351
|
Abstract
Pancreatic cancer is an aggressive and intractable malignancy with high mortality. This is due in part to a high resistance to chemotherapeutics and radiation treatment conferred by diverse regulatory mechanisms. Among these, constituents of the nuclear envelope play a significant role in regulating oncogenesis and pancreatic tumor biology, and this review focuses on three specific components and their roles in cancer. The LINC complex is a nuclear envelope component formed by proteins with SUN and KASH domains that interact in the periplasmic space of the nuclear envelope. These interactions functionally and structurally couple the cytoskeleton to chromatin and facilitates gene regulation informed by cytoplasmic activity. Furthermore, cancer cell invasiveness is impacted by LINC complex biology. The nuclear lamina is adjacent to the inner nuclear membrane of the nuclear envelope and can actively regulate chromatin in addition to providing structural integrity to the nucleus. A disrupted lamina can impart biophysical compromise to nuclear structure and function, as well as form dysfunctional micronuclei that may lead to genomic instability and chromothripsis. In close relationship to the nuclear lamina is the nuclear pore complex, a large megadalton structure that spans both outer and inner membranes of the nuclear envelope. The nuclear pore complex mediates bidirectional nucleocytoplasmic transport and is comprised of specialized proteins called nucleoporins that are overexpressed in many cancers and are diagnostic markers for oncogenesis. Furthermore, recent demonstration of gene regulatory functions for discrete nucleoporins independent of their nuclear trafficking function suggests that these proteins may contribute more to malignant phenotypes beyond serving as biomarkers. The nuclear envelope is thus a complex, intricate regulator of cell signaling, with roles in pancreatic tumorigenesis and general oncogenic transformation.
Collapse
Affiliation(s)
| | - Randolph S. Faustino
- Genetics and Genomics, Sanford Research, Sioux Falls, SD 57104, USA
- Department of Pediatrics, Sanford School of Medicine of the University of South Dakota, Sioux Falls, SD 57105, USA
| |
Collapse
|
352
|
Chen F, Zhang Q, Deng X, Zhang X, Chen C, Lv D, Li Y, Li D, Zhang Y, Li P, Diao Y, Kang L, Owen GI, Chen J, Li Z. Conflicts of CpG density and DNA methylation are proximally and distally involved in gene regulation in human and mouse tissues. Epigenetics 2018; 13:721-741. [PMID: 30009687 DOI: 10.1080/15592294.2018.1500057] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The relationship between CpG content and DNA methylation has attracted considerable interest in recent years. Direct or indirect methods have been developed to investigate their regulatory functions based on various hypotheses, large cohort studies, and meta-analyses. However, all of these analyses were performed at units of CpG blocks and, thus, the influence of finer genome structure has been neglected. Herein, we present a novel algorithm of base-pair resolution to systematically investigate the relationship between CpG contents and DNA methylation. By introducing the concept of 'complementary index' we examined the methylomes of 34 adult and 7 embryonic tissues and successfully fitted the relationship of DNA methylation and CpG density into a nonlinear mathematical model. A further algorithm was developed to locate the regions where CpG density does not match expectations from the model, termed 'conflict of gap' (COG) regions. Interestingly, COGs are highly concordant in human and mouse and their distributions display a tissue-specific pattern. Based on COG methylation patterns we correctly classified tissues according to their function or origin. We demonstrate that COGs based on our method can reveal more and deeper information than traditional differential methylation region (DMR) approaches. We also found that when COGs are located near to transcription start site (TSS), these regions can determine which promoters will be utilized for initiating gene transcription. Furthermore, COGs located far from the TSS perform as enhancers in terms of histone modification, sequence conservation, transcription factor binding, and DNase I-hypersensitivity.
Collapse
Affiliation(s)
- Fushun Chen
- a Center of Genome and Personalized Medicine , Institute of Cancer Stem Cell, Dalian Medical University , Dalian , China
| | - Qingzheng Zhang
- a Center of Genome and Personalized Medicine , Institute of Cancer Stem Cell, Dalian Medical University , Dalian , China
| | - Xiaodi Deng
- a Center of Genome and Personalized Medicine , Institute of Cancer Stem Cell, Dalian Medical University , Dalian , China
| | - Xia Zhang
- a Center of Genome and Personalized Medicine , Institute of Cancer Stem Cell, Dalian Medical University , Dalian , China
| | - Chengjun Chen
- a Center of Genome and Personalized Medicine , Institute of Cancer Stem Cell, Dalian Medical University , Dalian , China
| | - Dekang Lv
- a Center of Genome and Personalized Medicine , Institute of Cancer Stem Cell, Dalian Medical University , Dalian , China
| | - Yulong Li
- a Center of Genome and Personalized Medicine , Institute of Cancer Stem Cell, Dalian Medical University , Dalian , China
| | - Dan Li
- b The Second Hospital of Dalian Medical University , Dalian , China
| | - Yu Zhang
- a Center of Genome and Personalized Medicine , Institute of Cancer Stem Cell, Dalian Medical University , Dalian , China
| | - Peiying Li
- a Center of Genome and Personalized Medicine , Institute of Cancer Stem Cell, Dalian Medical University , Dalian , China
| | - Yunpeng Diao
- c Department of Pharmacy , Dalian Medical University , Dalian , China
| | - Lan Kang
- a Center of Genome and Personalized Medicine , Institute of Cancer Stem Cell, Dalian Medical University , Dalian , China
| | - Gareth I Owen
- d Faculty of Biological Sciences , Pontificia Universidad Católica de Chile , Santiago , Chile
| | - Jun Chen
- b The Second Hospital of Dalian Medical University , Dalian , China
| | - Zhiguang Li
- a Center of Genome and Personalized Medicine , Institute of Cancer Stem Cell, Dalian Medical University , Dalian , China
| |
Collapse
|
353
|
Alt FW, Schwer B. DNA double-strand breaks as drivers of neural genomic change, function, and disease. DNA Repair (Amst) 2018; 71:158-163. [PMID: 30195640 DOI: 10.1016/j.dnarep.2018.08.019] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Early work from about two decades ago implicated DNA double-strand break (DSB) formation and repair in neuronal development. Findings emerging from recent studies of DSBs in proliferating neural progenitors and in mature, non-dividing neurons suggest important roles of DSBs in brain physiology, aging, cancer, psychiatric and neurodegenerative disorders. We provide an overview of some findings and speculate on what may lie ahead.
Collapse
Affiliation(s)
- Frederick W Alt
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Department of Genetics, and Department of Pediatrics, Harvard Medical School, Boston, MA 02115, United States.
| | - Bjoern Schwer
- Department of Neurological Surgery and Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94158, United States.
| |
Collapse
|
354
|
Dynamic changes in ORC localization and replication fork progression during tissue differentiation. BMC Genomics 2018; 19:623. [PMID: 30134926 PMCID: PMC6103881 DOI: 10.1186/s12864-018-4992-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 08/02/2018] [Indexed: 12/23/2022] Open
Abstract
Background Genomic regions repressed for DNA replication, resulting in either delayed replication in S phase or underreplication in polyploid cells, are thought to be controlled by inhibition of replication origin activation. Studies in Drosophila polytene cells, however, raised the possibility that impeding replication fork progression also plays a major role. Results We exploited genomic regions underreplicated (URs) with tissue specificity in Drosophila polytene cells to analyze mechanisms of replication repression. By localizing the Origin Recognition Complex (ORC) in the genome of the larval fat body and comparing this to ORC binding in the salivary gland, we found that sites of ORC binding show extensive tissue specificity. In contrast, there are common domains nearly devoid of ORC in the salivary gland and fat body that also have reduced density of ORC binding sites in diploid cells. Strikingly, domains lacking ORC can still be replicated in some polytene tissues, showing absence of ORC and origins is insufficient to repress replication. Analysis of the width and location of the URs with respect to ORC position indicates that whether or not a genomic region lacking ORC is replicated is controlled by whether replication forks formed outside the region are inhibited. Conclusions These studies demonstrate that inhibition of replication fork progression can block replication across genomic regions that constitutively lack ORC. Replication fork progression can be inhibited in both tissue-specific and genome region-specific ways. Consequently, when evaluating sources of genome instability it is important to consider altered control of replication forks in response to differentiation. Electronic supplementary material The online version of this article (10.1186/s12864-018-4992-3) contains supplementary material, which is available to authorized users.
Collapse
|
355
|
Yang Y, Gu Q, Zhang Y, Sasaki T, Crivello J, O'Neill RJ, Gilbert DM, Ma J. Continuous-Trait Probabilistic Model for Comparing Multi-species Functional Genomic Data. Cell Syst 2018; 7:208-218.e11. [PMID: 29936186 PMCID: PMC6107375 DOI: 10.1016/j.cels.2018.05.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 05/17/2018] [Accepted: 05/29/2018] [Indexed: 01/22/2023]
Abstract
A large amount of multi-species functional genomic data from high-throughput assays are becoming available to help understand the molecular mechanisms for phenotypic diversity across species. However, continuous-trait probabilistic models, which are key to such comparative analysis, remain under-explored. Here we develop a new model, called phylogenetic hidden Markov Gaussian processes (Phylo-HMGP), to simultaneously infer heterogeneous evolutionary states of functional genomic features in a genome-wide manner. Both simulation studies and real data application demonstrate the effectiveness of Phylo-HMGP. Importantly, we applied Phylo-HMGP to analyze a new cross-species DNA replication timing (RT) dataset from the same cell type in five primate species (human, chimpanzee, orangutan, gibbon, and green monkey). We demonstrate that our Phylo-HMGP model enables discovery of genomic regions with distinct evolutionary patterns of RT. Our method provides a generic framework for comparative analysis of multi-species continuous functional genomic signals to help reveal regions with conserved or lineage-specific regulatory roles.
Collapse
Affiliation(s)
- Yang Yang
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Quanquan Gu
- Department of Computer Science, University of Virginia, Charlottesville, VA 22904, USA
| | - Yang Zhang
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Takayo Sasaki
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Julianna Crivello
- Institute for Systems Genomics, Department of Molecular & Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Rachel J O'Neill
- Institute for Systems Genomics, Department of Molecular & Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - David M Gilbert
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Jian Ma
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
| |
Collapse
|
356
|
Rivera-Mulia JC, Schwerer H, Besnard E, Desprat R, Trevilla-Garcia C, Sima J, Bensadoun P, Zouaoui A, Gilbert DM, Lemaitre JM. Cellular senescence induces replication stress with almost no affect on DNA replication timing. Cell Cycle 2018; 17:1667-1681. [PMID: 29963964 DOI: 10.1080/15384101.2018.1491235] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Organismal aging entails a gradual decline of normal physiological functions and a major contributor to this decline is withdrawal of the cell cycle, known as senescence. Senescence can result from telomere diminution leading to a finite number of population doublings, known as replicative senescence (RS), or from oncogene overexpression, as a protective mechanism against cancer. Senescence is associated with large-scale chromatin re-organization and changes in gene expression. Replication stress is a complex phenomenon, defined as the slowing or stalling of replication fork progression and/or DNA synthesis, which has serious implications for genome stability, and consequently in human diseases. Aberrant replication fork structures activate the replication stress response leading to the activation of dormant origins, which is thought to be a safeguard mechanism to complete DNA replication on time. However, the relationship between replicative stress and the changes in the spatiotemporal program of DNA replication in senescence progression remains unclear. Here, we studied the DNA replication program during senescence progression in proliferative and pre-senescent cells from donors of various ages by single DNA fiber combing of replicated DNA, origin mapping by sequencing short nascent strands and genome-wide profiling of replication timing (TRT). We demonstrate that, progression into RS leads to reduced replication fork rates and activation of dormant origins, which are the hallmarks of replication stress. However, with the exception of a delay in RT of the CREB5 gene in all pre-senescent cells, RT was globally unaffected by replication stress during entry into either oncogene-induced or RS. Consequently, we conclude that RT alterations associated with physiological and accelerated aging, do not result from senescence progression. Our results clarify the interplay between senescence, aging and replication programs and demonstrate that RT is largely resistant to replication stress.
Collapse
Affiliation(s)
| | - Hélène Schwerer
- b Laboratory of Genome and Stem Cell Plasticity in Development and Aging , Institute of Regenerative Medicine, U1183, Université de Montpellier , Montpellier Cedex , France
| | - Emilie Besnard
- b Laboratory of Genome and Stem Cell Plasticity in Development and Aging , Institute of Regenerative Medicine, U1183, Université de Montpellier , Montpellier Cedex , France
| | - Romain Desprat
- c Stem cell Core Facility SAFE-iPS INGESTEM , CHU Montpellier, Saint Eloi Hospital , Montpellier Cedex , France
| | | | - Jiao Sima
- a Department of Biological Science , Florida State University , Tallahassee , FL , USA
| | - Paul Bensadoun
- b Laboratory of Genome and Stem Cell Plasticity in Development and Aging , Institute of Regenerative Medicine, U1183, Université de Montpellier , Montpellier Cedex , France
| | - Anissa Zouaoui
- c Stem cell Core Facility SAFE-iPS INGESTEM , CHU Montpellier, Saint Eloi Hospital , Montpellier Cedex , France
| | - David M Gilbert
- a Department of Biological Science , Florida State University , Tallahassee , FL , USA.,d Center for Genomics and Personalized Medicine , Florida State University , Tallahassee , FL , USA
| | - Jean-Marc Lemaitre
- b Laboratory of Genome and Stem Cell Plasticity in Development and Aging , Institute of Regenerative Medicine, U1183, Université de Montpellier , Montpellier Cedex , France.,c Stem cell Core Facility SAFE-iPS INGESTEM , CHU Montpellier, Saint Eloi Hospital , Montpellier Cedex , France
| |
Collapse
|
357
|
Petryk N, Dalby M, Wenger A, Stromme CB, Strandsby A, Andersson R, Groth A. MCM2 promotes symmetric inheritance of modified histones during DNA replication. Science 2018; 361:1389-1392. [PMID: 30115746 DOI: 10.1126/science.aau0294] [Citation(s) in RCA: 168] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 08/06/2018] [Indexed: 12/13/2022]
Abstract
During genome replication, parental histones are recycled to newly replicated DNA with their posttranslational modifications (PTMs). Whether sister chromatids inherit modified histones evenly remains unknown. We measured histone PTM partition to sister chromatids in embryonic stem cells. We found that parental histones H3-H4 segregate to both daughter DNA strands with a weak leading-strand bias, skewing partition at topologically associating domain (TAD) borders and enhancers proximal to replication initiation zones. Segregation of parental histones to the leading strand increased markedly in cells with histone-binding mutations in MCM2, part of the replicative helicase, exacerbating histone PTM sister chromatid asymmetry. This work reveals how histones are inherited to sister chromatids and identifies a mechanism by which the replication machinery ensures symmetric cell division.
Collapse
Affiliation(s)
- Nataliya Petryk
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark.,Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Maria Dalby
- The Bioinformatics Centre, Department of Biology, Faculty of Science, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Alice Wenger
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark.,Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Caroline B Stromme
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Anne Strandsby
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Robin Andersson
- The Bioinformatics Centre, Department of Biology, Faculty of Science, University of Copenhagen, 2200 Copenhagen, Denmark.
| | - Anja Groth
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark. .,Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| |
Collapse
|
358
|
Decoding topologically associating domains with ultra-low resolution Hi-C data by graph structural entropy. Nat Commun 2018; 9:3265. [PMID: 30111883 PMCID: PMC6093941 DOI: 10.1038/s41467-018-05691-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 07/18/2018] [Indexed: 01/09/2023] Open
Abstract
Submegabase-size topologically associating domains (TAD) have been observed in high-throughput chromatin interaction data (Hi-C). However, accurate detection of TADs depends on ultra-deep sequencing and sophisticated normalization procedures. Here we propose a fast and normalization-free method to decode the domains of chromosomes (deDoc) that utilizes structural information theory. By treating Hi-C contact matrix as a representation of a graph, deDoc partitions the graph into segments with minimal structural entropy. We show that structural entropy can also be used to determine the proper bin size of the Hi-C data. By applying deDoc to pooled Hi-C data from 10 single cells, we detect megabase-size TAD-like domains. This result implies that the modular structure of the genome spatial organization may be fundamental to even a small cohort of single cells. Our algorithms may facilitate systematic investigations of chromosomal domains on a larger scale than hitherto have been possible.
Collapse
|
359
|
Diament A, Tuller T. Modeling three-dimensional genomic organization in evolution and pathogenesis. Semin Cell Dev Biol 2018; 90:78-93. [PMID: 30030143 DOI: 10.1016/j.semcdb.2018.07.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 07/08/2018] [Indexed: 12/17/2022]
Abstract
The regulation of gene expression is mediated via the complex three-dimensional (3D) conformation of the genetic material and its interactions with various intracellular factors. Various experimental and computational approaches have been developed in recent years for understating the relation between the 3D conformation of the genome and the phenotypes of cells in normal condition and diseases. In this review, we will discuss novel approaches for analyzing and modeling the 3D genomic conformation, focusing on deciphering disease-causing mutations that affect gene expression. We conclude that as this is a very challenging mission, an important direction should involve the comparative analysis of various 3D models from various organisms or cells.
Collapse
Affiliation(s)
- Alon Diament
- Dept. of Biomedical Engineering, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Tamir Tuller
- Dept. of Biomedical Engineering, Tel Aviv University, Tel Aviv 6997801, Israel; The Sagol School of Neuroscience, Tel-Aviv University, Tel Aviv 6997801, Israel.
| |
Collapse
|
360
|
Umlauf D, Mourad R. The 3D genome: From fundamental principles to disease and cancer. Semin Cell Dev Biol 2018; 90:128-137. [PMID: 30030142 DOI: 10.1016/j.semcdb.2018.07.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 07/03/2018] [Indexed: 12/18/2022]
Abstract
In higher eukaryotes, the three-dimensional (3D) organization of the genome is intimately related to numerous key biological functions including gene expression, DNA repair and DNA replication regulations. Alteration of this 3D organization is detrimental to the organism and can give rise to a broad range of diseases such as cancers. Here, we review recent advances in the field. We first describe how the genome is packed in 3D to form chromosome territories, compartments and domains. We also give an overview of the recent techniques that allow to map the genome in 3D up to the kilobase resolution. We then discuss potential mechanisms by which genome misfolding can affect proper gene expression by distal enhancers, and how the 3D genome influences the formation of genomic rearrangements.
Collapse
Affiliation(s)
- David Umlauf
- LBME, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France.
| | - Raphaël Mourad
- LBCMCP, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France.
| |
Collapse
|
361
|
D'Ippolito AM, McDowell IC, Barrera A, Hong LK, Leichter SM, Bartelt LC, Vockley CM, Majoros WH, Safi A, Song L, Gersbach CA, Crawford GE, Reddy TE. Pre-established Chromatin Interactions Mediate the Genomic Response to Glucocorticoids. Cell Syst 2018; 7:146-160.e7. [PMID: 30031775 DOI: 10.1016/j.cels.2018.06.007] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 02/27/2018] [Accepted: 06/12/2018] [Indexed: 10/28/2022]
Abstract
The glucocorticoid receptor (GR) is a hormone-inducible transcription factor involved in metabolic and anti-inflammatory gene expression responses. To investigate what controls interactions between GR binding sites and their target genes, we used in situ Hi-C to generate high-resolution, genome-wide maps of chromatin interactions before and after glucocorticoid treatment. We found that GR binding to the genome typically does not cause new chromatin interactions to target genes but instead acts through chromatin interactions that already exist prior to hormone treatment. Both glucocorticoid-induced and glucocorticoid-repressed genes increased interactions with distal GR binding sites. In addition, while glucocorticoid-induced genes increased interactions with transcriptionally active chromosome compartments, glucocorticoid-repressed genes increased interactions with transcriptionally silent compartments. Lastly, while the architectural DNA-binding proteins CTCF and RAD21 were bound to most chromatin interactions, we found that glucocorticoid-responsive chromatin interactions were depleted for CTCF binding but enriched for RAD21. Together, these findings offer new insights into the mechanisms underlying GC-mediated gene activation and repression.
Collapse
Affiliation(s)
- Anthony M D'Ippolito
- University Program in Genetics and Genomics, Duke University, Durham, NC 27708, USA; Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA
| | - Ian C McDowell
- Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA; Computational Biology and Bioinformatics Graduate Program, Duke University, Durham, NC 27708, USA
| | - Alejandro Barrera
- Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA; Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC 27710, USA
| | - Linda K Hong
- Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA; Department of Pediatrics, Duke University Medical Center, Durham, NC 27710, USA
| | - Sarah M Leichter
- Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA
| | - Luke C Bartelt
- Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA
| | - Christopher M Vockley
- Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA; Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC 27710, USA
| | - William H Majoros
- Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA; Computational Biology and Bioinformatics Graduate Program, Duke University, Durham, NC 27708, USA
| | - Alexias Safi
- Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA; Department of Pediatrics, Duke University Medical Center, Durham, NC 27710, USA
| | - Lingyun Song
- Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA; Department of Pediatrics, Duke University Medical Center, Durham, NC 27710, USA
| | - Charles A Gersbach
- University Program in Genetics and Genomics, Duke University, Durham, NC 27708, USA; Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA; Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Department of Orthopedic Surgery, Duke University Medical Center, Durham, NC 27708, USA
| | - Gregory E Crawford
- University Program in Genetics and Genomics, Duke University, Durham, NC 27708, USA; Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA; Department of Pediatrics, Duke University Medical Center, Durham, NC 27710, USA; Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Timothy E Reddy
- University Program in Genetics and Genomics, Duke University, Durham, NC 27708, USA; Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA; Computational Biology and Bioinformatics Graduate Program, Duke University, Durham, NC 27708, USA; Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC 27710, USA; Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA.
| |
Collapse
|
362
|
Genetic predisposition to B-cell acute lymphoblastic leukemia at 14q11.2 is mediated by a CEBPE promoter polymorphism. Leukemia 2018; 33:1-14. [PMID: 29977016 PMCID: PMC6327050 DOI: 10.1038/s41375-018-0184-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 05/21/2018] [Accepted: 05/30/2018] [Indexed: 01/08/2023]
Abstract
Acute lymphoblastic leukaemia (ALL) is the most common paediatric malignancy. Genome-wide association studies have shown variation at 14q11.2 influences ALL risk. We sought to decipher causal variant(s) at 14q11.2 and the mechanism of tumorigenesis. We show rs2239630 G>A resides in the promoter of the CCAT enhancer-binding protein epsilon (CEBPE) gene. The rs2239630-A risk allele is associated with increased promotor activity and CEBPE expression. Depletion of CEBPE in ALL cells reduces cell growth, correspondingly CEBPE binds to the promoters of electron transport and energy generation genes. RNA-seq in CEBPE depleted cells demonstrates CEBPE regulates the expression of genes involved in B-cell development (IL7R), apoptosis (BCL2), and methotrexate resistance (RASS4L). CEBPE regulated genes significantly overlapped in CEBPE depleted cells, ALL blasts and IGH-CEBPE translocated ALL. This suggests CEBPE regulates a similar set of genes in each, consistent with a common biological mechanism of leukemogenesis for rs2239630 associated and CEBPE translocated ALL. Finally, we map IGH-CEBPE translocation breakpoints in two cases, implicating RAG recombinase activity in their formation.
Collapse
|
363
|
Pavlaki I, Docquier F, Chernukhin I, Kita G, Gretton S, Clarkson CT, Teif VB, Klenova E. Poly(ADP-ribosyl)ation associated changes in CTCF-chromatin binding and gene expression in breast cells. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1861:718-730. [PMID: 29981477 PMCID: PMC6074063 DOI: 10.1016/j.bbagrm.2018.06.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 06/23/2018] [Accepted: 06/23/2018] [Indexed: 12/11/2022]
Abstract
CTCF is an evolutionarily conserved and ubiquitously expressed architectural protein regulating a plethora of cellular functions via different molecular mechanisms. CTCF can undergo a number of post-translational modifications which change its properties and functions. One such modifications linked to cancer is poly(ADP-ribosyl)ation (PARylation). The highly PARylated CTCF form has an apparent molecular mass of 180 kDa (referred to as CTCF180), which can be distinguished from hypo- and non-PARylated CTCF with the apparent molecular mass of 130 kDa (referred to as CTCF130). The existing data accumulated so far have been mainly related to CTCF130. However, the properties of CTCF180 are not well understood despite its abundance in a number of primary tissues. In this study we performed ChIP-seq and RNA-seq analyses in human breast cells 226LDM, which display predominantly CTCF130 when proliferating, but CTCF180 upon cell cycle arrest. We observed that in the arrested cells the majority of sites lost CTCF, whereas fewer sites gained CTCF or remain bound (i.e. common sites). The classical CTCF binding motif was found in the lost and common, but not in the gained sites. The changes in CTCF occupancies in the lost and common sites were associated with increased chromatin densities and altered expression from the neighboring genes. Based on these results we propose a model integrating the CTCF130/180 transition with CTCF-DNA binding and gene expression changes. This study also issues an important cautionary note concerning the design and interpretation of any experiments using cells and tissues where CTCF180 may be present.
Collapse
Affiliation(s)
- Ioanna Pavlaki
- University of Essex, School of Biological Sciences, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK
| | - France Docquier
- University of Essex, School of Biological Sciences, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK
| | - Igor Chernukhin
- University of Essex, School of Biological Sciences, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK
| | - Georgia Kita
- University of Essex, School of Biological Sciences, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK
| | - Svetlana Gretton
- University of Essex, School of Biological Sciences, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK
| | - Christopher T Clarkson
- University of Essex, School of Biological Sciences, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK
| | - Vladimir B Teif
- University of Essex, School of Biological Sciences, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK.
| | - Elena Klenova
- University of Essex, School of Biological Sciences, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK.
| |
Collapse
|
364
|
Lazar NH, Nevonen KA, O'Connell B, McCann C, O'Neill RJ, Green RE, Meyer TJ, Okhovat M, Carbone L. Epigenetic maintenance of topological domains in the highly rearranged gibbon genome. Genome Res 2018; 28:983-997. [PMID: 29914971 PMCID: PMC6028127 DOI: 10.1101/gr.233874.117] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 06/01/2018] [Indexed: 12/27/2022]
Abstract
The relationship between evolutionary genome remodeling and the three-dimensional structure of the genome remain largely unexplored. Here, we use the heavily rearranged gibbon genome to examine how evolutionary chromosomal rearrangements impact genome-wide chromatin interactions, topologically associating domains (TADs), and their epigenetic landscape. We use high-resolution maps of gibbon-human breaks of synteny (BOS), apply Hi-C in gibbon, measure an array of epigenetic features, and perform cross-species comparisons. We find that gibbon rearrangements occur at TAD boundaries, independent of the parameters used to identify TADs. This overlap is supported by a remarkable genetic and epigenetic similarity between BOS and TAD boundaries, namely presence of CpG islands and SINE elements, and enrichment in CTCF and H3K4me3 binding. Cross-species comparisons reveal that regions orthologous to BOS also correspond with boundaries of large (400-600 kb) TADs in human and other mammalian species. The colocalization of rearrangement breakpoints and TAD boundaries may be due to higher chromatin fragility at these locations and/or increased selective pressure against rearrangements that disrupt TAD integrity. We also examine the small portion of BOS that did not overlap with TAD boundaries and gave rise to novel TADs in the gibbon genome. We postulate that these new TADs generally lack deleterious consequences. Last, we show that limited epigenetic homogenization occurs across breakpoints, irrespective of their time of occurrence in the gibbon lineage. Overall, our findings demonstrate remarkable conservation of chromatin interactions and epigenetic landscape in gibbons, in spite of extensive genomic shuffling.
Collapse
Affiliation(s)
- Nathan H Lazar
- Bioinformatics and Computational Biology Division, Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Kimberly A Nevonen
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Brendan O'Connell
- Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA
| | - Christine McCann
- Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut 06269, USA
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Rachel J O'Neill
- Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut 06269, USA
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Richard E Green
- Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA
| | - Thomas J Meyer
- Bioinformatics and Computational Biology Division, Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Mariam Okhovat
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Lucia Carbone
- Bioinformatics and Computational Biology Division, Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, Oregon 97239, USA
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon 97239, USA
- Oregon National Primate Research Center, Beaverton, Oregon 97006, USA
| |
Collapse
|
365
|
Schoenfelder S, Javierre BM, Furlan-Magaril M, Wingett SW, Fraser P. Promoter Capture Hi-C: High-resolution, Genome-wide Profiling of Promoter Interactions. J Vis Exp 2018. [PMID: 30010637 PMCID: PMC6102006 DOI: 10.3791/57320] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The three-dimensional organization of the genome is linked to its function. For example, regulatory elements such as transcriptional enhancers control the spatio-temporal expression of their target genes through physical contact, often bridging considerable (in some cases hundreds of kilobases) genomic distances and bypassing nearby genes. The human genome harbors an estimated one million enhancers, the vast majority of which have unknown gene targets. Assigning distal regulatory regions to their target genes is thus crucial to understand gene expression control. We developed Promoter Capture Hi-C (PCHi-C) to enable the genome-wide detection of distal promoter-interacting regions (PIRs), for all promoters in a single experiment. In PCHi-C, highly complex Hi-C libraries are specifically enriched for promoter sequences through in-solution hybrid selection with thousands of biotinylated RNA baits complementary to the ends of all promoter-containing restriction fragments. The aim is to then pull-down promoter sequences and their frequent interaction partners such as enhancers and other potential regulatory elements. After high-throughput paired-end sequencing, a statistical test is applied to each promoter-ligated restriction fragment to identify significant PIRs at the restriction fragment level. We have used PCHi-C to generate an atlas of long-range promoter interactions in dozens of human and mouse cell types. These promoter interactome maps have contributed to a greater understanding of mammalian gene expression control by assigning putative regulatory regions to their target genes and revealing preferential spatial promoter-promoter interaction networks. This information also has high relevance to understanding human genetic disease and the identification of potential disease genes, by linking non-coding disease-associated sequence variants in or near control sequences to their target genes.
Collapse
Affiliation(s)
- Stefan Schoenfelder
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus;
| | - Biola-Maria Javierre
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus; IJC Building, Campus ICO-Germans Trias i Pujol, Josep Carreras Leukemia Research Institute;
| | - Mayra Furlan-Magaril
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus; Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México
| | - Steven W Wingett
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus; Bioinformatics Group, The Babraham Institute, Babraham Research Campus
| | - Peter Fraser
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus; Department of Biological Science, Florida State University;
| |
Collapse
|
366
|
Genome organization at different scales: nature, formation and function. Curr Opin Cell Biol 2018; 52:145-153. [DOI: 10.1016/j.ceb.2018.03.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 03/06/2018] [Accepted: 03/23/2018] [Indexed: 02/01/2023]
|
367
|
Arbona JM, Goldar A, Hyrien O, Arneodo A, Audit B. The eukaryotic bell-shaped temporal rate of DNA replication origin firing emanates from a balance between origin activation and passivation. eLife 2018; 7:35192. [PMID: 29856315 PMCID: PMC6033540 DOI: 10.7554/elife.35192] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 05/31/2018] [Indexed: 01/22/2023] Open
Abstract
The time-dependent rate I(t) of origin firing per length of unreplicated DNA presents a universal bell shape in eukaryotes that has been interpreted as the result of a complex time-evolving interaction between origins and limiting firing factors. Here, we show that a normal diffusion of replication fork components towards localized potential replication origins (p-oris) can more simply account for the I(t) universal bell shape, as a consequence of a competition between the origin firing time and the time needed to replicate DNA separating two neighboring p-oris. We predict the I(t) maximal value to be the product of the replication fork speed with the squared p-ori density. We show that this relation is robustly observed in simulations and in experimental data for several eukaryotes. Our work underlines that fork-component recycling and potential origins localization are sufficient spatial ingredients to explain the universality of DNA replication kinetics. Before a cell can divide, it must duplicate its DNA. In eukaryotes – organisms such as animals and fungi, which store their DNA in the cell’s nucleus – DNA replication starts at specific sites in the genome called replication origins. At each origin sits a protein complex that will activate when it randomly captures an activating protein that diffuses within the nucleus. Once a replication origin activates or “fires”, the complex then splits into two new complexes that move away from each other as they duplicate the DNA. If an active complex collides with an inactive one at another origin, the latter is inactivated – a phenomenon known as origin passivation. When two active complexes meet, they release the activating proteins, which diffuse away and eventually activate other origins in unreplicated DNA. The number of origins that activate each minute divided by the length of unreplicated DNA is referred to as the “rate of origin firing”. In all eukaryotes, this rate – also known as I(t) – follows the same pattern. First, it increases until more than half of the DNA is duplicated. Then it decreases until everything is duplicated. This means that, if plotted out, the graph of origin firing rate would always be a bell-shaped curve, even for organisms with genomes of different sizes that have different numbers of origins. The reason for this universal shape remained unclear. Scientists had tried to create numerical simulations that model the rate of origin firing. However, for these simulations to reproduce the bell-shape curve, a number of untested assumptions had to be made about how DNA replication takes place. In addition, these models ignored the fact that it takes time to replicate the DNA between origins. To take this time into account, Arbona et al. instead decided to model the replication origins as discrete and distinct entities. This way of building the mathematical model succeeded in reproducing the universal bell curve shape without additional assumptions. With this simulation, the balance between origin activation and passivation is enough to achieve the observed pattern. The new model also predicts that the maximum rate of origin firing is determined by the speed of DNA replication and the density of origins in the genome. Arbona et al. verified this prediction in yeast, fly, frog and human cells – organisms with different sized genomes that take between 20 minutes and 8 hours to replicate their DNA. Lastly, the prediction also held true in yeast treated with hydroxyurea, an anticancer drug that slows DNA replication. A better understanding of DNA replication can help scientists to understand how this process is perturbed in cancers and how drugs that target DNA replication can treat these diseases. Future work will explore how the 3D organization of the genome affects the diffusion of activating proteins within the cell nucleus.
Collapse
Affiliation(s)
- Jean-Michel Arbona
- Laboratoire de Physique, Université de Lyon, Ens de Lyon, Université Claude Bernard Lyon 1, CNRS, Lyon, France
| | | | - Olivier Hyrien
- Institut de Biologie de l'Ecole Normale Supérieure, Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France
| | - Alain Arneodo
- LOMA, Univ de Bordeaux, CNRS, UMR 5798, Talence, France
| | - Benjamin Audit
- Laboratoire de Physique, Université de Lyon, Ens de Lyon, Université Claude Bernard Lyon 1, CNRS, Lyon, France
| |
Collapse
|
368
|
Kim JH, Titus KR, Gong W, Beagan JA, Cao Z, Phillips-Cremins JE. 5C-ID: Increased resolution Chromosome-Conformation-Capture-Carbon-Copy with in situ 3C and double alternating primer design. Methods 2018; 142:39-46. [PMID: 29772275 PMCID: PMC5993643 DOI: 10.1016/j.ymeth.2018.05.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Revised: 03/01/2018] [Accepted: 05/08/2018] [Indexed: 01/13/2023] Open
Abstract
Mammalian genomes are folded in a hierarchy of compartments, topologically associating domains (TADs), subTADs, and looping interactions. Currently, there is a great need to evaluate the link between chromatin topology and genome function across many biological conditions and genetic perturbations. Hi-C can generate genome-wide maps of looping interactions but is intractable for high-throughput comparison of loops across multiple conditions due to the enormous number of reads (>6 Billion) required per library. Here, we describe 5C-ID, a new version of Chromosome-Conformation-Capture-Carbon-Copy (5C) with restriction digest and ligation performed in the nucleus (in situ Chromosome-Conformation-Capture (3C)) and ligation-mediated amplification performed with a double alternating primer design. We demonstrate that 5C-ID produces higher-resolution 3D genome folding maps with reduced spatial noise using markedly lower cell numbers than canonical 5C. 5C-ID enables the creation of high-resolution, high-coverage maps of chromatin loops in up to a 30 Megabase subset of the genome at a fraction of the cost of Hi-C.
Collapse
Affiliation(s)
- Ji Hun Kim
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Katelyn R Titus
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Wanfeng Gong
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jonathan A Beagan
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Zhendong Cao
- Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jennifer E Phillips-Cremins
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| |
Collapse
|
369
|
Fu H, Baris A, Aladjem MI. Replication timing and nuclear structure. Curr Opin Cell Biol 2018; 52:43-50. [PMID: 29414592 PMCID: PMC5988923 DOI: 10.1016/j.ceb.2018.01.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 01/05/2018] [Accepted: 01/14/2018] [Indexed: 12/12/2022]
Abstract
DNA replication proceeds along spatially and temporally coordinated patterns within the nucleus, thus protecting the genome during the synthesis of new genetic material. While we have been able to visualize replication patterns on DNA fibers for 50 years, recent developments and discoveries have provided a greater insight into how DNA replication is controlled. In this review, we highlight many of these discoveries. Of great interest are the physiological role of the replication timing program, cis and trans-acting factors that modulate replication timing and the effects of chromatin structure on the replication timing program. We also discuss future directions in the study of replication timing.
Collapse
Affiliation(s)
- Haiqing Fu
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, 37 Convent Drive, Bethesda, MD 20892, United States
| | - Adrian Baris
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, 37 Convent Drive, Bethesda, MD 20892, United States
| | - Mirit I Aladjem
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, 37 Convent Drive, Bethesda, MD 20892, United States.
| |
Collapse
|
370
|
Rivera-Mulia JC, Dimond A, Vera D, Trevilla-Garcia C, Sasaki T, Zimmerman J, Dupont C, Gribnau J, Fraser P, Gilbert DM. Allele-specific control of replication timing and genome organization during development. Genome Res 2018; 28:800-811. [PMID: 29735606 PMCID: PMC5991511 DOI: 10.1101/gr.232561.117] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 04/26/2018] [Indexed: 12/14/2022]
Abstract
DNA replication occurs in a defined temporal order known as the replication-timing (RT) program. RT is regulated during development in discrete chromosomal units, coordinated with transcriptional activity and 3D genome organization. Here, we derived distinct cell types from F1 hybrid musculus × castaneus mouse crosses and exploited the high single-nucleotide polymorphism (SNP) density to characterize allelic differences in RT (Repli-seq), genome organization (Hi-C and promoter-capture Hi-C), gene expression (total nuclear RNA-seq), and chromatin accessibility (ATAC-seq). We also present HARP, a new computational tool for sorting SNPs in phased genomes to efficiently measure allele-specific genome-wide data. Analysis of six different hybrid mESC clones with different genomes (C57BL/6, 129/sv, and CAST/Ei), parental configurations, and gender revealed significant RT asynchrony between alleles across ∼12% of the autosomal genome linked to subspecies genomes but not to parental origin, growth conditions, or gender. RT asynchrony in mESCs strongly correlated with changes in Hi-C compartments between alleles but not as strongly with SNP density, gene expression, imprinting, or chromatin accessibility. We then tracked mESC RT asynchronous regions during development by analyzing differentiated cell types, including extraembryonic endoderm stem (XEN) cells, four male and female primary mouse embryonic fibroblasts (MEFs), and neural precursor cells (NPCs) differentiated in vitro from mESCs with opposite parental configurations. We found that RT asynchrony and allelic discordance in Hi-C compartments seen in mESCs were largely lost in all differentiated cell types, accompanied by novel sites of allelic asynchrony at a considerably smaller proportion of the genome, suggesting that genome organization of homologs converges to similar folding patterns during cell fate commitment.
Collapse
Affiliation(s)
- Juan Carlos Rivera-Mulia
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306-4295, USA
| | - Andrew Dimond
- The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom
| | - Daniel Vera
- Center for Genomics and Personalized Medicine, Florida State University, Tallahassee, Florida 32306, USA
| | - Claudia Trevilla-Garcia
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306-4295, USA
| | - Takayo Sasaki
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306-4295, USA
| | - Jared Zimmerman
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306-4295, USA
| | - Catherine Dupont
- Department of Reproduction and Development, Erasmus MC, University Medical Center, 3015GE Rotterdam, The Netherlands
| | - Joost Gribnau
- Department of Reproduction and Development, Erasmus MC, University Medical Center, 3015GE Rotterdam, The Netherlands
| | - Peter Fraser
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306-4295, USA
- The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom
- Center for Genomics and Personalized Medicine, Florida State University, Tallahassee, Florida 32306, USA
| | - David M Gilbert
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306-4295, USA
- Center for Genomics and Personalized Medicine, Florida State University, Tallahassee, Florida 32306, USA
| |
Collapse
|
371
|
Rao S, Ghani M, Guo Z, Deming Y, Wang K, Sims R, Mao C, Yao Y, Cruchaga C, Stephan DA, Rogaeva E. An APOE-independent cis-eSNP on chromosome 19q13.32 influences tau levels and late-onset Alzheimer's disease risk. Neurobiol Aging 2018; 66:178.e1-178.e8. [PMID: 29395286 PMCID: PMC7050280 DOI: 10.1016/j.neurobiolaging.2017.12.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 11/18/2017] [Accepted: 12/27/2017] [Indexed: 10/18/2022]
Abstract
Although multiple susceptibility loci for late-onset Alzheimer's disease (LOAD) have been identified, a large portion of the genetic risk for this disease remains unexplained. LOAD risk may be associated with single-nucleotide polymorphisms responsible for changes in gene expression (eSNPs). To detect eSNPs associated with LOAD, we integrated data from LOAD genome-wide association studies and expression quantitative trait loci using Sherlock (a Bayesian statistical method). We identified a cis-regulatory eSNP (rs2927438) located on chromosome 19q13.32, for which subsequent analyses confirmed the association with both LOAD risk and the expression level of several nearby genes. Importantly, rs2927438 may represent an APOE-independent LOAD eSNP according to the weak linkage disequilibrium of rs2927438 with the 2 polymorphisms (rs7412 and rs429358) defining the APOE-ε2, -ε3, and -ε4 alleles. Furthermore, rs2927438 does not influence chromatin interaction events at the APOE locus or cis-regulation of APOE expression. Further exploratory analysis revealed that rs2927438 is significantly associated with tau levels in the cerebrospinal fluid. Our findings suggest that rs2927438 may confer APOE-independent risk for LOAD.
Collapse
Affiliation(s)
- Shuquan Rao
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, China.
| | - Mahdi Ghani
- Tanz Centre for Research in Neurodegenerative Diseases, and Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Zhiyun Guo
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, China
| | - Yuetiva Deming
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Kesheng Wang
- Department of Biostatistics and Epidemiology, College of Public Health, East Tennessee State University, Johnson City, TN, USA
| | - Rebecca Sims
- Institute of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, UK
| | - Canquan Mao
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, China
| | - Yao Yao
- Department of Fundamental Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA; Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Dietrich A Stephan
- Department of Human Genetics, Graduate School of Public Health, Pittsburgh, PA, USA
| | - Ekaterina Rogaeva
- Tanz Centre for Research in Neurodegenerative Diseases, and Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
372
|
Fang K, Chen X, Li X, Shen Y, Sun J, Czajkowsky DM, Shao Z. Super-resolution Imaging of Individual Human Subchromosomal Regions in Situ Reveals Nanoscopic Building Blocks of Higher-Order Structure. ACS NANO 2018; 12:4909-4918. [PMID: 29715004 DOI: 10.1021/acsnano.8b01963] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
It is widely recognized that the higher-order spatial organization of the genome, beyond the nucleosome, plays an important role in many biological processes. However, to date, direct information on even such fundamental structural details as the typical sizes and DNA content of these higher-order structures in situ is poorly characterized. Here, we examine the nanoscopic DNA organization within human nuclei using super-resolution direct stochastic optical reconstruction microscopy (dSTORM) imaging and 5-ethynyl-2'-deoxyuridine click chemistry, studying single fully labeled chromosomes within an otherwise unlabeled nuclei to improve the attainable resolution. We find that, regardless of nuclear position, individual subchromosomal regions consist of three different levels of DNA compaction: (i) dispersed chromatin; (ii) nanodomains of sizes ranging tens of nanometers containing a few kilobases (kb) of DNA; and (iii) clusters of nanodomains. Interestingly, the sizes and DNA content of the nanodomains are approximately the same at the nuclear periphery, nucleolar proximity, and nuclear interior, suggesting that these nanodomains share a roughly common higher-order architecture. Overall, these results suggest that DNA compaction within the eukaryote nucleus occurs via the condensation of DNA into few-kb nanodomains of approximately similar structure, with further compaction occurring via the clustering of nanodomains.
Collapse
|
373
|
Matthews BJ, Waxman DJ. Computational prediction of CTCF/cohesin-based intra-TAD loops that insulate chromatin contacts and gene expression in mouse liver. eLife 2018; 7:e34077. [PMID: 29757144 PMCID: PMC5986275 DOI: 10.7554/elife.34077] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 04/30/2018] [Indexed: 12/18/2022] Open
Abstract
CTCF and cohesin are key drivers of 3D-nuclear organization, anchoring the megabase-scale Topologically Associating Domains (TADs) that segment the genome. Here, we present and validate a computational method to predict cohesin-and-CTCF binding sites that form intra-TAD DNA loops. The intra-TAD loop anchors identified are structurally indistinguishable from TAD anchors regarding binding partners, sequence conservation, and resistance to cohesin knockdown; further, the intra-TAD loops retain key functional features of TADs, including chromatin contact insulation, blockage of repressive histone mark spread, and ubiquity across tissues. We propose that intra-TAD loops form by the same loop extrusion mechanism as the larger TAD loops, and that their shorter length enables finer regulatory control in restricting enhancer-promoter interactions, which enables selective, high-level expression of gene targets of super-enhancers and genes located within repressive nuclear compartments. These findings elucidate the role of intra-TAD cohesin-and-CTCF binding in nuclear organization associated with widespread insulation of distal enhancer activity.
Collapse
Affiliation(s)
- Bryan J Matthews
- Department of Biology and Bioinformatics ProgramBoston UniversityBostonUnited States
| | - David J Waxman
- Department of Biology and Bioinformatics ProgramBoston UniversityBostonUnited States
| |
Collapse
|
374
|
Kang S, Kang MS, Ryu E, Myung K. Eukaryotic DNA replication: Orchestrated action of multi-subunit protein complexes. Mutat Res 2018; 809:58-69. [PMID: 28501329 DOI: 10.1016/j.mrfmmm.2017.04.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 04/13/2017] [Accepted: 04/30/2017] [Indexed: 06/07/2023]
Abstract
Genome duplication is an essential process to preserve genetic information between generations. The eukaryotic cell cycle is composed of functionally distinct phases: G1, S, G2, and M. One of the key replicative proteins that participate at every stage of DNA replication is the Mcm2-7 complex, a replicative helicase. In the G1 phase, inactive Mcm2-7 complexes are loaded on the replication origins by replication-initiator proteins, ORC and Cdc6. Two kinases, S-CDK and DDK, convert the inactive origin-loaded Mcm2-7 complex to an active helicase, the CMG complex in the S phase. The activated CMG complex begins DNA unwinding and recruits enzymes essential for DNA synthesis to assemble a replisome at the replication fork. After completion of DNA synthesis, the inactive CMG complex on the replicated DNA is removed from chromatin to terminate DNA replication. In this review, we will discuss the structure, function, and regulation of the molecular machines involved in each step of DNA replication.
Collapse
Affiliation(s)
- Sukhyun Kang
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea.
| | - Mi-Sun Kang
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
| | - Eunjin Ryu
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea; School of Life Sciences, Ulsan National Institute for Science and Technology, Ulsan 44919, Republic of Korea
| | - Kyungjae Myung
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea; School of Life Sciences, Ulsan National Institute for Science and Technology, Ulsan 44919, Republic of Korea
| |
Collapse
|
375
|
Siefert JC, Clowdus EA, Goins D, Koren A, Sansam CL. Profiling DNA Replication Timing Using Zebrafish as an In Vivo Model System. J Vis Exp 2018. [PMID: 29757277 DOI: 10.3791/57146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
DNA replication timing is an important cellular characteristic, exhibiting significant relationships with chromatin structure, transcription, and DNA mutation rates. Changes in replication timing occur during development and in cancer, but the role replication timing plays in development and disease is not known. Zebrafish were recently established as an in vivo model system to study replication timing. Here is detailed the protocols for using the zebrafish to determine DNA replication timing. After sorting cells from embryos and adult zebrafish, high-resolution genome-wide DNA replication timing patterns can be constructed by determining changes in DNA copy number through analysis of next generation sequencing data. The zebrafish model system allows for evaluation of the replication timing changes that occur in vivo throughout development, and can also be used to assess changes in individual cell types, disease models, or mutant lines. These methods will enable studies investigating the mechanisms and determinants of replication timing establishment and maintenance during development, the role replication timing plays in mutations and tumorigenesis, and the effects of perturbing replication timing on development and disease.
Collapse
Affiliation(s)
- Joseph C Siefert
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation; Department of Cell Biology, University of Oklahoma Health Sciences Center
| | - Emily A Clowdus
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation; Department of Cell Biology, University of Oklahoma Health Sciences Center
| | - Duane Goins
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University
| | - Christopher L Sansam
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation; Department of Cell Biology, University of Oklahoma Health Sciences Center;
| |
Collapse
|
376
|
|
377
|
Chromatin conformation regulates the coordination between DNA replication and transcription. Nat Commun 2018; 9:1590. [PMID: 29686321 PMCID: PMC5913246 DOI: 10.1038/s41467-018-03539-8] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 02/21/2018] [Indexed: 12/26/2022] Open
Abstract
Chromatin is the template for the basic processes of replication and transcription, making the maintenance of chromosomal integrity critical for cell viability. To elucidate how dividing cells respond to alterations in chromatin structure, here we analyse the replication programme of primary cells with altered chromatin configuration caused by the genetic ablation of the HMGB1 gene, or three histone H1 genes. We find that loss of chromatin compaction in H1-depleted cells triggers the accumulation of stalled forks and DNA damage as a consequence of transcription–replication conflicts. In contrast, reductions in nucleosome occupancy due to the lack of HMGB1 cause faster fork progression without impacting the initiation landscape or fork stability. Thus, perturbations in chromatin integrity elicit a range of responses in the dynamics of DNA replication and transcription, with different consequences on replicative stress. These findings have broad implications for our understanding of how defects in chromatin structure contribute to genomic instability. The maintenance of chromatin integrity during replication is critical for cell viability. Here the authors study how dividing cells respond to alterations in chromatin structure and find that these elicit a range of responses in the dynamics of DNA replication and consequences on replicative stress.
Collapse
|
378
|
Kolesnikova TD, Goncharov FP, Zhimulev IF. Similarity in replication timing between polytene and diploid cells is associated with the organization of the Drosophila genome. PLoS One 2018; 13:e0195207. [PMID: 29659604 PMCID: PMC5902040 DOI: 10.1371/journal.pone.0195207] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 03/19/2018] [Indexed: 12/21/2022] Open
Abstract
Morphologically, polytene chromosomes of Drosophila melanogaster consist of compact “black” bands alternating with less compact “grey” bands and interbands. We developed a comprehensive approach that combines cytological mapping data of FlyBase-annotated genes and novel tools for predicting cytogenetic features of chromosomes on the basis of their protein composition and determined the genomic coordinates for all black bands of polytene chromosome 2R. By a PCNA immunostaining assay, we obtained the replication timetable for all the bands mapped. The results allowed us to compare replication timing between polytene chromosomes in salivary glands and chromosomes from cultured diploid cell lines and to observe a substantial similarity in the global replication patterns at the band resolution level. In both kinds of chromosomes, the intervals between black bands correspond to early replication initiation zones. Black bands are depleted of replication initiation events and are characterized by a gradient of replication timing; therefore, the time of replication completion correlates with the band length. The bands are characterized by low gene density, contain predominantly tissue-specific genes, and are represented by silent chromatin types in various tissues. The borders of black bands correspond well to the borders of topological domains as well as to the borders of the zones showing H3K27me3, SUUR, and LAMIN enrichment. In conclusion, the characteristic pattern of polytene chromosomes reflects partitioning of the Drosophila genome into two global types of domains with contrasting properties. This partitioning is conserved in different tissues and determines replication timing in Drosophila.
Collapse
Affiliation(s)
- Tatyana D. Kolesnikova
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
- * E-mail:
| | - Fedor P. Goncharov
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, Russia
| | - Igor F. Zhimulev
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| |
Collapse
|
379
|
Barutcu AR, Maass PG, Lewandowski JP, Weiner CL, Rinn JL. A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus. Nat Commun 2018; 9:1444. [PMID: 29654311 PMCID: PMC5899154 DOI: 10.1038/s41467-018-03614-0] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 02/27/2018] [Indexed: 12/22/2022] Open
Abstract
The binding of the transcriptional regulator CTCF to the genome has been implicated in the formation of topologically associated domains (TADs). However, the general mechanisms of folding the genome into TADs are not fully understood. Here we test the effects of deleting a CTCF-rich locus on TAD boundary formation. Using genome-wide chromosome conformation capture (Hi-C), we focus on one TAD boundary on chromosome X harboring ~ 15 CTCF binding sites and located at the long non-coding RNA (lncRNA) locus Firre. Specifically, this TAD boundary is invariant across evolution, tissues, and temporal dynamics of X-chromosome inactivation. We demonstrate that neither the deletion of this locus nor the ectopic insertion of Firre cDNA or its ectopic expression are sufficient to alter TADs in a sex-specific or allele-specific manner. In contrast, Firre's deletion disrupts the chromatin super-loop formation of the inactive X-chromosome. Collectively, our findings suggest that apart from CTCF binding, additional mechanisms may play roles in establishing TAD boundary formation.
Collapse
Affiliation(s)
- A Rasim Barutcu
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA.
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA.
| | - Philipp G Maass
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Jordan P Lewandowski
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, 02215, USA
| | - Catherine L Weiner
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, 02215, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, 02138, USA
| | - John L Rinn
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA.
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA.
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, 02215, USA.
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, 02138, USA.
- Department of Biochemistry, University of Colorado, BioFrontiers Institute, Boulder, CO, 80301, USA.
| |
Collapse
|
380
|
Schuijers J, Manteiga JC, Weintraub AS, Day DS, Zamudio AV, Hnisz D, Lee TI, Young RA. Transcriptional Dysregulation of MYC Reveals Common Enhancer-Docking Mechanism. Cell Rep 2018; 23:349-360. [PMID: 29641996 PMCID: PMC5929158 DOI: 10.1016/j.celrep.2018.03.056] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 02/09/2018] [Accepted: 03/14/2018] [Indexed: 12/11/2022] Open
Abstract
Transcriptional dysregulation of the MYC oncogene is among the most frequent events in aggressive tumor cells, and this is generally accomplished by acquisition of a super-enhancer somewhere within the 2.8 Mb TAD where MYC resides. We find that these diverse cancer-specific super-enhancers, differing in size and location, interact with the MYC gene through a common and conserved CTCF binding site located 2 kb upstream of the MYC promoter. Genetic perturbation of this enhancer-docking site in tumor cells reduces CTCF binding, super-enhancer interaction, MYC gene expression, and cell proliferation. CTCF binding is highly sensitive to DNA methylation, and this enhancer-docking site, which is hypomethylated in diverse cancers, can be inactivated through epigenetic editing with dCas9-DNMT. Similar enhancer-docking sites occur at other genes, including genes with prominent roles in multiple cancers, suggesting a mechanism by which tumor cell oncogenes can generally hijack enhancers. These results provide insights into mechanisms that allow a single target gene to be regulated by diverse enhancer elements in different cell types.
Collapse
Affiliation(s)
- Jurian Schuijers
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | - John Colonnese Manteiga
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Abraham Selby Weintraub
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Daniel Sindt Day
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | - Alicia Viridiana Zamudio
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Denes Hnisz
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | - Tong Ihn Lee
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | - Richard Allen Young
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| |
Collapse
|
381
|
Bellush JM, Whitehouse I. DNA replication through a chromatin environment. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0287. [PMID: 28847824 DOI: 10.1098/rstb.2016.0287] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/18/2017] [Indexed: 01/03/2023] Open
Abstract
Compaction of the genome into the nuclear space is achieved by wrapping DNA around octameric assemblies of histone proteins to form nucleosomes, the fundamental repeating unit of chromatin. Aside from providing a means by which to fit larger genomes into the cell, chromatinization of DNA is a crucial means by which the cell regulates access to the genome. While the complex role that chromatin plays in gene transcription has been appreciated for a long time, it is now also apparent that crucial aspects of DNA replication are linked to the biology of chromatin. This review will focus on recent advances in our understanding of how the chromatin environment influences key aspects of DNA replication.This article is part of the themed issue 'Chromatin modifiers and remodellers in DNA repair and signalling'.
Collapse
Affiliation(s)
- James M Bellush
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA.,BCMB Graduate Program, Weill Cornell Medical College, 1300 York Avenue, New York, NY, USA
| | - Iestyn Whitehouse
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| |
Collapse
|
382
|
Razin SV, Gavrilov AA. Structural–Functional Domains of the Eukaryotic Genome. BIOCHEMISTRY (MOSCOW) 2018; 83:302-312. [DOI: 10.1134/s0006297918040028] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 11/27/2017] [Indexed: 08/30/2023]
|
383
|
Takahashi S, Kobayashi S, Hiratani I. Epigenetic differences between naïve and primed pluripotent stem cells. Cell Mol Life Sci 2018; 75:1191-1203. [PMID: 29134247 PMCID: PMC5843680 DOI: 10.1007/s00018-017-2703-x] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 10/22/2017] [Accepted: 10/30/2017] [Indexed: 02/07/2023]
Abstract
It has been 8 years since the concept of naïve and primed pluripotent stem cell states was first proposed. Both are states of pluripotency, but exhibit slightly different properties. The naïve state represents the cellular state of the preimplantation mouse blastocyst inner cell mass, while the primed state is representative of the post-implantation epiblast cells. These two cell types exhibit clearly distinct developmental potential, as evidenced by the fact that naïve cells are able to contribute to blastocyst chimeras, while primed cells cannot. However, the epigenetic differences that underlie the distinct developmental potential of these cell types remain unclear, which is rather surprising given the large amount of active investigation over the years. Elucidating such epigenetic differences should lead to a better understanding of the fundamental properties of these states of pluripotency and the means by which the naïve-to-primed transition occurs, which may provide insights into the essence of stem cell commitment.
Collapse
Affiliation(s)
- Saori Takahashi
- Laboratory for Developmental Epigenetics, RIKEN Center for Developmental Biology, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Shin Kobayashi
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koutou-ku, Tokyo, 135-0064, Japan.
- Department of Epigenetics, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan.
| | - Ichiro Hiratani
- Laboratory for Developmental Epigenetics, RIKEN Center for Developmental Biology, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan.
| |
Collapse
|
384
|
Genome-wide analysis of replication timing by next-generation sequencing with E/L Repli-seq. Nat Protoc 2018; 13:819-839. [PMID: 29599440 DOI: 10.1038/nprot.2017.148] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
This protocol is an extension to: Nat. Protoc. 6, 870-895 (2014); doi:10.1038/nprot.2011.328; published online 02 June 2011Cycling cells duplicate their DNA content during S phase, following a defined program called replication timing (RT). Early- and late-replicating regions differ in terms of mutation rates, transcriptional activity, chromatin marks and subnuclear position. Moreover, RT is regulated during development and is altered in diseases. Here, we describe E/L Repli-seq, an extension of our Repli-chip protocol. E/L Repli-seq is a rapid, robust and relatively inexpensive protocol for analyzing RT by next-generation sequencing (NGS), allowing genome-wide assessment of how cellular processes are linked to RT. Briefly, cells are pulse-labeled with BrdU, and early and late S-phase fractions are sorted by flow cytometry. Labeled nascent DNA is immunoprecipitated from both fractions and sequenced. Data processing leads to a single bedGraph file containing the ratio of nascent DNA from early versus late S-phase fractions. The results are comparable to those of Repli-chip, with the additional benefits of genome-wide sequence information and an increased dynamic range. We also provide computational pipelines for downstream analyses, for parsing phased genomes using single-nucleotide polymorphisms (SNPs) to analyze RT allelic asynchrony, and for direct comparison to Repli-chip data. This protocol can be performed in up to 3 d before sequencing, and requires basic cellular and molecular biology skills, as well as a basic understanding of Unix and R.
Collapse
|
385
|
Xiang W, Roberti MJ, Hériché JK, Huet S, Alexander S, Ellenberg J. Correlative live and super-resolution imaging reveals the dynamic structure of replication domains. J Cell Biol 2018; 217:1973-1984. [PMID: 29572382 PMCID: PMC5987722 DOI: 10.1083/jcb.201709074] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 01/19/2018] [Accepted: 03/06/2018] [Indexed: 12/15/2022] Open
Abstract
Combining fluorescence labeling with live-cell confocal and correlative super-resolution microscopy, Xiang et al. characterize biophysical parameters defining the internal organization, spacing, and mechanical coupling of replication domains. Chromosome organization in higher eukaryotes controls gene expression, DNA replication, and DNA repair. Genome mapping has revealed the functional units of chromatin at the submegabase scale as self-interacting regions called topologically associating domains (TADs) and showed they correspond to replication domains (RDs). A quantitative structural and dynamic description of RD behavior in the nucleus is, however, missing because visualization of dynamic subdiffraction-sized RDs remains challenging. Using fluorescence labeling of RDs combined with correlative live and super-resolution microscopy in situ, we determined biophysical parameters to characterize the internal organization, spacing, and mechanical coupling of RDs. We found that RDs are typically 150 nm in size and contain four co-replicating regions spaced 60 nm apart. Spatially neighboring RDs are spaced 300 nm apart and connected by highly flexible linker regions that couple their motion only <550 nm. Our pipeline allows a robust quantitative characterization of chromosome structure in situ and provides important biophysical parameters to understand general principles of chromatin organization.
Collapse
Affiliation(s)
- Wanqing Xiang
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - M Julia Roberti
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jean-Karim Hériché
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Sébastien Huet
- Université de Rennes 1, Structure fédérative de recherche Biosit, Rennes, France.,Centre National de la Recherche Scientifique, UMR 6290, Institut Génétique et Développement de Rennes, Rennes, France
| | - Stephanie Alexander
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jan Ellenberg
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| |
Collapse
|
386
|
Arzate-Mejía RG, Recillas-Targa F, Corces VG. Developing in 3D: the role of CTCF in cell differentiation. Development 2018; 145:dev137729. [PMID: 29567640 PMCID: PMC5897592 DOI: 10.1242/dev.137729] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
CTCF is a highly conserved zinc-finger DNA-binding protein that mediates interactions between distant sequences in the genome. As a consequence, CTCF regulates enhancer-promoter interactions and contributes to the three-dimensional organization of the genome. Recent studies indicate that CTCF is developmentally regulated, suggesting that it plays a role in cell type-specific genome organization. Here, we review these studies and discuss how CTCF functions during the development of various cell and tissue types, ranging from embryonic stem cells and gametes, to neural, muscle and cardiac cells. We propose that the lineage-specific control of CTCF levels, and its partnership with lineage-specific transcription factors, allows for the control of cell type-specific gene expression via chromatin looping.
Collapse
Affiliation(s)
- Rodrigo G Arzate-Mejía
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, 04510 Ciudad de México, México
| | - Félix Recillas-Targa
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, 04510 Ciudad de México, México
| | - Victor G Corces
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| |
Collapse
|
387
|
Huang J, Li K, Cai W, Liu X, Zhang Y, Orkin SH, Xu J, Yuan GC. Dissecting super-enhancer hierarchy based on chromatin interactions. Nat Commun 2018; 9:943. [PMID: 29507293 PMCID: PMC5838163 DOI: 10.1038/s41467-018-03279-9] [Citation(s) in RCA: 135] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 02/01/2018] [Indexed: 02/06/2023] Open
Abstract
Recent studies have highlighted super-enhancers (SEs) as important regulatory elements for gene expression, but their intrinsic properties remain incompletely characterized. Through an integrative analysis of Hi-C and ChIP-seq data, here we find that a significant fraction of SEs are hierarchically organized, containing both hub and non-hub enhancers. Hub enhancers share similar histone marks with non-hub enhancers, but are distinctly associated with cohesin and CTCF binding sites and disease-associated genetic variants. Genetic ablation of hub enhancers results in profound defects in gene activation and local chromatin landscape. As such, hub enhancers are the major constituents responsible for SE functional and structural organization.
Collapse
Affiliation(s)
- Jialiang Huang
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA
- Division of Hematology/Oncology, Boston Childrens Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA
| | - Kailong Li
- Department of Pediatrics, Childrens Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Wenqing Cai
- Division of Hematology/Oncology, Boston Childrens Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA
| | - Xin Liu
- Department of Pediatrics, Childrens Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Yuannyu Zhang
- Department of Pediatrics, Childrens Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Stuart H Orkin
- Division of Hematology/Oncology, Boston Childrens Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA
- Howard Hughes Medical Institute, Boston, MA, 02215, USA
| | - Jian Xu
- Department of Pediatrics, Childrens Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
| | - Guo-Cheng Yuan
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA.
| |
Collapse
|
388
|
Concia L, Brooks AM, Wheeler E, Zynda GJ, Wear EE, LeBlanc C, Song J, Lee TJ, Pascuzzi PE, Martienssen RA, Vaughn MW, Thompson WF, Hanley-Bowdoin L. Genome-Wide Analysis of the Arabidopsis Replication Timing Program. PLANT PHYSIOLOGY 2018; 176:2166-2185. [PMID: 29301956 PMCID: PMC5841712 DOI: 10.1104/pp.17.01537] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 01/03/2018] [Indexed: 05/21/2023]
Abstract
Eukaryotes use a temporally regulated process, known as the replication timing program, to ensure that their genomes are fully and accurately duplicated during S phase. Replication timing programs are predictive of genomic features and activity and are considered to be functional readouts of chromatin organization. Although replication timing programs have been described for yeast and animal systems, much less is known about the temporal regulation of plant DNA replication or its relationship to genome sequence and chromatin structure. We used the thymidine analog, 5-ethynyl-2'-deoxyuridine, in combination with flow sorting and Repli-Seq to describe, at high-resolution, the genome-wide replication timing program for Arabidopsis (Arabidopsis thaliana) Col-0 suspension cells. We identified genomic regions that replicate predominantly during early, mid, and late S phase, and correlated these regions with genomic features and with data for chromatin state, accessibility, and long-distance interaction. Arabidopsis chromosome arms tend to replicate early while pericentromeric regions replicate late. Early and mid-replicating regions are gene-rich and predominantly euchromatic, while late regions are rich in transposable elements and primarily heterochromatic. However, the distribution of chromatin states across the different times is complex, with each replication time corresponding to a mixture of states. Early and mid-replicating sequences interact with each other and not with late sequences, but early regions are more accessible than mid regions. The replication timing program in Arabidopsis reflects a bipartite genomic organization with early/mid-replicating regions and late regions forming separate, noninteracting compartments. The temporal order of DNA replication within the early/mid compartment may be modulated largely by chromatin accessibility.
Collapse
Affiliation(s)
- Lorenzo Concia
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695
| | - Ashley M Brooks
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695
| | - Emily Wheeler
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695
| | - Gregory J Zynda
- Texas Advanced Computing Center, University of Texas at Austin, Austin, Texas 78758
| | - Emily E Wear
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695
| | - Chantal LeBlanc
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724
| | - Jawon Song
- Texas Advanced Computing Center, University of Texas at Austin, Austin, Texas 78758
| | - Tae-Jin Lee
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695
| | - Pete E Pascuzzi
- Purdue University Libraries, Purdue University, West Lafayette, Indiana 47907
| | - Robert A Martienssen
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724
| | - Matthew W Vaughn
- Texas Advanced Computing Center, University of Texas at Austin, Austin, Texas 78758
| | - William F Thompson
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695
| | - Linda Hanley-Bowdoin
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695
| |
Collapse
|
389
|
Sima J, Bartlett DA, Gordon MR, Gilbert DM. Bacterial artificial chromosomes establish replication timing and sub-nuclear compartment de novo as extra-chromosomal vectors. Nucleic Acids Res 2018; 46:1810-1820. [PMID: 29294101 PMCID: PMC5829748 DOI: 10.1093/nar/gkx1265] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Revised: 11/27/2017] [Accepted: 12/06/2017] [Indexed: 12/11/2022] Open
Abstract
The role of DNA sequence in determining replication timing (RT) and chromatin higher order organization remains elusive. To address this question, we have developed an extra-chromosomal replication system (E-BACs) consisting of ∼200 kb human bacterial artificial chromosomes (BACs) modified with Epstein-Barr virus (EBV) stable segregation elements. E-BACs were stably maintained as autonomous mini-chromosomes in EBNA1-expressing HeLa or human induced pluripotent stem cells (hiPSCs) and established distinct RT patterns. An E-BAC harboring an early replicating chromosomal region replicated early during S phase, while E-BACs derived from RT transition regions (TTRs) and late replicating regions replicated in mid to late S phase. Analysis of E-BAC interactions with cellular chromatin (4C-seq) revealed that the early replicating E-BAC interacted broadly throughout the genome and preferentially with the early replicating compartment of the nucleus. In contrast, mid- to late-replicating E-BACs interacted with more specific late replicating chromosomal segments, some of which were shared between different E-BACs. Together, we describe a versatile system in which to study the structure and function of chromosomal segments that are stably maintained separately from the influence of cellular chromosome context.
Collapse
Affiliation(s)
- Jiao Sima
- Department of Biological Science, 319 Stadium Drive, Florida State University, Tallahassee, FL 32306, USA
| | - Daniel A Bartlett
- Department of Biological Science, 319 Stadium Drive, Florida State University, Tallahassee, FL 32306, USA
| | - Molly R Gordon
- Department of Biological Science, 319 Stadium Drive, Florida State University, Tallahassee, FL 32306, USA
| | - David M Gilbert
- Department of Biological Science, 319 Stadium Drive, Florida State University, Tallahassee, FL 32306, USA
| |
Collapse
|
390
|
Perrot A, Millington CL, Gómez-Escoda B, Schausi-Tiffoche D, Wu PYJ. CDK activity provides temporal and quantitative cues for organizing genome duplication. PLoS Genet 2018; 14:e1007214. [PMID: 29466359 PMCID: PMC5821308 DOI: 10.1371/journal.pgen.1007214] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 01/22/2018] [Indexed: 12/17/2022] Open
Abstract
In eukaryotes, the spatial and temporal organization of genome duplication gives rise to distinctive profiles of replication origin usage along the chromosomes. While it has become increasingly clear that these programs are important for cellular physiology, the mechanisms by which they are determined and modulated remain elusive. Replication initiation requires the function of cyclin-dependent kinases (CDKs), which associate with various cyclin partners to drive cell proliferation. Surprisingly, although we possess detailed knowledge of the CDK regulators and targets that are crucial for origin activation, little is known about whether CDKs play a critical role in establishing the genome-wide pattern of origin selection. We have addressed this question in the fission yeast, taking advantage of a simplified cell cycle network in which cell proliferation is driven by a single cyclin-CDK module. This system allows us to precisely control CDK activity in vivo using chemical genetics. First, in contrast to previous reports, our results clearly show that distinct cyclin-CDK pairs are not essential for regulating specific subsets of origins and for establishing a normal replication program. Importantly, we then demonstrate that the timing at which CDK activity reaches the S phase threshold is critical for the organization of replication in distinct efficiency domains, while the level of CDK activity at the onset of S phase is a dose-dependent modulator of overall origin efficiencies. Our study therefore implicates these different aspects of CDK regulation as versatile mechanisms for shaping the architecture of DNA replication across the genome. The duplication of the genetic material is a highly conserved and tightly regulated process that is essential for cell proliferation. DNA synthesis initiates at sites called origins that are distributed throughout the genome. Replication origins are not all used equivalently, and their patterns of activation along the chromosomes give rise to specific profiles, or programs, of DNA replication. These programs change during development and in response to external stimuli, and we have previously shown that they have important consequences for cellular function. However, we still do not understand the mechanisms by which cells establish different replication patterns. Here we investigate the role of the cyclin-dependent kinase (CDK) family of proteins, whose activities are critical for cell cycle progression, in regulating the organization of genome duplication. Taking advantage of a system that allows us to precisely modulate CDK activity levels in living cells, we demonstrate that both the temporal and quantitative controls of CDK function are crucial for determining distinct programs of DNA replication. Our work therefore uncovers a fundamental link between CDK activity, a central input in a variety of cellular and developmental processes, and the architecture of genome duplication.
Collapse
Affiliation(s)
- Anthony Perrot
- Genome Duplication and Maintenance Team, Institute of Genetics and Development, CNRS UMR, Rennes, France
| | - Christopher Lee Millington
- Genome Duplication and Maintenance Team, Institute of Genetics and Development, CNRS UMR, Rennes, France
| | - Blanca Gómez-Escoda
- Genome Duplication and Maintenance Team, Institute of Genetics and Development, CNRS UMR, Rennes, France
| | - Diane Schausi-Tiffoche
- Genome Duplication and Maintenance Team, Institute of Genetics and Development, CNRS UMR, Rennes, France
| | - Pei-Yun Jenny Wu
- Genome Duplication and Maintenance Team, Institute of Genetics and Development, CNRS UMR, Rennes, France
- * E-mail:
| |
Collapse
|
391
|
Palmigiano A, Santaniello F, Cerutti A, Penkov D, Purushothaman D, Makhija E, Luzi L, di Fagagna FD, Pelicci PG, Shivashankar V, Dellino GI, Blasi F. PREP1 tumor suppressor protects the late-replicating DNA by controlling its replication timing and symmetry. Sci Rep 2018; 8:3198. [PMID: 29453404 PMCID: PMC5816642 DOI: 10.1038/s41598-018-21363-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 02/01/2018] [Indexed: 12/15/2022] Open
Abstract
The synthesis of middle-to-late-replicating DNA can be affected independently of the rest of the genome by down-regulating the tumor suppressor PREP1 (PKNOX1). Indeed, DNA combing shows that PREP1 down-regulation affects DNA replication rate, increases the number of simultaneously firing origins and the asymmetry of DNA replication, leading to DNA damage. Genome-wide analysis of replication timing by Repli-seq shows that, upon PREP1 down-regulation, 25% of the genome is replicated earlier in the S-phase. The targeted DNA sequences correspond to Lamin-Associated Domains (LADs), and include late-replicating (LRRs) and temporal transition regions (TTRs). Notably, the distribution of PREP1 DNA binding sites and of its target genes indicates that DNA replication defects are independent of the overall PREP1 transcriptional activity. Finally, PREP1 down-regulation causes a substantial decrease in Lamin B1 levels. This suggests that DNA is released from the nuclear lamina earlier than in the control cells and is available for replication, thus explaining timing defects and DNA damage.This is the first evidence that the replication timing of a specific fraction of the human genome is affected by PREP1 tumor suppressor. This previously unknown function might significantly contribute to the genomic instability observed in human tumors.
Collapse
Affiliation(s)
- Angela Palmigiano
- IFOM (Foundation FIRC Institute of Molecular Oncology), via Adamello 16, 20139, Milan, Italy
- Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, via Olgettina 60, Milan, 20138, Italy
| | - Francesco Santaniello
- Department of Experimental Oncology, European Institute of Oncology, via Adamello 16, 20139, Milan, Italy
| | - Aurora Cerutti
- IFOM (Foundation FIRC Institute of Molecular Oncology), via Adamello 16, 20139, Milan, Italy
- Oncogenomics Department, Netherland Cancer Institute (NKI), Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Dmitry Penkov
- IFOM (Foundation FIRC Institute of Molecular Oncology), via Adamello 16, 20139, Milan, Italy
- Lomonosov Moscow State University, Leninskiye Gori 1, 119991, Moscow, Russia
| | - Divya Purushothaman
- IFOM (Foundation FIRC Institute of Molecular Oncology), via Adamello 16, 20139, Milan, Italy
| | - Ekta Makhija
- Mechano-Biology Institute, National University of Singapore, Singapore, Singapore
| | - Lucilla Luzi
- Department of Experimental Oncology, European Institute of Oncology, via Adamello 16, 20139, Milan, Italy
| | - Fabrizio d'Adda di Fagagna
- IFOM (Foundation FIRC Institute of Molecular Oncology), via Adamello 16, 20139, Milan, Italy
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), Via Abbiategrasso 207, 27100, Pavia, Italy
| | - Pier Giuseppe Pelicci
- Department of Experimental Oncology, European Institute of Oncology, via Adamello 16, 20139, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Via Santa Sofia 9, 20142, Milan, Italy
| | - Viveswara Shivashankar
- IFOM (Foundation FIRC Institute of Molecular Oncology), via Adamello 16, 20139, Milan, Italy
- Mechano-Biology Institute, National University of Singapore, Singapore, Singapore
| | - Gaetano Ivan Dellino
- Department of Experimental Oncology, European Institute of Oncology, via Adamello 16, 20139, Milan, Italy.
- Department of Oncology and Hemato-Oncology, University of Milan, Via Santa Sofia 9, 20142, Milan, Italy.
| | - Francesco Blasi
- IFOM (Foundation FIRC Institute of Molecular Oncology), via Adamello 16, 20139, Milan, Italy.
| |
Collapse
|
392
|
Xia K. Sequence-based multiscale modeling for high-throughput chromosome conformation capture (Hi-C) data analysis. PLoS One 2018; 13:e0191899. [PMID: 29408904 PMCID: PMC5800693 DOI: 10.1371/journal.pone.0191899] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 01/12/2018] [Indexed: 11/18/2022] Open
Abstract
In this paper, we introduce sequence-based multiscale modeling for biomolecular data analysis. We employ spectral clustering method in our modeling and reveal the difference between sequence-based global scale clustering and local scale clustering. Essentially, two types of distances, i.e., Euclidean (or spatial) distance and genomic (or sequential) distance, can be used in data clustering. Clusters from sequence-based global scale models optimize spatial distances, meaning spatially adjacent loci are more likely to be assigned into the same cluster. Sequence-based local scale models, on the other hand, result in clusters that optimize genomic distances. That is to say, in these models, sequentially adjoining loci tend to be cluster together. We propose two sequence-based multiscale models (SeqMMs) for the study of chromosome hierarchical structures, including genomic compartments and topological associated domains (TADs). We find that genomic compartments are determined only by global scale information in the Hi-C data. The removal of all the local interactions within a band region as large as 10 Mb in genomic distance has almost no significant influence on the final compartment results. Further, in TAD analysis, we find that when the sequential scale is small, a tiny variation of diagonal band region in a contact map will result in a great change in the predicted TAD boundaries. When the scale value is larger than a threshold value, the TAD boundaries become very consistent. This threshold value is highly related to TAD sizes. By the comparison of our results with those previously obtained using a spectral clustering model, we find that our method is more robust and reliable. Finally, we demonstrate that almost all TAD boundaries from both clustering methods are local minimum of a TAD summation function.
Collapse
Affiliation(s)
- Kelin Xia
- Division of Mathematical Sciences, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore 637371, Singapore
| |
Collapse
|
393
|
Buckley RM, Kortschak RD, Raison JM, Adelson DL. Similar Evolutionary Trajectories for Retrotransposon Accumulation in Mammals. Genome Biol Evol 2018; 9:2336-2353. [PMID: 28945883 PMCID: PMC5610350 DOI: 10.1093/gbe/evx179] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/01/2017] [Indexed: 12/19/2022] Open
Abstract
The factors guiding retrotransposon insertion site preference are not well understood. Different types of retrotransposons share common replication machinery and yet occupy distinct genomic domains. Autonomous long interspersed elements accumulate in gene-poor domains and their nonautonomous short interspersed elements accumulate in gene-rich domains. To determine genomic factors that contribute to this discrepancy we analyzed the distribution of retrotransposons within the framework of chromosomal domains and regulatory elements. Using comparative genomics, we identified large-scale conserved patterns of retrotransposon accumulation across several mammalian genomes. Importantly, retrotransposons that were active after our sample-species diverged accumulated in orthologous regions. This suggested a similar evolutionary interaction between retrotransposon activity and conserved genome architecture across our species. In addition, we found that retrotransposons accumulated at regulatory element boundaries in open chromatin, where accumulation of particular retrotransposon types depended on insertion size and local regulatory element density. From our results, we propose a model where density and distribution of genes and regulatory elements canalize retrotransposon accumulation. Through conservation of synteny, gene regulation and nuclear organization, mammalian genomes with dissimilar retrotransposons follow similar evolutionary trajectories.
Collapse
Affiliation(s)
- Reuben M Buckley
- Department of Genetics and Evolution, The University of Adelaide, South Australia, Australia
| | - R Daniel Kortschak
- Department of Genetics and Evolution, The University of Adelaide, South Australia, Australia
| | - Joy M Raison
- Department of Genetics and Evolution, The University of Adelaide, South Australia, Australia
| | - David L Adelson
- Department of Genetics and Evolution, The University of Adelaide, South Australia, Australia
| |
Collapse
|
394
|
Rennie S, Dalby M, van Duin L, Andersson R. Transcriptional decomposition reveals active chromatin architectures and cell specific regulatory interactions. Nat Commun 2018; 9:487. [PMID: 29402885 PMCID: PMC5799294 DOI: 10.1038/s41467-017-02798-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Accepted: 12/29/2017] [Indexed: 12/29/2022] Open
Abstract
Transcriptional regulation is tightly coupled with chromosomal positioning and three-dimensional chromatin architecture. However, it is unclear what proportion of transcriptional activity is reflecting such organisation, how much can be informed by RNA expression alone and how this impacts disease. Here, we develop a computational transcriptional decomposition approach separating the proportion of expression associated with genome organisation from independent effects not directly related to genomic positioning. We show that positionally attributable expression accounts for a considerable proportion of total levels and is highly informative of topological associating domain activities and organisation, revealing boundaries and chromatin compartments. Furthermore, expression data alone accurately predict individual enhancer-promoter interactions, drawing features from expression strength, stabilities, insulation and distance. We characterise predictions in 76 human cell types, observing extensive sharing of domains, yet highly cell-type-specific enhancer-promoter interactions and strong enrichments in relevant trait-associated variants. Overall, our work demonstrates a close relationship between transcription and chromatin architecture.
Collapse
Affiliation(s)
- Sarah Rennie
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200, Copenhagen, Denmark
| | - Maria Dalby
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200, Copenhagen, Denmark
| | - Lucas van Duin
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200, Copenhagen, Denmark
| | - Robin Andersson
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200, Copenhagen, Denmark.
| |
Collapse
|
395
|
Stadhouders R, Vidal E, Serra F, Di Stefano B, Le Dily F, Quilez J, Gomez A, Collombet S, Berenguer C, Cuartero Y, Hecht J, Filion GJ, Beato M, Marti-Renom MA, Graf T. Transcription factors orchestrate dynamic interplay between genome topology and gene regulation during cell reprogramming. Nat Genet 2018; 50:238-249. [PMID: 29335546 PMCID: PMC5810905 DOI: 10.1038/s41588-017-0030-7] [Citation(s) in RCA: 228] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Accepted: 12/01/2017] [Indexed: 01/28/2023]
Abstract
Chromosomal architecture is known to influence gene expression, yet its role in controlling cell fate remains poorly understood. Reprogramming of somatic cells into pluripotent stem cells (PSCs) by the transcription factors (TFs) OCT4, SOX2, KLF4 and MYC offers an opportunity to address this question but is severely limited by the low proportion of responding cells. We have recently developed a highly efficient reprogramming protocol that synchronously converts somatic into pluripotent stem cells. Here, we used this system to integrate time-resolved changes in genome topology with gene expression, TF binding and chromatin-state dynamics. The results showed that TFs drive topological genome reorganization at multiple architectural levels, often before changes in gene expression. Removal of locus-specific topological barriers can explain why pluripotency genes are activated sequentially, instead of simultaneously, during reprogramming. Together, our results implicate genome topology as an instructive force for implementing transcriptional programs and cell fate in mammals.
Collapse
Affiliation(s)
- Ralph Stadhouders
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
- Department of Pulmonary Medicine, Erasmus MC, Rotterdam, the Netherlands.
| | - Enrique Vidal
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - François Serra
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Structural Genomics Group, CNAG-CRG, BIST, Barcelona, Spain
| | - Bruno Di Stefano
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University and Harvard Medical School, Cambridge, MA, USA
| | - François Le Dily
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Structural Genomics Group, CNAG-CRG, BIST, Barcelona, Spain
| | - Javier Quilez
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Antonio Gomez
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Samuel Collombet
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR8197, INSERM U1024, Paris, France
| | - Clara Berenguer
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Yasmina Cuartero
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Structural Genomics Group, CNAG-CRG, BIST, Barcelona, Spain
| | - Jochen Hecht
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Genomics Unit, CRG, BIST, Barcelona, Spain
| | - Guillaume J Filion
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Miguel Beato
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Marc A Marti-Renom
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
- Structural Genomics Group, CNAG-CRG, BIST, Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
| | - Thomas Graf
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
| |
Collapse
|
396
|
Dileep V, Gilbert DM. Single-cell replication profiling to measure stochastic variation in mammalian replication timing. Nat Commun 2018; 9:427. [PMID: 29382831 PMCID: PMC5789892 DOI: 10.1038/s41467-017-02800-w] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 12/27/2017] [Indexed: 01/17/2023] Open
Abstract
Mammalian DNA replication is regulated via multi-replicon segments that replicate in a defined temporal order during S-phase. Further, early/late replication of RDs corresponds to active/inactive chromatin interaction compartments. Although replication origins are selected stochastically, variation in replication timing is poorly understood. Here we devise a strategy to measure variation in replication timing using DNA copy number in single mouse embryonic stem cells. We find that borders between replicated and unreplicated DNA are highly conserved between cells, demarcating active and inactive compartments of the nucleus. Fifty percent of replication events deviated from their average replication time by ± 15% of S phase. This degree of variation is similar between cells, between homologs within cells and between all domains genomewide, regardless of their replication timing. These results demonstrate that stochastic variation in replication timing is independent of elements that dictate timing or extrinsic environmental variation.
Collapse
Affiliation(s)
- Vishnu Dileep
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL, 32306, USA
| | - David M Gilbert
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL, 32306, USA.
| |
Collapse
|
397
|
Dekker J, Belmont AS, Guttman M, Leshyk VO, Lis JT, Lomvardas S, Mirny LA, O'Shea CC, Park PJ, Ren B, Politz JCR, Shendure J, Zhong S. The 4D nucleome project. Nature 2018; 549:219-226. [PMID: 28905911 DOI: 10.1038/nature23884] [Citation(s) in RCA: 437] [Impact Index Per Article: 72.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 07/27/2017] [Indexed: 12/19/2022]
Abstract
The 4D Nucleome Network aims to develop and apply approaches to map the structure and dynamics of the human and mouse genomes in space and time with the goal of gaining deeper mechanistic insights into how the nucleus is organized and functions. The project will develop and benchmark experimental and computational approaches for measuring genome conformation and nuclear organization, and investigate how these contribute to gene regulation and other genome functions. Validated experimental technologies will be combined with biophysical approaches to generate quantitative models of spatial genome organization in different biological states, both in cell populations and in single cells.
Collapse
Affiliation(s)
- Job Dekker
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Howard Hughes Medical Institute, Worcester, Massachusetts 01605, USA
| | - Andrew S Belmont
- Department of Cell and Developmental Biology, University of Illinois, Urbana-Champaign, Illinois 61801, USA
| | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Victor O Leshyk
- Department of Bioengineering, University of California San Diego, La Jolla, California 92093, USA
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Stavros Lomvardas
- Department of Biochemistry and Molecular Biophysics, Mortimer B. Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, New York 10027, USA
| | - Leonid A Mirny
- Institute for Medical Engineering and Science, and Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Clodagh C O'Shea
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, Moores Cancer Center, University of California San Diego, La Jolla California 92093, USA
| | - Joan C Ritland Politz
- Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, Washington 98109, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Howard Hughes Medical Institute, Seattle, Washington 98109, USA
| | - Sheng Zhong
- Department of Bioengineering, University of California San Diego, La Jolla, California 92093, USA
| | | |
Collapse
|
398
|
Le Dily F, Beato M. Signaling by Steroid Hormones in the 3D Nuclear Space. Int J Mol Sci 2018; 19:E306. [PMID: 29360755 PMCID: PMC5855546 DOI: 10.3390/ijms19020306] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 01/18/2018] [Accepted: 01/19/2018] [Indexed: 01/30/2023] Open
Abstract
Initial studies showed that ligand-activated hormone receptors act by binding to the proximal promoters of individual target genes. Genome-wide studies have now revealed that regulation of transcription by steroid hormones mainly depends on binding of the receptors to distal regulatory elements. Those distal elements, either enhancers or silencers, act on the regulation of target genes by chromatin looping to the gene promoters. In the nucleus, this level of chromatin folding is integrated within dynamic higher orders of genome structures, which are organized in a non-random fashion. Terminally differentiated cells exhibit a tissue-specific three-dimensional (3D) organization of the genome that favors or restrains the activity of transcription factors and modulates the function of steroid hormone receptors, which are transiently activated upon hormone exposure. Conversely, integration of the hormones signal may require modifications of the 3D organization to allow appropriate transcriptional outcomes. In this review, we summarize the main levels of organization of the genome, review how they can modulate the response to steroids in a cell specific manner and discuss the role of receptors in shaping and rewiring the structure in response to hormone. Taking into account the dynamics of 3D genome organization will contribute to a better understanding of the pleiotropic effects of steroid hormones in normal and cancer cells.
Collapse
Affiliation(s)
- François Le Dily
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Doctor Aiguader 88, 08003 Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain.
| | - Miguel Beato
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Doctor Aiguader 88, 08003 Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain.
| |
Collapse
|
399
|
Zhao PA, Rivera-Mulia JC, Gilbert DM. Replication Domains: Genome Compartmentalization into Functional Replication Units. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1042:229-257. [DOI: 10.1007/978-981-10-6955-0_11] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
400
|
Wang Q, Sun Q, Czajkowsky DM, Shao Z. Sub-kb Hi-C in D. melanogaster reveals conserved characteristics of TADs between insect and mammalian cells. Nat Commun 2018; 9:188. [PMID: 29335463 PMCID: PMC5768742 DOI: 10.1038/s41467-017-02526-9] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 12/06/2017] [Indexed: 01/19/2023] Open
Abstract
Topologically associating domains (TADs) are fundamental elements of the eukaryotic genomic structure. However, recent studies suggest that the insulating complexes, CTCF/cohesin, present at TAD borders in mammals are absent from those in Drosophila melanogaster, raising the possibility that border elements are not conserved among metazoans. Using in situ Hi-C with sub-kb resolution, here we show that the D. melanogaster genome is almost completely partitioned into >4000 TADs, nearly sevenfold more than previously identified. The overwhelming majority of these TADs are demarcated by the insulator complexes, BEAF-32/CP190, or BEAF-32/Chromator, indicating that these proteins may play an analogous role in flies as that of CTCF/cohesin in mammals. Moreover, extended regions previously thought to be unstructured are shown to consist of small contiguous TADs, a property also observed in mammals upon re-examination. Altogether, our work demonstrates that fundamental features associated with the higher-order folding of the genome are conserved from insects to mammals.
Collapse
Affiliation(s)
- Qi Wang
- Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Qiu Sun
- Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Daniel M Czajkowsky
- State Key Laboratory for Oncogenes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, 200240, Shanghai, China.
| | - Zhifeng Shao
- State Key Laboratory for Oncogenes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, 200240, Shanghai, China.
| |
Collapse
|