERM, U900, F-75005, Paris, France.,Institut Curie, Mines ParisTech, PSL Research University, F-75005, Paris, France.,Institut Cochin, INSERM U1016, CNRS UMR 8104, Université Paris Descartes UMR-S1016, F-75014 Paris, France
| | - Allison C Mallory
- Institut Curie, PSL Research University, INSERM U934, CNRS UMR 3215, F-75005, Paris, France
| | - Angelo Bitetti
- Institut Curie, PSL Research University, INSERM U934, CNRS UMR 3215, F-75005, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, F-75005, Paris, France
| | - Sara Majello
- Institut Curie, PSL Research University, INSERM U934, CNRS UMR 3215, F-75005, Paris, France
| | - Emmanuel Barillot
- INSERM, U900, F-75005, Paris, France.,Institut Curie, Mines ParisTech, PSL Research University, F-75005, Paris, France
| | - Alena Shkumatava
- Institut Curie, PSL Research University, INSERM U934, CNRS UMR 3215, F-75005, Paris, France
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137
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TET proteins regulate the lineage specification and TCR-mediated expansion of iNKT cells. Nat Immunol 2016; 18:45-53. [PMID: 27869820 DOI: 10.1038/ni.3630] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2016] [Accepted: 10/25/2016] [Indexed: 12/12/2022]
Abstract
TET proteins oxidize 5-methylcytosine in DNA to 5-hydroxymethylcytosine and other oxidation products. We found that simultaneous deletion of Tet2 and Tet3 in mouse CD4+CD8+ double-positive thymocytes resulted in dysregulated development and proliferation of invariant natural killer T cells (iNKT cells). Tet2-Tet3 double-knockout (DKO) iNKT cells displayed pronounced skewing toward the NKT17 lineage, with increased DNA methylation and impaired expression of genes encoding the key lineage-specifying factors T-bet and ThPOK. Transfer of purified Tet2-Tet3 DKO iNKT cells into immunocompetent recipient mice resulted in an uncontrolled expansion that was dependent on the nonclassical major histocompatibility complex (MHC) protein CD1d, which presents lipid antigens to iNKT cells. Our data indicate that TET proteins regulate iNKT cell fate by ensuring their proper development and maturation and by suppressing aberrant proliferation mediated by the T cell antigen receptor (TCR).
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138
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Symmons O, Pan L, Remeseiro S, Aktas T, Klein F, Huber W, Spitz F. The Shh Topological Domain Facilitates the Action of Remote Enhancers by Reducing the Effects of Genomic Distances. Dev Cell 2016; 39:529-543. [PMID: 27867070 PMCID: PMC5142843 DOI: 10.1016/j.devcel.2016.10.015] [Citation(s) in RCA: 150] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 08/01/2016] [Accepted: 10/18/2016] [Indexed: 11/18/2022]
Abstract
Gene expression often requires interaction between promoters and distant enhancers, which occur within the context of highly organized topologically associating domains (TADs). Using a series of engineered chromosomal rearrangements at the Shh locus, we carried out an extensive fine-scale characterization of the factors that govern the long-range regulatory interactions controlling Shh expression. We show that Shh enhancers act pervasively, yet not uniformly, throughout the TAD. Importantly, changing intra-TAD distances had no impact on Shh expression. In contrast, inversions disrupting the TAD altered global folding of the region and prevented regulatory contacts in a distance-dependent manner. Our data indicate that the Shh TAD promotes distance-independent contacts between distant regions that would otherwise interact only sporadically, enabling functional communication between them. In large genomes where genomic distances per se can limit regulatory interactions, this function of TADs could be as essential for gene expression as the formation of insulated neighborhoods.
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Affiliation(s)
- Orsolya Symmons
- Developmental Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Leslie Pan
- Developmental Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Silvia Remeseiro
- Developmental Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Tugce Aktas
- Developmental Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Felix Klein
- Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Wolfgang Huber
- Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - François Spitz
- Developmental Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany; Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
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139
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Melamed P, Yosefzon Y, Rudnizky S, Pnueli L. Transcriptional enhancers: Transcription, function and flexibility. Transcription 2016; 7:26-31. [PMID: 26934309 DOI: 10.1080/21541264.2015.1128517] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Active transcriptional enhancers are often transcribed to eRNAs, whose changing levels mirror those of the target gene mRNA. We discuss some of the reported functions of these eRNAs and their likely diversity to allow utilization of distinct cis regulatory regions to enhance transcription in diverse developmental and cellular contexts.
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Affiliation(s)
- Philippa Melamed
- a Faculty of Biology, Technion-Israel Institute of Technology , Haifa , Israel
| | - Yahav Yosefzon
- a Faculty of Biology, Technion-Israel Institute of Technology , Haifa , Israel
| | - Sergei Rudnizky
- a Faculty of Biology, Technion-Israel Institute of Technology , Haifa , Israel
| | - Lilach Pnueli
- a Faculty of Biology, Technion-Israel Institute of Technology , Haifa , Israel
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140
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Abstract
Genetic variation associated with disease often appears in non-coding parts of the genome. Understanding the mechanisms by which this phenomenon leads to disease is necessary to translate results from genetic association studies to the clinic. Assigning function to this type of variation is notoriously difficult because the human genome harbours a complex regulatory landscape with a dizzying array of transcriptional regulatory sequences, such as enhancers that have unpredictable, promiscuous and context-dependent behaviour. In this Review, we discuss how technological advances have provided increasingly detailed information on genome folding; for example, genome folding forms loops that bring enhancers and target genes into close proximity. We also now know that enhancers function within topologically associated domains, which are structural and functional units of chromosomes. Studying disease-associated mutations and chromosomal rearrangements in the context of the 3D genome will enable the identification of dysregulated target genes and aid the progression from descriptive genetic association results to discovering molecular mechanisms underlying disease.
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141
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Cai L, Chang H, Fang Y, Li G. A Comprehensive Characterization of the Function of LincRNAs in Transcriptional Regulation Through Long-Range Chromatin Interactions. Sci Rep 2016; 6:36572. [PMID: 27824113 PMCID: PMC5099911 DOI: 10.1038/srep36572] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 10/18/2016] [Indexed: 11/13/2022] Open
Abstract
LincRNAs are emerging as important regulators with various cellular functions. However, the mechanisms behind their role in transcriptional regulation have not yet been fully explored. In this report, we proposed to characterize the diverse functions of lincRNAs in transcription regulation through an examination of their long-range chromatin interactions. We found that the promoter regions of lincRNAs displayed two distinct patterns of chromatin states, promoter-like and enhancer-like, indicating different regulatory functions for lincRNAs. Notably, the chromatin interactions between lincRNA genes and other genes suggested a potential mechanism for lincRNAs in the regulation of other genes at the RNA level because the transcribed lincRNAs could function at local spaces on other genes that interact with the lincRNAs at the DNA level. These results represent a novel way to predict the functions of lincRNAs. The GWAS-identification of SNPs within the lincRNAs revealed that some lincRNAs were disease-associated, and the chromatin interactions with those lincRNAs suggested that they were potential target genes of these lincRNA-associated SNPs. Our study provides new insights into the roles that lincRNAs play in transcription regulation.
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Affiliation(s)
- Liuyang Cai
- National Key Laboratory of Crop Genetic Improvement, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Huidan Chang
- National Key Laboratory of Crop Genetic Improvement, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yaping Fang
- National Key Laboratory of Crop Genetic Improvement, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Guoliang Li
- National Key Laboratory of Crop Genetic Improvement, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, China
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142
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Szałaj P, Tang Z, Michalski P, Pietal MJ, Luo OJ, Sadowski M, Li X, Radew K, Ruan Y, Plewczynski D. An integrated 3-Dimensional Genome Modeling Engine for data-driven simulation of spatial genome organization. Genome Res 2016; 26:1697-1709. [PMID: 27789526 PMCID: PMC5131821 DOI: 10.1101/gr.205062.116] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 10/20/2016] [Indexed: 02/03/2023]
Abstract
ChIA-PET is a high-throughput mapping technology that reveals long-range chromatin interactions and provides insights into the basic principles of spatial genome organization and gene regulation mediated by specific protein factors. Recently, we showed that a single ChIA-PET experiment provides information at all genomic scales of interest, from the high-resolution locations of binding sites and enriched chromatin interactions mediated by specific protein factors, to the low resolution of nonenriched interactions that reflect topological neighborhoods of higher-order chromosome folding. This multilevel nature of ChIA-PET data offers an opportunity to use multiscale 3D models to study structural-functional relationships at multiple length scales, but doing so requires a structural modeling platform. Here, we report the development of 3D-GNOME (3-Dimensional Genome Modeling Engine), a complete computational pipeline for 3D simulation using ChIA-PET data. 3D-GNOME consists of three integrated components: a graph-distance-based heat map normalization tool, a 3D modeling platform, and an interactive 3D visualization tool. Using ChIA-PET and Hi-C data derived from human B-lymphocytes, we demonstrate the effectiveness of 3D-GNOME in building 3D genome models at multiple levels, including the entire genome, individual chromosomes, and specific segments at megabase (Mb) and kilobase (kb) resolutions of single average and ensemble structures. Further incorporation of CTCF-motif orientation and high-resolution looping patterns in 3D simulation provided additional reliability of potential biologically plausible topological structures.
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Affiliation(s)
- Przemysław Szałaj
- Centre of New Technologies, Warsaw University, 02-097 Warsaw, Poland.,Centre for Innovative Research, Medical University of Bialystok, 15-089 Białystok, Poland.,I-BioStat, Hasselt University, BE3590 Hasselt, Belgium
| | - Zhonghui Tang
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06032, USA
| | - Paul Michalski
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06032, USA
| | - Michal J Pietal
- Centre of New Technologies, Warsaw University, 02-097 Warsaw, Poland
| | - Oscar J Luo
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06032, USA
| | - Michał Sadowski
- Centre of New Technologies, Warsaw University, 02-097 Warsaw, Poland
| | - Xingwang Li
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06032, USA
| | - Kamen Radew
- Centre of New Technologies, Warsaw University, 02-097 Warsaw, Poland
| | - Yijun Ruan
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06032, USA.,Department of Genetics and Genome Sciences, UConn Health, Farmington, Connecticut 06032, USA
| | - Dariusz Plewczynski
- Centre of New Technologies, Warsaw University, 02-097 Warsaw, Poland.,Centre for Innovative Research, Medical University of Bialystok, 15-089 Białystok, Poland.,Faculty of Pharmacy, Medical University of Warsaw, 02-097 Warsaw, Poland
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143
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Sacilotto N, Chouliaras KM, Nikitenko LL, Lu YW, Fritzsche M, Wallace MD, Nornes S, García-Moreno F, Payne S, Bridges E, Liu K, Biggs D, Ratnayaka I, Herbert SP, Molnár Z, Harris AL, Davies B, Bond GL, Bou-Gharios G, Schwarz JJ, De Val S. MEF2 transcription factors are key regulators of sprouting angiogenesis. Genes Dev 2016; 30:2297-2309. [PMID: 27898394 PMCID: PMC5110996 DOI: 10.1101/gad.290619.116] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 09/29/2016] [Indexed: 12/24/2022]
Abstract
Angiogenesis, the fundamental process by which new blood vessels form from existing ones, depends on precise spatial and temporal gene expression within specific compartments of the endothelium. However, the molecular links between proangiogenic signals and downstream gene expression remain unclear. During sprouting angiogenesis, the specification of endothelial cells into the tip cells that lead new blood vessel sprouts is coordinated by vascular endothelial growth factor A (VEGFA) and Delta-like ligand 4 (Dll4)/Notch signaling and requires high levels of Notch ligand DLL4. Here, we identify MEF2 transcription factors as crucial regulators of sprouting angiogenesis directly downstream from VEGFA. Through the characterization of a Dll4 enhancer directing expression to endothelial cells at the angiogenic front, we found that MEF2 factors directly transcriptionally activate the expression of Dll4 and many other key genes up-regulated during sprouting angiogenesis in both physiological and tumor vascularization. Unlike ETS-mediated regulation, MEF2-binding motifs are not ubiquitous to all endothelial gene enhancers and promoters but are instead overrepresented around genes associated with sprouting angiogenesis. MEF2 target gene activation is directly linked to VEGFA-induced release of repressive histone deacetylases and concurrent recruitment of the histone acetyltransferase EP300 to MEF2 target gene regulatory elements, thus establishing MEF2 factors as the transcriptional effectors of VEGFA signaling during angiogenesis.
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Affiliation(s)
- Natalia Sacilotto
- Ludwig Institute for Cancer Research Ltd., Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Kira M Chouliaras
- Ludwig Institute for Cancer Research Ltd., Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Leonid L Nikitenko
- Ludwig Institute for Cancer Research Ltd., Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Yao Wei Lu
- Center for Cardiovascular Sciences, Albany Medical College, Albany, New York 12208, USA
| | - Martin Fritzsche
- Ludwig Institute for Cancer Research Ltd., Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Marsha D Wallace
- Ludwig Institute for Cancer Research Ltd., Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Svanhild Nornes
- Ludwig Institute for Cancer Research Ltd., Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Fernando García-Moreno
- Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford OX1 3QX, United Kingdom
| | - Sophie Payne
- Ludwig Institute for Cancer Research Ltd., Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Esther Bridges
- Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 7LJ, United Kingdom
| | - Ke Liu
- Institute of Aging and Chronic Disease, University of Liverpool, Liverpool L7 8TX, United Kingdom
| | - Daniel Biggs
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Indrika Ratnayaka
- Ludwig Institute for Cancer Research Ltd., Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Shane P Herbert
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Zoltán Molnár
- Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford OX1 3QX, United Kingdom
| | - Adrian L Harris
- Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 7LJ, United Kingdom
| | - Benjamin Davies
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Gareth L Bond
- Ludwig Institute for Cancer Research Ltd., Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - George Bou-Gharios
- Institute of Aging and Chronic Disease, University of Liverpool, Liverpool L7 8TX, United Kingdom
| | - John J Schwarz
- Center for Cardiovascular Sciences, Albany Medical College, Albany, New York 12208, USA
| | - Sarah De Val
- Ludwig Institute for Cancer Research Ltd., Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom
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144
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Abstract
Chromatin immunoprecipitation with massively parallel DNA sequencing (ChIP-Seq) has been used extensively to determine the genome-wide location of DNA-binding factors, such as transcription factors, posttranscriptionally modified histones, and members of the transcription complex, to assess regulatory input, epigenetic modifications, and transcriptional activity, respectively. Here we describe methods to isolate chromatin from tissues, immunoprecipitate DNA bound to a protein of interest, and perform next-generation sequencing to identify a genome-wide DNA-binding pattern.
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Affiliation(s)
- Karyn L Sheaffer
- Department of Genetics, and Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jonathan Schug
- Department of Genetics, and Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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145
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Cico A, Andrieu-Soler C, Soler E. Enhancers and their dynamics during hematopoietic differentiation and emerging strategies for therapeutic action. FEBS Lett 2016; 590:4084-4104. [DOI: 10.1002/1873-3468.12424] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Revised: 09/08/2016] [Accepted: 09/12/2016] [Indexed: 12/18/2022]
Affiliation(s)
- Alba Cico
- Inserm UMR967, CEA/DRF/iRCM; Fontenay-aux-Roses France
| | - Charlotte Andrieu-Soler
- Inserm UMR967, CEA/DRF/iRCM; Fontenay-aux-Roses France
- CNRS; Institute of Molecular Genetics (IGMM); Montpellier France
| | - Eric Soler
- Inserm UMR967, CEA/DRF/iRCM; Fontenay-aux-Roses France
- CNRS; Institute of Molecular Genetics (IGMM); Montpellier France
- Laboratory of Excellence GR-Ex; Paris France
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146
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Suppression by T FR cells leads to durable and selective inhibition of B cell effector function. Nat Immunol 2016; 17:1436-1446. [PMID: 27695002 DOI: 10.1038/ni.3578] [Citation(s) in RCA: 154] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 09/07/2016] [Indexed: 12/14/2022]
Abstract
Follicular regulatory T cells (TFR cells) inhibit follicular helper T cell (TFH cell)-mediated antibody production. The mechanisms by which TFR cells exert their key immunoregulatory functions are largely unknown. Here we found that TFR cells induced a distinct suppressive state in TFH cells and B cells, in which effector transcriptional signatures were maintained but key effector molecules and metabolic pathways were suppressed. The suppression of B cell antibody production and metabolism by TFR cells was durable and persisted even in the absence of TFR cells. This durable suppression was due in part to epigenetic changes. The cytokine IL-21 was able to overcome TFR cell-mediated suppression and inhibited TFR cells and stimulated B cells. By determining mechanisms of TFR cell-mediated suppression, we have identified methods for modulating the function of TFR cells and antibody production.
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147
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Resetting the epigenome for heart regeneration. Semin Cell Dev Biol 2016; 58:2-13. [DOI: 10.1016/j.semcdb.2015.12.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 12/29/2015] [Indexed: 12/27/2022]
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148
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Kim KD, Tanizawa H, Iwasaki O, Noma KI. Transcription factors mediate condensin recruitment and global chromosomal organization in fission yeast. Nat Genet 2016; 48:1242-52. [PMID: 27548313 PMCID: PMC5042855 DOI: 10.1038/ng.3647] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 07/22/2016] [Indexed: 12/13/2022]
Abstract
It is becoming clear that structural-maintenance-of-chromosomes (SMC) complexes such as condensin and cohesin are involved in three-dimensional genome organization, yet their exact roles in functional organization remain unclear. We used chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) to comprehensively identify genome-wide associations mediated by condensin and cohesin in fission yeast. We found that although cohesin and condensin often bind to the same loci, they direct different association networks and generate small and larger chromatin domains, respectively. Cohesin mediates associations between loci positioned within 100 kb of each other; condensin can drive longer-range associations. Moreover, condensin, but not cohesin, connects cell cycle-regulated genes bound by mitotic transcription factors. This study describes the different functions of condensin and cohesin in genome organization and how specific transcription factors function in condensin loading, cell cycle-dependent genome organization and mitotic chromosome organization to support faithful chromosome segregation.
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149
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Babu D, Fullwood MJ. 3D genome organization in health and disease: emerging opportunities in cancer translational medicine. Nucleus 2016; 6:382-93. [PMID: 26553406 PMCID: PMC4915485 DOI: 10.1080/19491034.2015.1106676] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Organizing the DNA to fit inside a spatially constrained nucleus is a challenging problem that has attracted the attention of scientists across all disciplines of science. Increasing evidence has demonstrated the importance of genome geometry in several cellular contexts that affect human health. Among several approaches, the application of sequencing technologies has substantially increased our understanding of this intricate organization, also known as chromatin interactions. These structures are involved in transcriptional control of gene expression by connecting distal regulatory elements with their target genes and regulating co-transcriptional splicing. In addition, chromatin interactions play pivotal roles in the organization of the genome, the formation of structural variants, recombination, DNA replication and cell division. Mutations in factors that regulate chromatin interactions lead to the development of pathological conditions, for example, cancer. In this review, we discuss key findings that have shed light on the importance of these structures in the context of cancers, and highlight the applicability of chromatin interactions as potential biomarkers in molecular medicine as well as therapeutic implications of chromatin interactions.
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Affiliation(s)
- Deepak Babu
- a Cancer Science Institute of Singapore: Singapore; National University of Singapore ; Singapore
| | - Melissa J Fullwood
- a Cancer Science Institute of Singapore: Singapore; National University of Singapore ; Singapore.,b School of Biological Sciences; Nanyang Technological University ; Singapore.,c Institute of Molecular and Cell Biology; Agency for Science; Technology and Research (A*STAR) ; Singapore.,d Yale-NUS Liberal Arts College ; Singapore
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150
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Abstract
We are beginning to understand the function of 3D genome architecture in the immune system. In this issue, Bunting et al. (2016) reported massive multi-layer genome reorganization from naive B cells to germinal center B cells, centered on a locus control region of Bcl6.
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Affiliation(s)
- Gangqing Hu
- Systems Biology Center, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Keji Zhao
- Systems Biology Center, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA.
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