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Thayer M, Heskett MB, Smith LG, Spellman PT, Yates PA. ASAR lncRNAs control DNA replication timing through interactions with multiple hnRNP/RNA binding proteins. eLife 2024; 13:RP95898. [PMID: 38896448 PMCID: PMC11186638 DOI: 10.7554/elife.95898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024] Open
Abstract
ASARs are a family of very-long noncoding RNAs that control replication timing on individual human autosomes, and are essential for chromosome stability. The eight known ASAR lncRNAs remain closely associated with their parent chromosomes. Analysis of RNA-protein interaction data (from ENCODE) revealed numerous RBPs with significant interactions with multiple ASAR lncRNAs, with several hnRNPs as abundant interactors. An ~7 kb domain within the ASAR6-141 lncRNA shows a striking density of RBP interaction sites. Genetic deletion and ectopic integration assays indicate that this ~7 kb RNA binding protein domain contains functional sequences for controlling replication timing of entire chromosomes in cis. shRNA-mediated depletion of 10 different RNA binding proteins, including HNRNPA1, HNRNPC, HNRNPL, HNRNPM, HNRNPU, or HNRNPUL1, results in dissociation of ASAR lncRNAs from their chromosome territories, and disrupts the synchronous replication that occurs on all autosome pairs, recapitulating the effect of individual ASAR knockouts on a genome-wide scale. Our results further demonstrate the role that ASARs play during the temporal order of genome-wide replication, and we propose that ASARs function as essential RNA scaffolds for the assembly of hnRNP complexes that help maintain the structural integrity of each mammalian chromosome.
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Affiliation(s)
- Mathew Thayer
- Department of Chemical Physiology and Biochemistry,Oregon Health & Science UniversityPortlandUnited States
| | - Michael B Heskett
- Department of Molecular and Medical Genetics, Oregon Health & Science UniversityPortlandUnited States
- Stanford Cancer InstituteStanfordUnited States
| | - Leslie G Smith
- Department of Chemical Physiology and Biochemistry,Oregon Health & Science UniversityPortlandUnited States
| | - Paul T Spellman
- Department of Molecular and Medical Genetics, Oregon Health & Science UniversityPortlandUnited States
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science UniversityPortlandUnited States
| | - Phillip A Yates
- Department of Chemical Physiology and Biochemistry,Oregon Health & Science UniversityPortlandUnited States
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2
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Irastorza-Azcarate I, Kukalev A, Kempfer R, Thieme CJ, Mastrobuoni G, Markowski J, Loof G, Sparks TM, Brookes E, Natarajan KN, Sauer S, Fisher AG, Nicodemi M, Ren B, Schwarz RF, Kempa S, Pombo A. Extensive folding variability between homologous chromosomes in mammalian cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.08.591087. [PMID: 38766012 PMCID: PMC11100664 DOI: 10.1101/2024.05.08.591087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Genetic variation and 3D chromatin structure have major roles in gene regulation. Due to challenges in mapping chromatin conformation with haplotype-specific resolution, the effects of genetic sequence variation on 3D genome structure and gene expression imbalance remain understudied. Here, we applied Genome Architecture Mapping (GAM) to a hybrid mouse embryonic stem cell (mESC) line with high density of single nucleotide polymorphisms (SNPs). GAM resolved haplotype-specific 3D genome structures with high sensitivity, revealing extensive allelic differences in chromatin compartments, topologically associating domains (TADs), long-range enhancer-promoter contacts, and CTCF loops. Architectural differences often coincide with allele-specific differences in gene expression, mediated by Polycomb repression. We show that histone genes are expressed with allelic imbalance in mESCs, are involved in haplotype-specific chromatin contact marked by H3K27me3, and are targets of Polycomb repression through conditional knockouts of Ezh2 or Ring1b. Our work reveals highly distinct 3D folding structures between homologous chromosomes, and highlights their intricate connections with allelic gene expression.
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3
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Ubieto-Capella P, Ximénez-Embún P, Giménez-Llorente D, Losada A, Muñoz J, Méndez J. A rewiring of DNA replication mediated by MRE11 exonuclease underlies primed-to-naive cell de-differentiation. Cell Rep 2024; 43:114024. [PMID: 38581679 DOI: 10.1016/j.celrep.2024.114024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 02/01/2024] [Accepted: 03/15/2024] [Indexed: 04/08/2024] Open
Abstract
Mouse embryonic stem cells (mESCs) in the primed pluripotency state, which resembles the post-implantation epiblast, can be de-differentiated in culture to a naive state that resembles the pre-implantation inner cell mass. We report that primed-to-naive mESC transition entails a significant slowdown of DNA replication forks and the compensatory activation of dormant origins. Using isolation of proteins on nascent DNA coupled to mass spectrometry, we identify key changes in replisome composition that are responsible for these effects. Naive mESC forks are enriched in MRE11 nuclease and other DNA repair proteins. MRE11 is recruited to newly synthesized DNA in response to transcription-replication conflicts, and its inhibition or genetic downregulation in naive mESCs is sufficient to restore the fork rate of primed cells. Transcriptomic analyses indicate that MRE11 exonuclease activity is required for the complete primed-to-naive mESC transition, demonstrating a direct link between DNA replication dynamics and the mESC de-differentiation process.
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Affiliation(s)
- Patricia Ubieto-Capella
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Pilar Ximénez-Embún
- Proteomics Unit-ProteoRed-ISCIII, Biotechnology Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Daniel Giménez-Llorente
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Ana Losada
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Javier Muñoz
- Proteomics Unit-ProteoRed-ISCIII, Biotechnology Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Juan Méndez
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain.
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4
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Simon NM, Kim Y, Bautista DM, Dutton JR, Brem RB. Stem cell transcriptional profiles from mouse subspecies reveal cis-regulatory evolution at translation genes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.18.549406. [PMID: 37503246 PMCID: PMC10370129 DOI: 10.1101/2023.07.18.549406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
A key goal of evolutionary genomics is to harness molecular data to draw inferences about selective forces that have acted on genomes. The field progresses in large part through the development of advanced molecular-evolution analysis methods. Here we explored the intersection between classical sequence-based tests for selection and an empirical expression-based approach, using stem cells from Mus musculus subspecies as a model. Using a test of directional, cis-regulatory evolution across genes in pathways, we discovered a unique program of induction of translation genes in stem cells of the Southeast Asian mouse M. m. castaneus relative to its sister taxa. As a complement, we used sequence analyses to find population-genomic signatures of selection in M. m. castaneus, at the upstream regions of the translation genes, including at transcription factor binding sites. We interpret our data under a model of changes in lineage-specific pressures across Mus musculus in stem cells with high translational capacity. Together, our findings underscore the rigor of integrating expression and sequence-based methods to generate hypotheses about evolutionary events from long ago.
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Affiliation(s)
- Noah M. Simon
- Biology of Aging Doctoral Program, Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089
- Buck Institute for Research on Aging, Novato, CA 94945, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley CA 94720, USA
| | - Yujin Kim
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Diana M. Bautista
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley CA 94720
| | - James R. Dutton
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Rachel B. Brem
- Buck Institute for Research on Aging, Novato, CA 94945, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley CA 94720, USA
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5
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Lin Y, Li J, Gu Y, Jin L, Bai J, Zhang J, Wang Y, Liu P, Long K, He M, Li D, Liu C, Han Z, Zhang Y, Li X, Zeng B, Lu L, Kong F, Sun Y, Fan Y, Wang X, Wang T, Jiang A, Ma J, Shen L, Zhu L, Jiang Y, Tang G, Fan X, Liu Q, Li H, Wang J, Chen L, Ge L, Li X, Tang Q, Li M. Haplotype-resolved 3D chromatin architecture of the hybrid pig. Genome Res 2024; 34:310-325. [PMID: 38479837 PMCID: PMC10984390 DOI: 10.1101/gr.278101.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 02/15/2024] [Indexed: 03/22/2024]
Abstract
In diploid mammals, allele-specific three-dimensional (3D) genome architecture may lead to imbalanced gene expression. Through ultradeep in situ Hi-C sequencing of three representative somatic tissues (liver, skeletal muscle, and brain) from hybrid pigs generated by reciprocal crosses of phenotypically and physiologically divergent Berkshire and Tibetan pigs, we uncover extensive chromatin reorganization between homologous chromosomes across multiple scales. Haplotype-based interrogation of multi-omic data revealed the tissue dependence of 3D chromatin conformation, suggesting that parent-of-origin-specific conformation may drive gene imprinting. We quantify the effects of genetic variations and histone modifications on allelic differences of long-range promoter-enhancer contacts, which likely contribute to the phenotypic differences between the parental pig breeds. We also observe the fine structure of somatically paired homologous chromosomes in the pig genome, which has a functional implication genome-wide. This work illustrates how allele-specific chromatin architecture facilitates concomitant shifts in allele-biased gene expression, as well as the possible consequential phenotypic changes in mammals.
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Affiliation(s)
- Yu Lin
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jing Li
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China;
| | - Yiren Gu
- College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu 610066, China
| | - Long Jin
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jingyi Bai
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiaman Zhang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yujie Wang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Pengliang Liu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Keren Long
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Mengnan He
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Diyan Li
- School of Pharmacy, Chengdu University, Chengdu 610106, China
| | - Can Liu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Ziyin Han
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yu Zhang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaokai Li
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Bo Zeng
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Lu Lu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Fanli Kong
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Ying Sun
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Institute of Geriatric Health, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China
| | - Yongliang Fan
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xun Wang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Tao Wang
- School of Pharmacy, Chengdu University, Chengdu 610106, China
| | - An'an Jiang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jideng Ma
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Linyuan Shen
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Li Zhu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yanzhi Jiang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Guoqing Tang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaolan Fan
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Qingyou Liu
- Animal Molecular Design and Precise Breeding Key Laboratory of Guangdong Province, School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Hua Li
- Animal Molecular Design and Precise Breeding Key Laboratory of Guangdong Province, School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Jinyong Wang
- Pig Industry Sciences Key Laboratory of Ministry of Agriculture and Rural Affairs, Chongqing Academy of Animal Sciences, Chongqing 402460, China
- National Center of Technology Innovation for Pigs, Chongqing 402460, China
| | - Li Chen
- Pig Industry Sciences Key Laboratory of Ministry of Agriculture and Rural Affairs, Chongqing Academy of Animal Sciences, Chongqing 402460, China
- National Center of Technology Innovation for Pigs, Chongqing 402460, China
| | - Liangpeng Ge
- Pig Industry Sciences Key Laboratory of Ministry of Agriculture and Rural Affairs, Chongqing Academy of Animal Sciences, Chongqing 402460, China
- National Center of Technology Innovation for Pigs, Chongqing 402460, China
| | - Xuewei Li
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Qianzi Tang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China;
| | - Mingzhou Li
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China;
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6
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Nakatani T, Schauer T, Altamirano-Pacheco L, Klein KN, Ettinger A, Pal M, Gilbert DM, Torres-Padilla ME. Emergence of replication timing during early mammalian development. Nature 2024; 625:401-409. [PMID: 38123678 PMCID: PMC10781638 DOI: 10.1038/s41586-023-06872-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 11/16/2023] [Indexed: 12/23/2023]
Abstract
DNA replication enables genetic inheritance across the kingdoms of life. Replication occurs with a defined temporal order known as the replication timing (RT) programme, leading to organization of the genome into early- or late-replicating regions. RT is cell-type specific, is tightly linked to the three-dimensional nuclear organization of the genome1,2 and is considered an epigenetic fingerprint3. In spite of its importance in maintaining the epigenome4, the developmental regulation of RT in mammals in vivo has not been explored. Here, using single-cell Repli-seq5, we generated genome-wide RT maps of mouse embryos from the zygote to the blastocyst stage. Our data show that RT is initially not well defined but becomes defined progressively from the 4-cell stage, coinciding with strengthening of the A and B compartments. We show that transcription contributes to the precision of the RT programme and that the difference in RT between the A and B compartments depends on RNA polymerase II at zygotic genome activation. Our data indicate that the establishment of nuclear organization precedes the acquisition of defined RT features and primes the partitioning of the genome into early- and late-replicating domains. Our work sheds light on the establishment of the epigenome at the beginning of mammalian development and reveals the organizing principles of genome organization.
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Affiliation(s)
| | - Tamas Schauer
- Institute of Epigenetics and Stem Cells, Helmholtz Munich, Munich, Germany
| | | | - Kyle N Klein
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Andreas Ettinger
- Institute of Epigenetics and Stem Cells, Helmholtz Munich, Munich, Germany
| | - Mrinmoy Pal
- Institute of Epigenetics and Stem Cells, Helmholtz Munich, Munich, Germany
| | - David M Gilbert
- Laboratory of Chromosome Replication and Epigenome Regulation, San Diego Biomedical Research Institute, San Diego, CA, USA
| | - Maria-Elena Torres-Padilla
- Institute of Epigenetics and Stem Cells, Helmholtz Munich, Munich, Germany.
- Faculty of Biology, Ludwig-Maximilians Universität, Munich, Germany.
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7
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Neikes HK, Kliza KW, Gräwe C, Wester RA, Jansen PWTC, Lamers LA, Baltissen MP, van Heeringen SJ, Logie C, Teichmann SA, Lindeboom RGH, Vermeulen M. Quantification of absolute transcription factor binding affinities in the native chromatin context using BANC-seq. Nat Biotechnol 2023; 41:1801-1809. [PMID: 36973556 DOI: 10.1038/s41587-023-01715-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 02/16/2023] [Indexed: 03/29/2023]
Abstract
Transcription factor binding across the genome is regulated by DNA sequence and chromatin features. However, it is not yet possible to quantify the impact of chromatin context on transcription factor binding affinities. Here, we report a method called binding affinities to native chromatin by sequencing (BANC-seq) to determine absolute apparent binding affinities of transcription factors to native DNA across the genome. In BANC-seq, a concentration range of a tagged transcription factor is added to isolated nuclei. Concentration-dependent binding is then measured per sample to quantify apparent binding affinities across the genome. BANC-seq adds a quantitative dimension to transcription factor biology, which enables stratification of genomic targets based on transcription factor concentration and prediction of transcription factor binding sites under non-physiological conditions, such as disease-associated overexpression of (onco)genes. Notably, whereas consensus DNA binding motifs for transcription factors are important to establish high-affinity binding sites, these motifs are not always strictly required to generate nanomolar-affinity interactions in the genome.
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Affiliation(s)
- Hannah K Neikes
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Katarzyna W Kliza
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Cathrin Gräwe
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Roelof A Wester
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Pascal W T C Jansen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Lieke A Lamers
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Marijke P Baltissen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Simon J van Heeringen
- Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Colin Logie
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | | | - Rik G H Lindeboom
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- The Netherlands Cancer Institute, Amsterdam, the Netherlands.
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, the Netherlands.
- The Netherlands Cancer Institute, Amsterdam, the Netherlands.
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8
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Weiner AC, Williams MJ, Shi H, Vázquez-García I, Salehi S, Rusk N, Aparicio S, Shah SP, McPherson A. Single-cell DNA replication dynamics in genomically unstable cancers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.10.536250. [PMID: 37090647 PMCID: PMC10120671 DOI: 10.1101/2023.04.10.536250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Dysregulated DNA replication is both a cause and a consequence of aneuploidy, yet the dynamics of DNA replication in aneuploid cell populations remains understudied. We developed a new method, PERT, for inferring cell-specific DNA replication states from single-cell whole genome sequencing, and investigated clone-specific DNA replication dynamics in >50,000 cells obtained from a collection of aneuploid and clonally heterogeneous cell lines, xenografts and primary cancer tissues. Clone replication timing (RT) profiles correlated with future copy number changes in serially passaged cell lines. Cell type was the strongest determinant of RT heterogeneity, while whole genome doubling and mutational process were associated with accumulation of late S-phase cells and weaker RT associations. Copy number changes affecting chromosome X had striking impact on RT, with loss of the inactive X allele shifting replication earlier, and loss of inactive Xq resulting in reactivation of Xp. Finally, analysis of time series xenografts illustrate how cell cycle distributions approximate clone proliferation, recapitulating expected relationships between proliferation and fitness in treatment-naive and chemotherapeutic contexts.
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Affiliation(s)
- Adam C Weiner
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Marc J Williams
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hongyu Shi
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ignacio Vázquez-García
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sohrab Salehi
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nicole Rusk
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Samuel Aparicio
- Department of Molecular Oncology, British Columbia Cancer, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Sohrab P Shah
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrew McPherson
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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9
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Balasooriya GI, Spector DL. Allele pairing at Sun1-enriched domains at the nuclear periphery via T1A3 tandem DNA repeats. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.07.536031. [PMID: 37066204 PMCID: PMC10104147 DOI: 10.1101/2023.04.07.536031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Spatiotemporal gene regulation is fundamental to the biology of diploid cells. Therefore, effective communication between two alleles and their geometry in the nucleus is important. However, the mechanism that fine-tunes the expression from each of the two alleles of an autosome is enigmatic. Establishing an allele-specific gene expression visualization system in living cells, we show that alleles of biallelically expressed Cth and Ttc4 genes are paired prior to acquiring monoallelic expression. We found that active alleles of monoallelic genes are preferentially localized at Sun1-enriched domains at the nuclear periphery. These peripherally localized active DNA loci are enriched with adenine-thymidine-rich tandem repeats that interact with Hnrnpd and reside in a Hi-C-defined A compartment within the B compartment. Our results demonstrate the biological significance of T 1 A 3 tandem repeat sequences in genome organization and how the regulation of gene expression, at the level of individual alleles, relates to their spatial arrangement.
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10
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Zhang L, Wu J, Liang J, Lin R, Sun C, Dai Q, Zhang L, Guo H, Zhao R, Wang X. Conserved noncoding sequences correlate with distant gene contacts in Arabidopsis and Brassica. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023. [PMID: 36762577 DOI: 10.1111/jipb.13465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
Physical contact between genes distant on chromosomes is a potentially important way for genes to coordinate their expressions. To investigate the potential importance of distant contacts, we performed high-throughput chromatin conformation capture (Hi-C) experiments on leaf nuclei isolated from Brassica rapa and Brassica oleracea. We then combined our results with published Hi-C data from Arabidopsis thaliana. We found that distant genes come into physical contact and do so preferentially between the proximal promoter of one gene and the downstream region of another gene. Genes with higher numbers of conserved noncoding sequences (CNSs) nearby were more likely to have contact with distant genes. With more CNSs came higher numbers of transcription factor binding sites and more histone modifications associated with the activity. In addition, for the genes we studied, distant contacting genes with CNSs were more likely to be transcriptionally coordinated. These observations suggest that CNSs may enrich active histone modifications and recruit transcription factors, correlating with distant contacts to ensure coordinated expression. This study advances our knowledge of gene contacts and provides insights into the relationship between CNSs and distant gene contacts in plants.
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Affiliation(s)
- Lei Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jian Wu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jianli Liang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Runmao Lin
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chao Sun
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Qirui Dai
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lupeng Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Huiling Guo
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ranze Zhao
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaowu Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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11
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Rivera-Mulia JC, Trevilla-Garcia C, Martinez-Cifuentes S. Optimized Repli-seq: improved DNA replication timing analysis by next-generation sequencing. Chromosome Res 2022; 30:401-414. [PMID: 35781769 PMCID: PMC10124313 DOI: 10.1007/s10577-022-09703-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 06/15/2022] [Accepted: 06/15/2022] [Indexed: 01/25/2023]
Abstract
The human genome is divided into functional units that replicate at specific times during S-phase. This temporal program is known as replication timing (RT) and is coordinated with the spatial organization of the genome and transcriptional activity. RT is also cell type-specific, dynamically regulated during development, and alterations in RT are observed in multiple diseases. Thus, the precise measure of RT is critical to understand the role of RT in gene function regulation. Distinct methods for assaying the RT program exist; however, conventional methods require thousands of cells as input, prohibiting its applicability to samples with limited cell numbers such as those from disease patients or from early developing embryos. Although single-cell RT analyses have been developed, these methods are low throughput, require generation of numerous libraries, increased sequencing costs, and produce low resolution data. Here, we developed an improved method to measure RT genome-wide that enables high-resolution analysis of low input samples. This method incorporates direct cell sorting into lysis buffer, as well as DNA fragmentation and library preparation in a single tube, resulting in higher yields, increased quality, and reproducibility with decreased costs. We also performed a systematic data processing analysis to provide standardized parameters for RT measurement. This optimized method facilitates RT analysis and will enable its application to a broad range of studies investigating the role of RT in gene expression, nuclear architecture, and disease.
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Affiliation(s)
- Juan Carlos Rivera-Mulia
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, MN, USA.
- Stem Cell Institute, University of Minnesota Medical School, Minneapolis, MN, USA.
- Masonic Cancer Center, University of Minnesota Medical School, Minneapolis, MN, USA.
| | - Claudia Trevilla-Garcia
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Santiago Martinez-Cifuentes
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, MN, USA
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12
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Heskett MB, Vouzas AE, Smith LG, Yates PA, Boniface C, Bouhassira EE, Spellman PT, Gilbert DM, Thayer MJ. Epigenetic control of chromosome-associated lncRNA genes essential for replication and stability. Nat Commun 2022; 13:6301. [PMID: 36273230 PMCID: PMC9588035 DOI: 10.1038/s41467-022-34099-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 10/13/2022] [Indexed: 01/18/2023] Open
Abstract
ASARs are long noncoding RNA genes that control replication timing of entire human chromosomes in cis. The three known ASAR genes are located on human chromosomes 6 and 15, and are essential for chromosome integrity. To identify ASARs on all human chromosomes we utilize a set of distinctive ASAR characteristics that allow for the identification of hundreds of autosomal loci with epigenetically controlled, allele-restricted behavior in expression and replication timing of coding and noncoding genes, and is distinct from genomic imprinting. Disruption of noncoding RNA genes at five of five tested loci result in chromosome-wide delayed replication and chromosomal instability, validating their ASAR activity. In addition to the three known essential cis-acting chromosomal loci, origins, centromeres, and telomeres, we propose that all mammalian chromosomes also contain "Inactivation/Stability Centers" that display allele-restricted epigenetic regulation of protein coding and noncoding ASAR genes that are essential for replication and stability of each chromosome.
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Affiliation(s)
- Michael B Heskett
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Molecular and Medical Genetics Oregon Health & Science University, Portland, OR, 97239, USA
| | - Athanasios E Vouzas
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| | - Leslie G Smith
- Department of Chemical Physiology and Biochemistry Oregon Health & Science University, Portland, OR, 97239, USA
| | - Phillip A Yates
- Department of Chemical Physiology and Biochemistry Oregon Health & Science University, Portland, OR, 97239, USA
| | - Christopher Boniface
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute Oregon Health & Science University, Portland, OR, 97239, USA
| | - Eric E Bouhassira
- Department of Cell Biology and Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Paul T Spellman
- Department of Molecular and Medical Genetics Oregon Health & Science University, Portland, OR, 97239, USA
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute Oregon Health & Science University, Portland, OR, 97239, USA
| | - David M Gilbert
- San Diego Biomedical Research Institute, San Diego, CA, 92121, USA
| | - Mathew J Thayer
- Department of Chemical Physiology and Biochemistry Oregon Health & Science University, Portland, OR, 97239, USA.
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13
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Balasooriya GI, Spector DL. Allele-specific differential regulation of monoallelically expressed autosomal genes in the cardiac lineage. Nat Commun 2022; 13:5984. [PMID: 36216821 PMCID: PMC9550772 DOI: 10.1038/s41467-022-33722-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 09/27/2022] [Indexed: 11/29/2022] Open
Abstract
Each mammalian autosomal gene is represented by two alleles in diploid cells. To our knowledge, no insights have been made in regard to allele-specific regulatory mechanisms of autosomes. Here we use allele-specific single cell transcriptomic analysis to elucidate the establishment of monoallelic gene expression in the cardiac lineage. We find that monoallelically expressed autosomal genes in mESCs and mouse blastocyst cells are differentially regulated based on the genetic background of the parental alleles. However, the genetic background of the allele does not affect the establishment of monoallelic genes in differentiated cardiomyocytes. Additionally, we observe epigenetic differences between deterministic and random autosomal monoallelic genes. Moreover, we also find a greater contribution of the maternal versus paternal allele to the development and homeostasis of cardiac tissue and in cardiac health, highlighting the importance of maternal influence in male cardiac tissue homeostasis. Our findings emphasize the significance of allele-specific insights into gene regulation in development, homeostasis and disease.
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14
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Massey DJ, Koren A. Telomere-to-telomere human DNA replication timing profiles. Sci Rep 2022; 12:9560. [PMID: 35688856 PMCID: PMC9187705 DOI: 10.1038/s41598-022-13638-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/26/2022] [Indexed: 11/23/2022] Open
Abstract
The spatiotemporal organization of DNA replication produces a highly robust and reproducible replication timing profile. Sequencing-based methods for assaying replication timing genome-wide have become commonplace, but regions of high repeat content in the human genome have remained refractory to analysis. Here, we report the first nearly-gapless telomere-to-telomere replication timing profiles in human, using the T2T-CHM13 genome assembly and sequencing data for five cell lines. We find that replication timing can be successfully assayed in centromeres and large blocks of heterochromatin. Centromeric regions replicate in mid-to-late S-phase and contain replication-timing peaks at a similar density to other genomic regions, while distinct families of heterochromatic satellite DNA differ in their bias for replicating in late S-phase. The high degree of consistency in centromeric replication timing across chromosomes within each cell line prompts further investigation into the mechanisms dictating that some cell lines replicate their centromeres earlier than others, and what the consequences of this variation are.
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Affiliation(s)
- Dashiell J Massey
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA.
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15
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Screening thousands of transcribed coding and non-coding regions reveals sequence determinants of RNA polymerase II elongation potential. Nat Struct Mol Biol 2022; 29:613-620. [PMID: 35681023 DOI: 10.1038/s41594-022-00785-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 04/28/2022] [Indexed: 01/07/2023]
Abstract
Precise regulation of transcription by RNA polymerase II (RNAPII) is critical for organismal growth and development. However, what determines whether an engaged RNAPII will synthesize a full-length transcript or terminate prematurely is poorly understood. Notably, RNAPII is far more susceptible to termination when transcribing non-coding RNAs than when synthesizing protein-coding mRNAs, but the mechanisms underlying this are unclear. To investigate the impact of transcribed sequence on elongation potential, we developed a method to screen the effects of thousands of INtegrated Sequences on Expression of RNA and Translation using high-throughput sequencing (INSERT-seq). We found that higher AT content in non-coding RNAs, rather than specific sequence motifs, drives RNAPII termination. Further, we demonstrate that 5' splice sites autonomously stimulate processive transcription, even in the absence of polyadenylation signals. Our results reveal a potent role for the transcribed sequence in dictating gene output and demonstrate the power of INSERT-seq toward illuminating these contributions.
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16
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Miura H, Hiratani I. Cell cycle dynamics and developmental dynamics of the 3D genome: toward linking the two timescales. Curr Opin Genet Dev 2022; 73:101898. [PMID: 35026526 DOI: 10.1016/j.gde.2021.101898] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/11/2021] [Accepted: 12/15/2021] [Indexed: 11/03/2022]
Abstract
In the mammalian cell nucleus, chromosomes are folded differently in interphase and mitosis. Interphase chromosomes are relatively decondensed and display at least two unique layers of higher-order organization: topologically associating domains (TADs) and cell-type-specific A/B compartments, which correlate well with early/late DNA replication timing (RT). In mitosis, these structures rapidly disappear but are gradually reconstructed during G1 phase, coincident with the establishment of the RT program. However, these structures also change dynamically during cell differentiation and reprogramming, and yet we are surprisingly ignorant about the relationship between their cell cycle dynamics and developmental dynamics. In this review, we summarize the recent findings on this topic, discuss how these two processes might be coordinated with each other and its potential significance.
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Affiliation(s)
- Hisashi Miura
- Laboratory for Developmental Epigenetics, RIKEN Center for Biosystems Dynamics Research (BDR), 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047 Japan
| | - Ichiro Hiratani
- Laboratory for Developmental Epigenetics, RIKEN Center for Biosystems Dynamics Research (BDR), 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047 Japan.
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17
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Bergman Y, Simon I, Cedar H. Asynchronous Replication Timing: A Mechanism for Monoallelic Choice During Development. Front Cell Dev Biol 2021; 9:737681. [PMID: 34660595 PMCID: PMC8517340 DOI: 10.3389/fcell.2021.737681] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 09/14/2021] [Indexed: 11/13/2022] Open
Abstract
Developmental programming is carried out by a sequence of molecular choices that epigenetically mark the genome to generate the stable cell types which make up the total organism. A number of important processes, such as genomic imprinting, selection of immune or olfactory receptors, and X-chromosome inactivation in females are dependent on the ability to stably choose one single allele in each cell. In this perspective, we propose that asynchronous replication timing (ASRT) serves as the basis for a sophisticated universal mechanism for mediating and maintaining these decisions.
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Affiliation(s)
- Yehudit Bergman
- Department of Developmental Biology and Cancer Research, Hebrew University Hadassah Medical School, Jerusalem, Israel
| | - Itamar Simon
- Department of Microbiology and Molecular Genetics, Hebrew University Hadassah Medical School, The Institute for Medical Research Israel-Canada (IMRIC), Jerusalem, Israel
| | - Howard Cedar
- Department of Developmental Biology and Cancer Research, Hebrew University Hadassah Medical School, Jerusalem, Israel
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18
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Papathanasiou S, Markoulaki S, Blaine LJ, Leibowitz ML, Zhang CZ, Jaenisch R, Pellman D. Whole chromosome loss and genomic instability in mouse embryos after CRISPR-Cas9 genome editing. Nat Commun 2021; 12:5855. [PMID: 34615869 PMCID: PMC8494802 DOI: 10.1038/s41467-021-26097-y] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 09/13/2021] [Indexed: 12/26/2022] Open
Abstract
Karyotype alterations have emerged as on-target complications from CRISPR-Cas9 genome editing. However, the events that lead to these karyotypic changes in embryos after Cas9-treatment remain unknown. Here, using imaging and single-cell genome sequencing of 8-cell stage embryos, we track both spontaneous and Cas9-induced karyotype aberrations through the first three divisions of embryonic development. We observe the generation of abnormal structures of the nucleus that arise as a consequence of errors in mitosis, including micronuclei and chromosome bridges, and determine their contribution to common karyotype aberrations including whole chromosome loss that has been recently reported after editing in embryos. Together, these data demonstrate that Cas9-mediated germline genome editing can lead to unwanted on-target side effects, including major chromosome structural alterations that can be propagated over several divisions of embryonic development.
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Affiliation(s)
- Stamatis Papathanasiou
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Logan J Blaine
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mitchell L Leibowitz
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Cheng-Zhong Zhang
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Rudolf Jaenisch
- Whitehead Institute, Cambridge, MA, USA.
- Massachusetts Institute of Technology, Department of Biology, Cambridge, MA, USA.
| | - David Pellman
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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19
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Du Q, Smith GC, Luu PL, Ferguson JM, Armstrong NJ, Caldon CE, Campbell EM, Nair SS, Zotenko E, Gould CM, Buckley M, Chia KM, Portman N, Lim E, Kaczorowski D, Chan CL, Barton K, Deveson IW, Smith MA, Powell JE, Skvortsova K, Stirzaker C, Achinger-Kawecka J, Clark SJ. DNA methylation is required to maintain both DNA replication timing precision and 3D genome organization integrity. Cell Rep 2021; 36:109722. [PMID: 34551299 DOI: 10.1016/j.celrep.2021.109722] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 06/22/2021] [Accepted: 08/25/2021] [Indexed: 02/08/2023] Open
Abstract
DNA replication timing and three-dimensional (3D) genome organization are associated with distinct epigenome patterns across large domains. However, whether alterations in the epigenome, in particular cancer-related DNA hypomethylation, affects higher-order levels of genome architecture is still unclear. Here, using Repli-Seq, single-cell Repli-Seq, and Hi-C, we show that genome-wide methylation loss is associated with both concordant loss of replication timing precision and deregulation of 3D genome organization. Notably, we find distinct disruption in 3D genome compartmentalization, striking gains in cell-to-cell replication timing heterogeneity and loss of allelic replication timing in cancer hypomethylation models, potentially through the gene deregulation of DNA replication and genome organization pathways. Finally, we identify ectopic H3K4me3-H3K9me3 domains from across large hypomethylated domains, where late replication is maintained, which we purport serves to protect against catastrophic genome reorganization and aberrant gene transcription. Our results highlight a potential role for the methylome in the maintenance of 3D genome regulation.
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Affiliation(s)
- Qian Du
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | - Grady C Smith
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Phuc Loi Luu
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | - James M Ferguson
- The Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Nicola J Armstrong
- Mathematics and Statistics, Murdoch University, Murdoch, WA 6150, Australia
| | - C Elizabeth Caldon
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | | | - Shalima S Nair
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | - Elena Zotenko
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Cathryn M Gould
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Michael Buckley
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Kee-Ming Chia
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Neil Portman
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Elgene Lim
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | - Dominik Kaczorowski
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Chia-Ling Chan
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Kirston Barton
- The Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Ira W Deveson
- St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia; The Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Martin A Smith
- St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia; The Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Joseph E Powell
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; UNSW Cellular Genomics Futures Institute, School of Medical Sciences, UNSW Sydney, NSW 2010, Australia
| | - Ksenia Skvortsova
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | - Clare Stirzaker
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | - Joanna Achinger-Kawecka
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | - Susan J Clark
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia.
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20
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Abstract
Saccharomyces cerevisiae rewires its transcriptional output to survive stressful environments, such as nitrogen scarcity under fermentative conditions. Although divergence in nitrogen metabolism among natural yeast populations has been reported, the impact of regulatory genetic variants modulating gene expression and nitrogen consumption remains to be investigated. Here, we employed an F1 hybrid from two contrasting S. cerevisiae strains, providing a controlled genetic environment to map cis factors involved in the divergence of gene expression regulation in response to nitrogen scarcity. We used a dual approach to obtain genome-wide allele-specific profiles of chromatin accessibility, transcription factor binding, and gene expression through ATAC-seq (assay for transposase accessible chromatin) and RNA-seq (transcriptome sequencing). We observed large variability in allele-specific expression and accessibility between the two genetic backgrounds, with a third of these differences specific to a deficient nitrogen environment. Furthermore, we discovered events of allelic bias in gene expression correlating with allelic bias in transcription factor binding solely under nitrogen scarcity, where the majority of these transcription factors orchestrates the nitrogen catabolite repression regulatory pathway and demonstrates a cis × environment-specific response. Our approach allowed us to find cis variants modulating gene expression, chromatin accessibility, and allelic differences in transcription factor binding in response to low nitrogen culture conditions. IMPORTANCE Historically, coding variants were prioritized when searching for causal mechanisms driving adaptation of natural populations to stressful environments. However, the recent focus on noncoding variants demonstrated their ubiquitous role in adaptation. Here, we performed genome-wide regulatory variation profiles between two divergent yeast strains when facing nitrogen nutritional stress. The open chromatin availability of several regulatory regions changes in response to nitrogen scarcity. Importantly, we describe regulatory events that deviate between strains. Our results demonstrate a widespread variation in gene expression regulation between naturally occurring populations in response to stressful environments.
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21
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Li J, Lin Y, Tang Q, Li M. Understanding three-dimensional chromatin organization in diploid genomes. Comput Struct Biotechnol J 2021; 19:3589-3598. [PMID: 34257838 PMCID: PMC8246089 DOI: 10.1016/j.csbj.2021.06.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 06/11/2021] [Accepted: 06/12/2021] [Indexed: 11/17/2022] Open
Abstract
The three-dimensional (3D) organization of chromatin in the nucleus of diploid eukaryotic organisms has fascinated biologists for many years. Despite major progress in chromatin conformation studies, current knowledge regarding the spatial organization of diploid (maternal and paternal) genomes is still limited. Recent advances in Hi-C technology and data processing approaches have enabled construction of diploid Hi-C contact maps. These maps greatly accelerated the pace of novel discoveries in haplotype-resolved 3D genome studies, revealing the role of allele biased chromatin conformation in transcriptional regulation. Here, we review emerging concepts and haplotype phasing strategies of Hi-C data in 3D diploid genome studies. We discuss new insights on homologous chromosomal organization and the interplay between allelic biased chromatin architecture and several nuclear functions, explaining how haplotype-resolved Hi-C technologies have been used to resolve important biological questions.
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Affiliation(s)
- Jing Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yu Lin
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Qianzi Tang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Mingzhou Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
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22
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Markowski J, Kempfer R, Kukalev A, Irastorza-Azcarate I, Loof G, Kehr B, Pombo A, Rahmann S, Schwarz RF. GAMIBHEAR: whole-genome haplotype reconstruction from Genome Architecture Mapping data. Bioinformatics 2021; 37:3128-3135. [PMID: 33830196 PMCID: PMC8504635 DOI: 10.1093/bioinformatics/btab238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 02/22/2021] [Accepted: 04/07/2021] [Indexed: 11/24/2022] Open
Abstract
Motivation Genome Architecture Mapping (GAM) was recently introduced as a digestion- and ligation-free method to detect chromatin conformation. Orthogonal to existing approaches based on chromatin conformation capture (3C), GAM’s ability to capture both inter- and intra-chromosomal contacts from low amounts of input data makes it particularly well suited for allele-specific analyses in a clinical setting. Allele-specific analyses are powerful tools to investigate the effects of genetic variants on many cellular phenotypes including chromatin conformation, but require the haplotypes of the individuals under study to be known a priori. So far, however, no algorithm exists for haplotype reconstruction and phasing of genetic variants from GAM data, hindering the allele-specific analysis of chromatin contact points in non-model organisms or individuals with unknown haplotypes. Results We present GAMIBHEAR, a tool for accurate haplotype reconstruction from GAM data. GAMIBHEAR aggregates allelic co-observation frequencies from GAM data and employs a GAM-specific probabilistic model of haplotype capture to optimize phasing accuracy. Using a hybrid mouse embryonic stem cell line with known haplotype structure as a benchmark dataset, we assess correctness and completeness of the reconstructed haplotypes, and demonstrate the power of GAMIBHEAR to infer accurate genome-wide haplotypes from GAM data. Availability and implementation GAMIBHEAR is available as an R package under the open-source GPL-2 license at https://bitbucket.org/schwarzlab/gamibhear. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Julia Markowski
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Hannoversche Str. 28, 10115 Berlin, Germany.,Department of Biology, Humboldt University of Berlin, Unter den Linden 6, 10099 Berlin, Germany
| | - Rieke Kempfer
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Hannoversche Str. 28, 10115 Berlin, Germany.,Department of Biology, Humboldt University of Berlin, Unter den Linden 6, 10099 Berlin, Germany
| | - Alexander Kukalev
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Hannoversche Str. 28, 10115 Berlin, Germany
| | - Ibai Irastorza-Azcarate
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Hannoversche Str. 28, 10115 Berlin, Germany
| | - Gesa Loof
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Hannoversche Str. 28, 10115 Berlin, Germany.,Department of Biology, Humboldt University of Berlin, Unter den Linden 6, 10099 Berlin, Germany
| | - Birte Kehr
- Berlin Institute of Health (BIH), Anna-Louisa-Karsch-Str. 2, 10178 Berlin, Germany.,Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, 10117 Berlin, Germany
| | - Ana Pombo
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Hannoversche Str. 28, 10115 Berlin, Germany.,Department of Biology, Humboldt University of Berlin, Unter den Linden 6, 10099 Berlin, Germany
| | - Sven Rahmann
- Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, 45122 Essen, Germany
| | - Roland F Schwarz
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Hannoversche Str. 28, 10115 Berlin, Germany
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23
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Chromosomal coordination and differential structure of asynchronous replicating regions. Nat Commun 2021; 12:1035. [PMID: 33589603 PMCID: PMC7884787 DOI: 10.1038/s41467-021-21348-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 01/18/2021] [Indexed: 02/05/2023] Open
Abstract
Stochastic asynchronous replication timing (AS-RT) is a phenomenon in which the time of replication of each allele is different, and the identity of the early allele varies between cells. By taking advantage of stable clonal pre-B cell populations derived from C57BL6/Castaneous mice, we have mapped the genome-wide AS-RT loci, independently of genetic differences. These regions are characterized by differential chromatin accessibility, mono-allelic expression and include new gene families involved in specifying cell identity. By combining population level mapping with single cell FISH, our data reveal the existence of a novel regulatory program that coordinates a fixed relationship between AS-RT regions on any given chromosome, with some loci set to replicate in a parallel and others set in the anti-parallel orientation. Our results show that AS-RT is a highly regulated epigenetic mark established during early embryogenesis that may be used for facilitating the programming of mono-allelic choice throughout development. Most regions of the mammalian genome replicate both alleles in a synchronous manner, but some loci have been found to replicate asynchronously and the time of replication of each allele is different. Here the authors, by employing clonal mouse cells from a hybrid strain chart replication timing over the entire genome, using polymorphisms to distinguish between the paternal and maternal alleles.
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Poonperm R, Hiratani I. Formation of a multi-layered 3-dimensional structure of the heterochromatin compartment during early mammalian development. Dev Growth Differ 2021; 63:5-17. [PMID: 33491197 DOI: 10.1111/dgd.12709] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 12/14/2020] [Accepted: 01/05/2021] [Indexed: 01/10/2023]
Abstract
During embryogenesis in mammals, the 3-dimensional (3D) genome organization changes globally in parallel with transcription changes in a cell-type specific manner. This involves the progressive formation of heterochromatin, the best example of which is the inactive X chromosome (Xi) in females, originally discovered as a compact 3D structure at the nuclear periphery known as the Barr body. The heterochromatin formation on the autosomes and the Xi is tightly associated with the differentiation state and the developmental potential of cells, making it an ideal readout of the cellular epigenetic state. At a glance, the heterochromatin appears to be uniform. However, recent studies are beginning to reveal a more complex picture, with multiple hierarchical levels co-existing within the heterochromatin compartment. Such hierarchical levels appear to exist in the heterochromatin compartment on autosomes as well as on the Xi. Here, we review recent progress in our understanding of the 3D genome organization changes during the period of differentiation surrounding pluripotency in vivo and in vitro, with a focus on the heterochromatin compartment. We first look at the whole genome, then focus on the Xi, and discuss their differences and similarities. Finally, we present a unified view of how the heterochromatin compartment is formed and regulated during early development. In particular, we emphasize that there are multiple layers within the heterochromatic compartment on both the autosomes and the Xi, with regulatory mechanisms common and specific to each layer.
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Affiliation(s)
- Rawin Poonperm
- Laboratory for Developmental Epigenetics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
| | - Ichiro Hiratani
- Laboratory for Developmental Epigenetics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
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Chandradoss KR, Chawla B, Dhuppar S, Nayak R, Ramachandran R, Kurukuti S, Mazumder A, Sandhu KS. CTCF-Mediated Genome Architecture Regulates the Dosage of Mitotically Stable Mono-allelic Expression of Autosomal Genes. Cell Rep 2020; 33:108302. [PMID: 33113374 DOI: 10.1016/j.celrep.2020.108302] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 07/31/2020] [Accepted: 09/30/2020] [Indexed: 11/30/2022] Open
Abstract
The mechanisms that guide the clonally stable random mono-allelic expression of autosomal genes remain enigmatic. We show that (1) mono-allelically expressed (MAE) genes are assorted and insulated from bi-allelically expressed (BAE) genes through CTCF-mediated chromatin loops; (2) the cell-type-specific dynamics of mono-allelic expression coincides with the gain and loss of chromatin insulator sites; (3) dosage of MAE genes is more sensitive to the loss of chromatin insulation than that of BAE genes; and (4) inactive alleles of MAE genes are significantly more insulated than active alleles and are de-repressed upon CTCF depletion. This alludes to a topology wherein the inactive alleles of MAE genes are insulated from the spatial interference of transcriptional states from the neighboring bi-allelic domains via CTCF-mediated loops. We propose that CTCF functions as a typical insulator on inactive alleles, but facilitates transcription through enhancer-linking on active allele of MAE genes, indicating widespread allele-specific regulatory roles of CTCF.
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Affiliation(s)
- Keerthivasan Raanin Chandradoss
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER)-Mohali, Knowledge City, Sector 81, SAS Nagar 140306, India
| | - Bindia Chawla
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER)-Mohali, Knowledge City, Sector 81, SAS Nagar 140306, India
| | - Shivnarayan Dhuppar
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research (TIFR) Hyderabad, 36/P, Gopanpally Village, Serilingampally Mandal, Hyderabad 500046, India
| | - Rakhee Nayak
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Prof. C.R. Rao Road, Gachibowli, Hyderabad 500046, India
| | - Rajesh Ramachandran
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER)-Mohali, Knowledge City, Sector 81, SAS Nagar 140306, India
| | - Sreenivasulu Kurukuti
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Prof. C.R. Rao Road, Gachibowli, Hyderabad 500046, India
| | - Aprotim Mazumder
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research (TIFR) Hyderabad, 36/P, Gopanpally Village, Serilingampally Mandal, Hyderabad 500046, India
| | - Kuljeet Singh Sandhu
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER)-Mohali, Knowledge City, Sector 81, SAS Nagar 140306, India.
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26
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Distinct features of nucleolus-associated domains in mouse embryonic stem cells. Chromosoma 2020; 129:121-139. [PMID: 32219510 DOI: 10.1007/s00412-020-00734-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 03/09/2020] [Accepted: 03/12/2020] [Indexed: 10/24/2022]
Abstract
Heterochromatin in eukaryotic interphase cells frequently localizes to the nucleolar periphery (nucleolus-associated domains (NADs)) and the nuclear lamina (lamina-associated domains (LADs)). Gene expression in somatic cell NADs is generally low, but NADs have not been characterized in mammalian stem cells. Here, we generated the first genome-wide map of NADs in mouse embryonic stem cells (mESCs) via deep sequencing of chromatin associated with biochemically purified nucleoli. As we had observed in mouse embryonic fibroblasts (MEFs), the large type I subset of NADs overlaps with constitutive LADs and is enriched for features of constitutive heterochromatin, including late replication timing and low gene density and expression levels. Conversely, the type II NAD subset overlaps with loci that are not lamina-associated, but in mESCs, type II NADs are much less abundant than in MEFs. mESC NADs are also much less enriched in H3K27me3 modified regions than are NADs in MEFs. Additionally, comparision of MEF and mESC NADs revealed enrichment of developmentally regulated genes in cell-type-specific NADs. Together, these data indicate that NADs are a developmentally dynamic component of heterochromatin. These studies implicate association with the nucleolar periphery as a mechanism for developmentally regulated gene expression and will facilitate future studies of NADs during mESC differentiation.
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Zhao PA, Sasaki T, Gilbert DM. High-resolution Repli-Seq defines the temporal choreography of initiation, elongation and termination of replication in mammalian cells. Genome Biol 2020; 21:76. [PMID: 32209126 PMCID: PMC7092589 DOI: 10.1186/s13059-020-01983-8] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 03/04/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND DNA replication in mammalian cells occurs in a defined temporal order during S phase, known as the replication timing (RT) programme. Replication timing is developmentally regulated and correlated with chromatin conformation and local transcriptional potential. Here, we present RT profiles of unprecedented temporal resolution in two human embryonic stem cell lines, human colon carcinoma line HCT116, and mouse embryonic stem cells and their neural progenitor derivatives. RESULTS Fine temporal windows revealed a remarkable degree of cell-to-cell conservation in RT, particularly at the very beginning and ends of S phase, and identified 5 temporal patterns of replication in all cell types, consistent with varying degrees of initiation efficiency. Zones of replication initiation (IZs) were detected throughout S phase and interacted in 3D space preferentially with other IZs of similar firing time. Temporal transition regions were resolved into segments of uni-directional replication punctuated at specific sites by small, inefficient IZs. Sites of convergent replication were divided into sites of termination or large constant timing regions consisting of many synchronous IZs in tandem. Developmental transitions in RT occured mainly by activating or inactivating individual IZs or occasionally by altering IZ firing time, demonstrating that IZs, rather than individual origins, are the units of developmental regulation. Finally, haplotype phasing revealed numerous regions of allele-specific and allele-independent asynchronous replication. Allele-independent asynchronous replication was correlated with the presence of previously mapped common fragile sites. CONCLUSIONS Altogether, these data provide a detailed temporal choreography of DNA replication in mammalian cells.
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Affiliation(s)
- Peiyao A Zhao
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL, 32306, USA
| | - Takayo Sasaki
- 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.
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Hulke ML, Massey DJ, Koren A. Genomic methods for measuring DNA replication dynamics. Chromosome Res 2020; 28:49-67. [PMID: 31848781 PMCID: PMC7131883 DOI: 10.1007/s10577-019-09624-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 11/30/2019] [Accepted: 12/03/2019] [Indexed: 12/27/2022]
Abstract
Genomic DNA replicates according to a defined temporal program in which early-replicating loci are associated with open chromatin, higher gene density, and increased gene expression levels, while late-replicating loci tend to be heterochromatic and show higher rates of genomic instability. The ability to measure DNA replication dynamics at genome scale has proven crucial for understanding the mechanisms and cellular consequences of DNA replication timing. Several methods, such as quantification of nucleotide analog incorporation and DNA copy number analyses, can accurately reconstruct the genomic replication timing profiles of various species and cell types. More recent developments have expanded the DNA replication genomic toolkit to assays that directly measure the activity of replication origins, while single-cell replication timing assays are beginning to reveal a new level of replication timing regulation. The combination of these methods, applied on a genomic scale and in multiple biological systems, promises to resolve many open questions and lead to a holistic understanding of how eukaryotic cells replicate their genomes accurately and efficiently.
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Affiliation(s)
- Michelle L Hulke
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Dashiell J Massey
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA.
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29
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Paluvai H, Di Giorgio E, Brancolini C. The Histone Code of Senescence. Cells 2020; 9:cells9020466. [PMID: 32085582 PMCID: PMC7072776 DOI: 10.3390/cells9020466] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 02/14/2020] [Accepted: 02/17/2020] [Indexed: 12/12/2022] Open
Abstract
Senescence is the end point of a complex cellular response that proceeds through a set of highly regulated steps. Initially, the permanent cell-cycle arrest that characterizes senescence is a pro-survival response to irreparable DNA damage. The maintenance of this prolonged condition requires the adaptation of the cells to an unfavorable, demanding and stressful microenvironment. This adaptation is orchestrated through a deep epigenetic resetting. A first wave of epigenetic changes builds a dam on irreparable DNA damage and sustains the pro-survival response and the cell-cycle arrest. Later on, a second wave of epigenetic modifications allows the genomic reorganization to sustain the transcription of pro-inflammatory genes. The balanced epigenetic dynamism of senescent cells influences physiological processes, such as differentiation, embryogenesis and aging, while its alteration leads to cancer, neurodegeneration and premature aging. Here we provide an overview of the most relevant histone modifications, which characterize senescence, aging and the activation of a prolonged DNA damage response.
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30
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Control of DNA replication timing in the 3D genome. Nat Rev Mol Cell Biol 2019; 20:721-737. [DOI: 10.1038/s41580-019-0162-y] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/18/2019] [Indexed: 12/27/2022]
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31
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Hou Y, Li F, Zhang R, Li S, Liu H, Qin ZS, Sun X. Integrative characterization of G-Quadruplexes in the three-dimensional chromatin structure. Epigenetics 2019; 14:894-911. [PMID: 31177910 PMCID: PMC6691997 DOI: 10.1080/15592294.2019.1621140] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 05/05/2019] [Accepted: 05/14/2019] [Indexed: 12/14/2022] Open
Abstract
DNA molecules are highly compacted in the eukaryotic nucleus where distal regulatory elements reach their targets through three-dimensional chromosomal interactions. G-quadruplexes, stable four-stranded non-canonical DNA structures, can change local chromatin organization through the exclusion of nucleosomes. However, the relationship between G-quadruplexes and higher-order genome organization remains unknown. Here, we found that G-quadruplexes are significantly enriched at boundaries of topological associated domains (TADs). Architectural protein occupancy, which plays critical roles in the formation of TADs, was highly correlated with the content of G-quadruplexes at TAD boundaries. Moreover, adjacent boundaries containing G-quadruplexes frequently interacted with each other because of the high enrichment of architectural protein binding sites. Similar to CCCTC-binding factor (CTCF) binding sites, G-quadruplexes also showed strong insulation ability in the separation of adjacent regions. Additionally, the insulation ability of CTCF binding sites and TAD boundaries was significantly reinforced by G-quadruplexes. Furthermore, G-quadruplex motifs on different strands were associated with the orientation of CTCF binding sites. These findings suggest a potential role for G-quadruplexes in loop extrusion. The enrichment of transcription factor binding sites (TFBSs) around regulatory elements containing G-quadruplexes led to frequent interactions between regulatory elements containing G-quadruplexes. Intriguingly, more than 99% of G-quadruplexes overlapped with TFBSs. The binding sites of CTCF and cohesin proteins were preferentially located surrounding G-quadruplexes. Accordingly, we proposed a new mechanism of long-distance gene regulation in which G-quadruplexes are involved in distal interactions between enhancers and promoters.
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Affiliation(s)
- Yue Hou
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, China
| | - Fuyu Li
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, China
| | - Rongxin Zhang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, China
| | - Sheng Li
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, China
| | - Hongde Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, China
| | - Zhaohui S. Qin
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, China
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA USA
| | - Xiao Sun
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, China
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32
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Rivera-Mulia JC, Kim S, Gabr H, Chakraborty A, Ay F, Kahveci T, Gilbert DM. Replication timing networks reveal a link between transcription regulatory circuits and replication timing control. Genome Res 2019; 29:1415-1428. [PMID: 31434679 PMCID: PMC6724675 DOI: 10.1101/gr.247049.118] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Accepted: 08/05/2019] [Indexed: 12/11/2022]
Abstract
DNA replication occurs in a defined temporal order known as the replication timing (RT) program and is regulated during development, coordinated with 3D genome organization and transcriptional activity. However, transcription and RT are not sufficiently coordinated to predict each other, suggesting an indirect relationship. Here, we exploit genome-wide RT profiles from 15 human cell types and intermediate differentiation stages derived from human embryonic stem cells to construct different types of RT regulatory networks. First, we constructed networks based on the coordinated RT changes during cell fate commitment to create highly complex RT networks composed of thousands of interactions that form specific functional subnetwork communities. We also constructed directional regulatory networks based on the order of RT changes within cell lineages, and identified master regulators of differentiation pathways. Finally, we explored relationships between RT networks and transcriptional regulatory networks (TRNs) by combining them into more complex circuitries of composite and bipartite networks. Results identified novel trans interactions linking transcription factors that are core to the regulatory circuitry of each cell type to RT changes occurring in those cell types. These core transcription factors were found to bind cooperatively to sites in the affected replication domains, providing provocative evidence that they constitute biologically significant directional interactions. Our findings suggest a regulatory link between the establishment of cell-type-specific TRNs and RT control during lineage specification.
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Affiliation(s)
- Juan Carlos Rivera-Mulia
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, Minnesota 55455, USA
| | - Sebo Kim
- Department of Computer and Information Sciences and Engineering, University of Florida, Gainesville, Florida 32611, USA
| | - Haitham Gabr
- Department of Computer and Information Sciences and Engineering, University of Florida, Gainesville, Florida 32611, USA
| | - Abhijit Chakraborty
- La Jolla Institute for Allergy and Immunology, La Jolla, California 92037, USA
| | - Ferhat Ay
- La Jolla Institute for Allergy and Immunology, La Jolla, California 92037, USA.,School of Medicine, University of California San Diego, La Jolla, California 92093, USA
| | - Tamer Kahveci
- Department of Computer and Information Sciences and Engineering, University of Florida, Gainesville, Florida 32611, 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
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Miura H, Takahashi S, Poonperm R, Tanigawa A, Takebayashi SI, Hiratani I. Single-cell DNA replication profiling identifies spatiotemporal developmental dynamics of chromosome organization. Nat Genet 2019; 51:1356-1368. [PMID: 31406346 DOI: 10.1038/s41588-019-0474-z] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 06/26/2019] [Indexed: 01/09/2023]
Abstract
In mammalian cells, chromosomes are partitioned into megabase-sized topologically associating domains (TADs). TADs can be in either A (active) or B (inactive) subnuclear compartments, which exhibit early and late replication timing (RT), respectively. Here, we show that A/B compartments change coordinately with RT changes genome wide during mouse embryonic stem cell (mESC) differentiation. While A to B compartment changes and early to late RT changes were temporally inseparable, B to A changes clearly preceded late to early RT changes and transcriptional activation. Compartments changed primarily by boundary shifting, altering the compartmentalization of TADs facing the A/B compartment interface, which was conserved during reprogramming and confirmed in individual cells by single-cell Repli-seq. Differentiating mESCs altered single-cell Repli-seq profiles gradually but uniformly, transiently resembling RT profiles of epiblast-derived stem cells (EpiSCs), suggesting that A/B compartments might also change gradually but uniformly toward a primed pluripotent state. These results provide insights into how megabase-scale chromosome organization changes in individual cells during differentiation.
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Affiliation(s)
- Hisashi Miura
- Laboratory for Developmental Epigenetics, RIKEN Center for Developmental Biology and Center for Biosystems Dynamics Research, Kobe, Japan
| | - Saori Takahashi
- Laboratory for Developmental Epigenetics, RIKEN Center for Developmental Biology and Center for Biosystems Dynamics Research, Kobe, Japan
| | - Rawin Poonperm
- Laboratory for Developmental Epigenetics, RIKEN Center for Developmental Biology and Center for Biosystems Dynamics Research, Kobe, Japan
| | - Akie Tanigawa
- Laboratory for Developmental Epigenetics, RIKEN Center for Developmental Biology and Center for Biosystems Dynamics Research, Kobe, Japan
| | - Shin-Ichiro Takebayashi
- Laboratory of Molecular & Cellular Biology, Graduate Schoold of Bioresources, Mie University, Tsu, Japan
| | - Ichiro Hiratani
- Laboratory for Developmental Epigenetics, RIKEN Center for Developmental Biology and Center for Biosystems Dynamics Research, Kobe, Japan. .,Japan Science and Technology Agency, PRESTO, Kawaguchi, Japan.
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34
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Dileep V, Wilson KA, Marchal C, Lyu X, Zhao PA, Li B, Poulet A, Bartlett DA, Rivera-Mulia JC, Qin ZS, Robins AJ, Schulz TC, Kulik MJ, McCord RP, Dekker J, Dalton S, Corces VG, Gilbert DM. Rapid Irreversible Transcriptional Reprogramming in Human Stem Cells Accompanied by Discordance between Replication Timing and Chromatin Compartment. Stem Cell Reports 2019; 13:193-206. [PMID: 31231024 PMCID: PMC6627004 DOI: 10.1016/j.stemcr.2019.05.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 05/20/2019] [Accepted: 05/20/2019] [Indexed: 02/02/2023] Open
Abstract
The temporal order of DNA replication is regulated during development and is highly correlated with gene expression, histone modifications and 3D genome architecture. We tracked changes in replication timing, gene expression, and chromatin conformation capture (Hi-C) A/B compartments over the first two cell cycles during differentiation of human embryonic stem cells to definitive endoderm. Remarkably, transcriptional programs were irreversibly reprogrammed within the first cell cycle and were largely but not universally coordinated with replication timing changes. Moreover, changes in A/B compartment and several histone modifications that normally correlate strongly with replication timing showed weak correlation during the early cell cycles of differentiation but showed increased alignment in later differentiation stages and in terminally differentiated cell lines. Thus, epigenetic cell fate transitions during early differentiation can occur despite dynamic and discordant changes in otherwise highly correlated genomic properties.
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Affiliation(s)
- Vishnu Dileep
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA
| | - Korey A Wilson
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA
| | - Claire Marchal
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA
| | - Xiaowen Lyu
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Peiyao A Zhao
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA
| | - Ben Li
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, 1518 Clifton Road NE, Atlanta, GA 30322, USA
| | - Axel Poulet
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, 1518 Clifton Road NE, Atlanta, GA 30322, USA
| | - Daniel A Bartlett
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA
| | - Juan Carlos Rivera-Mulia
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA
| | - Zhaohui S Qin
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, 1518 Clifton Road NE, Atlanta, GA 30322, USA
| | | | | | - Michael J Kulik
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Rachel Patton McCord
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Job Dekker
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Stephen Dalton
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Victor G Corces
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - David M Gilbert
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA.
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35
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Duriez B, Chilaka S, Bercher JF, Hercul E, Prioleau MN. Replication dynamics of individual loci in single living cells reveal changes in the degree of replication stochasticity through S phase. Nucleic Acids Res 2019; 47:5155-5169. [PMID: 30926993 PMCID: PMC6547449 DOI: 10.1093/nar/gkz220] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 03/18/2019] [Accepted: 03/21/2019] [Indexed: 12/22/2022] Open
Abstract
Eukaryotic genomes are replicated under the control of a highly sophisticated program during the restricted time period corresponding to S phase. The most widely used replication timing assays, which are performed on populations of millions of cells, suggest that most of the genome is synchronously replicated on homologous chromosomes. We investigated the stochastic nature of this temporal program, by comparing the precise replication times of allelic loci within single vertebrate cells progressing through S phase at six loci replicated from very early to very late. We show that replication timing is strictly controlled for the three loci replicated in the first half of S phase. Out of the three loci replicated in the second part of S phase, two present a significantly more stochastic pattern. Surprisingly, we find that the locus replicated at the very end of S phase, presents stochasticity similar to those replicated in early S phase. We suggest that the richness of loci in efficient origins of replication, which decreases from early- to late-replicating regions, and the strength of interaction with the nuclear lamina may underlie the variation of timing control during S phase.
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Affiliation(s)
- Bénédicte Duriez
- Domaines Chromatiniens et Réplication, Institut Jacques Monod, UMR7592 CNRS – Université Paris Diderot, Paris, France, Equipe labellisée ARC
| | - Sabarinadh Chilaka
- Domaines Chromatiniens et Réplication, Institut Jacques Monod, UMR7592 CNRS – Université Paris Diderot, Paris, France, Equipe labellisée ARC
| | | | - Eslande Hercul
- Domaines Chromatiniens et Réplication, Institut Jacques Monod, UMR7592 CNRS – Université Paris Diderot, Paris, France, Equipe labellisée ARC
| | - Marie-Noëlle Prioleau
- Domaines Chromatiniens et Réplication, Institut Jacques Monod, UMR7592 CNRS – Université Paris Diderot, Paris, France, Equipe labellisée ARC
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36
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Hiratani I, Takahashi S. DNA Replication Timing Enters the Single-Cell Era. Genes (Basel) 2019; 10:genes10030221. [PMID: 30884743 PMCID: PMC6470765 DOI: 10.3390/genes10030221] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 03/12/2019] [Accepted: 03/12/2019] [Indexed: 12/20/2022] Open
Abstract
In mammalian cells, DNA replication timing is controlled at the level of megabase (Mb)-sized chromosomal domains and correlates well with transcription, chromatin structure, and three-dimensional (3D) genome organization. Because of these properties, DNA replication timing is an excellent entry point to explore genome regulation at various levels and a variety of studies have been carried out over the years. However, DNA replication timing studies traditionally required at least tens of thousands of cells, and it was unclear whether the replication domains detected by cell population analyses were preserved at the single-cell level. Recently, single-cell DNA replication profiling methods became available, which revealed that the Mb-sized replication domains detected by cell population analyses were actually well preserved in individual cells. In this article, we provide a brief overview of our current knowledge on DNA replication timing regulation in mammals based on cell population studies, outline the findings from single-cell DNA replication profiling, and discuss future directions and challenges.
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Affiliation(s)
- Ichiro Hiratani
- Laboratory for Developmental Epigenetics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Hyogo 650-0047, Japan.
| | - Saori Takahashi
- Laboratory for Developmental Epigenetics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Hyogo 650-0047, Japan.
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37
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Genome-wide stability of the DNA replication program in single mammalian cells. Nat Genet 2019; 51:529-540. [PMID: 30804559 DOI: 10.1038/s41588-019-0347-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Accepted: 01/09/2019] [Indexed: 11/09/2022]
Abstract
Here, we report a single-cell DNA replication sequencing method, scRepli-seq, a genome-wide methodology that measures copy number differences between replicated and unreplicated DNA. Using scRepli-seq, we demonstrate that replication-domain organization is conserved among individual mouse embryonic stem cells (mESCs). Differentiated mESCs exhibited distinct profiles, which were also conserved among cells. Haplotype-resolved scRepli-seq revealed similar replication profiles of homologous autosomes, while the inactive X chromosome was clearly replicated later than its active counterpart. However, a small degree of cell-to-cell replication-timing heterogeneity was present, which was smallest at the beginning and the end of S phase. In addition, developmentally regulated domains were found to deviate from others and showed a higher degree of heterogeneity, thus suggesting a link to developmental plasticity. Moreover, allelic expression imbalance was found to strongly associate with replication-timing asynchrony. Our results form a foundation for single-cell-level understanding of DNA replication regulation and provide insights into three-dimensional genome organization.
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38
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Sima J, Chakraborty A, Dileep V, Michalski M, Klein KN, Holcomb NP, Turner JL, Paulsen MT, Rivera-Mulia JC, Trevilla-Garcia C, Bartlett DA, Zhao PA, Washburn BK, Nora EP, Kraft K, Mundlos S, Bruneau BG, Ljungman M, Fraser P, Ay F, Gilbert DM. Identifying cis Elements for Spatiotemporal Control of Mammalian DNA Replication. Cell 2019; 176:816-830.e18. [PMID: 30595451 PMCID: PMC6546437 DOI: 10.1016/j.cell.2018.11.036] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 10/01/2018] [Accepted: 11/21/2018] [Indexed: 01/09/2023]
Abstract
The temporal order of DNA replication (replication timing [RT]) is highly coupled with genome architecture, but cis-elements regulating either remain elusive. We created a series of CRISPR-mediated deletions and inversions of a pluripotency-associated topologically associating domain (TAD) in mouse ESCs. CTCF-associated domain boundaries were dispensable for RT. CTCF protein depletion weakened most TAD boundaries but had no effect on RT or A/B compartmentalization genome-wide. By contrast, deletion of three intra-TAD CTCF-independent 3D contact sites caused a domain-wide early-to-late RT shift, an A-to-B compartment switch, weakening of TAD architecture, and loss of transcription. The dispensability of TAD boundaries and the necessity of these "early replication control elements" (ERCEs) was validated by deletions and inversions at additional domains. Our results demonstrate that discrete cis-regulatory elements orchestrate domain-wide RT, A/B compartmentalization, TAD architecture, and transcription, revealing fundamental principles linking genome structure and function.
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Affiliation(s)
- Jiao Sima
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | | | - Vishnu Dileep
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Marco Michalski
- Nuclear Dynamics Program, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Kyle N Klein
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Nicolas P Holcomb
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Jesse L Turner
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Michelle T Paulsen
- Departments of Radiation Oncology and Environmental Health Sciences, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | | | | | - Daniel A Bartlett
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Peiyao A Zhao
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Brian K Washburn
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Elphège P Nora
- Gladstone Institute of Cardiovascular Disease and Roddenberry Center for Stem Cell Biology and Medicine, San Francisco, CA 94158, USA
| | - Katerina Kraft
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitäts Medizin Berlin, 13353 Berlin, Germany
| | - Stefan Mundlos
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitäts Medizin Berlin, 13353 Berlin, Germany
| | - Benoit G Bruneau
- Gladstone Institute of Cardiovascular Disease and Roddenberry Center for Stem Cell Biology and Medicine, San Francisco, CA 94158, USA; Department of Pediatrics, Cardiovascular Research Institute, University of California at San Francisco, San Francisco, CA 94158, USA; Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Mats Ljungman
- Departments of Radiation Oncology and Environmental Health Sciences, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Peter Fraser
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA; Nuclear Dynamics Program, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Ferhat Ay
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA; UC San Diego, School of Medicine, La Jolla, CA 92037, USA
| | - David M Gilbert
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA.
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39
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Linking the organization of DNA replication with genome maintenance. Curr Genet 2019; 65:677-683. [PMID: 30600398 DOI: 10.1007/s00294-018-0923-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 12/17/2018] [Accepted: 12/19/2018] [Indexed: 12/11/2022]
Abstract
The spatial and temporal organization of genome duplication, also referred to as the replication program, is defined by the distribution and the activities of the sites of replication initiation across the genome. Alterations to the replication profile are associated with cell fate changes during development and in pathologies, but the importance of undergoing S phase with distinct and specific programs remains largely unexplored. We have recently addressed this question, focusing on the interplay between the replication program and genome maintenance. In particular, we demonstrated that when cells encounter challenges to DNA synthesis, the organization of DNA replication drives the response to replication stress that is mediated by the ATR/Rad3 checkpoint pathway, thus shaping the pattern of genome instability along the chromosomes. In this review, we present the major findings of our study and discuss how they may bring new perspectives to our understanding of the biological importance of the replication program.
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40
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Schlesinger S, Meshorer E. Open Chromatin, Epigenetic Plasticity, and Nuclear Organization in Pluripotency. Dev Cell 2019; 48:135-150. [DOI: 10.1016/j.devcel.2019.01.003] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 10/30/2018] [Accepted: 12/31/2018] [Indexed: 12/27/2022]
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41
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Khamlichi AA, Feil R. Parallels between Mammalian Mechanisms of Monoallelic Gene Expression. Trends Genet 2018; 34:954-971. [PMID: 30217559 DOI: 10.1016/j.tig.2018.08.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 08/06/2018] [Accepted: 08/16/2018] [Indexed: 02/06/2023]
Abstract
Different types of monoallelic gene expression are present in mammals, some of which are highly flexible, whereas others are more rigid. These include allelic exclusion at antigen receptor loci, the expression of olfactory receptor genes, genomic imprinting, X-chromosome inactivation, and random monoallelic expression (MAE). Although these processes play diverse biological roles, and arose through different selective pressures, the underlying epigenetic mechanisms show striking resemblances. Regulatory transcriptional events are important in all systems, particularly in the specification of MAE. Combined with comparative studies between species, this suggests that the different MAE systems found in mammals may have evolved from analogous ancestral processes.
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Affiliation(s)
- Ahmed Amine Khamlichi
- Institute of Pharmacology and Structural Biology (IPBS), Centre National de la Recherche Scientifique (CNRS) and Paul Sabatier University (UPS), 205 route de Narbonne, 31077 Toulouse, France.
| | - Robert Feil
- Institute of Molecular Genetics of Montpellier (IGMM), CNRS and the University of Montpellier, 1919 route de Mende, 34293 Montpellier, France.
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42
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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.
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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.
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43
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Singh B, Wu PYJ. Regulation of the program of DNA replication by CDK: new findings and perspectives. Curr Genet 2018; 65:79-85. [PMID: 29926159 DOI: 10.1007/s00294-018-0860-6] [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] [Received: 06/04/2018] [Revised: 06/14/2018] [Accepted: 06/15/2018] [Indexed: 12/18/2022]
Abstract
Progression through the cell cycle is driven by the activities of the cyclin-dependent kinase (CDK) family of enzymes, which establish an ordered passage through the cell cycle phases. CDK activity is crucial for the cellular transitions from G1 to S and G2 to M, which are highly controlled to promote the faithful duplication of the genetic material and the transmission of the genome into daughter cells, respectively. While oscillations in CDK activity are essential for cell division, how its specific dynamics may shape cellular processes remains an open question. Recently, we have investigated the potential role of CDK in establishing the profile of replication initiation along the chromosomes, also referred to as the replication program. Our results demonstrated that the timing and level of CDK activity at G1/S provide two critical and independent inputs that modulate the pattern of origin usage. In this review, we will present the conclusions of our study and discuss the implications of our findings for cellular function and physiology.
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Affiliation(s)
- Balveer Singh
- CNRS, Institute of Genetics and Development of Rennes, University of Rennes, UMR 6290, 2 avenue du Pr. Léon Bernard, 35043, Rennes, France
| | - Pei-Yun Jenny Wu
- CNRS, Institute of Genetics and Development of Rennes, University of Rennes, UMR 6290, 2 avenue du Pr. Léon Bernard, 35043, Rennes, France.
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44
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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.
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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.
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