1
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Briggs EM, Marques CA, Reis-Cunha J, Black J, Campbell S, Damasceno J, Bartholomeu D, Crouch K, McCulloch R. Next-Generation Analysis of Trypanosomatid Genome Stability and Instability. Methods Mol Biol 2021; 2116:225-262. [PMID: 32221924 DOI: 10.1007/978-1-0716-0294-2_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Understanding the rate and patterns of genome variation is becoming ever more amenable to whole-genome analysis through advances in DNA sequencing, which may, at least in some circumstances, have supplanted more localized analyses by cellular and genetic approaches. Whole-genome analyses can utilize both short- and long-read sequence technologies. Here we describe how sequence generated by these approaches has been used in trypanosomatids to examine DNA replication dynamics, the accumulation of modified histone H2A due to genome damage, and evaluation of genome variation, focusing on ploidy change.
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Affiliation(s)
- Emma M Briggs
- Institute of Infection, Immunity and Inflammation, The Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, UK
| | - Catarina A Marques
- Institute of Infection, Immunity and Inflammation, The Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, UK
| | - Joao Reis-Cunha
- Departamento de Parasitologia, Universidade Federal de Minas Gerais-Instituto de Ciências Biológicas, Belo Horizonte, Brazil
| | - Jennifer Black
- Institute of Infection, Immunity and Inflammation, The Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, UK
| | - Samantha Campbell
- Institute of Infection, Immunity and Inflammation, The Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, UK
| | - Jeziel Damasceno
- Institute of Infection, Immunity and Inflammation, The Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, UK
| | - Daniella Bartholomeu
- Departamento de Parasitologia, Universidade Federal de Minas Gerais-Instituto de Ciências Biológicas, Belo Horizonte, Brazil
| | - Kathryn Crouch
- Institute of Infection, Immunity and Inflammation, The Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, UK
| | - Richard McCulloch
- Institute of Infection, Immunity and Inflammation, The Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, UK.
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2
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Miura H, Takahashi S, Shibata T, Nagao K, Obuse C, Okumura K, Ogata M, Hiratani I, Takebayashi SI. Mapping replication timing domains genome wide in single mammalian cells with single-cell DNA replication sequencing. Nat Protoc 2020; 15:4058-4100. [PMID: 33230331 DOI: 10.1038/s41596-020-0378-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 07/02/2020] [Indexed: 01/03/2023]
Abstract
Replication timing (RT) domains are stable units of chromosome structure that are regulated in the context of development and disease. Conventional genome-wide RT mapping methods require many S-phase cells for either the effective enrichment of replicating DNA through bromodeoxyuridine (BrdU) immunoprecipitation or the determination of copy-number differences during S-phase, which precludes their application to non-abundant cell types and single cells. Here, we provide a simple, cost-effective, and robust protocol for single-cell DNA replication sequencing (scRepli-seq). The scRepli-seq methodology relies on whole-genome amplification (WGA) of genomic DNA (gDNA) from single S-phase cells and next-generation sequencing (NGS)-based determination of copy-number differences that arise between replicated and unreplicated DNA. Haplotype-resolved scRepli-seq, which distinguishes pairs of homologous chromosomes within a single cell, is feasible by using single-nucleotide polymorphism (SNP)/indel information. We also provide computational pipelines for quality control, normalization, and binarization of the scRepli-seq data. The experimental portion of this protocol (before sequencing) takes 3 d.
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Affiliation(s)
- Hisashi Miura
- Laboratory for Developmental Epigenetics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
| | - Saori Takahashi
- Laboratory for Developmental Epigenetics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
| | - Takahiro Shibata
- Department of Biochemistry and Proteomics, Graduate School of Medicine, Mie University, Tsu, Japan.,Laboratory of Molecular & Cellular Biology, Graduate School of Bioresources, Mie University, Tsu, Japan
| | - Koji Nagao
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Chikashi Obuse
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Katsuzumi Okumura
- Laboratory of Molecular & Cellular Biology, Graduate School of Bioresources, Mie University, Tsu, Japan
| | - Masato Ogata
- Department of Biochemistry and Proteomics, Graduate School of Medicine, Mie University, Tsu, Japan
| | - Ichiro Hiratani
- Laboratory for Developmental Epigenetics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan.
| | - Shin-Ichiro Takebayashi
- Department of Biochemistry and Proteomics, Graduate School of Medicine, Mie University, Tsu, Japan. .,Laboratory of Molecular & Cellular Biology, Graduate School of Bioresources, Mie University, Tsu, Japan.
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3
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Shin G, Jeong D, Kim H, Im JS, Lee JK. RecQL4 tethering on the pre-replicative complex induces unscheduled origin activation and replication stress in human cells. J Biol Chem 2019; 294:16255-16265. [PMID: 31519754 DOI: 10.1074/jbc.ra119.009996] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 09/09/2019] [Indexed: 12/15/2022] Open
Abstract
Sequential activation of DNA replication origins is precisely programmed and critical to maintaining genome stability. RecQL4, a member of the conserved RecQ family of helicases, plays an essential role in the initiation of DNA replication in mammalian cells. Here, we showed that RecQL4 protein tethered on the pre-replicative complex (pre-RC) induces early activation of late replicating origins during S phase. Tethering of RecQL4 or its N terminus on pre-RCs via fusion with Orc4 protein resulted in the recruitment of essential initiation factors, such as Mcm10, And-1, Cdc45, and GINS, increasing nascent DNA synthesis in late replicating origins during early S phase. In this origin activation process, tethered RecQL4 was able to recruit Cdc45 even in the absence of cyclin-dependent kinase (CDK) activity, whereas CDK phosphorylation of RecQL4 N terminus was required for interaction with and origin recruitment of And-1 and GINS. In addition, forced activation of replication origins by RecQL4 tethering resulted in increased replication stress and the accumulation of ssDNAs, which can be recovered by transcription inhibition. Collectively, these results suggest that recruitment of RecQL4 to replication origins is an important step for temporal activation of replication origins during S phase. Further, perturbation of replication timing control by unscheduled origin activation significantly induces replication stress, which is mostly caused by transcription-replication conflicts.
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Affiliation(s)
- Gwangsu Shin
- Interdisciplinary Graduate Program in Genetic Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Dongsoo Jeong
- Interdisciplinary Graduate Program in Genetic Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hyunsup Kim
- Interdisciplinary Graduate Program in Genetic Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jun-Sub Im
- Department of Biology Education, Seoul National University, Seoul, 08826, Republic of Korea
| | - Joon-Kyu Lee
- Interdisciplinary Graduate Program in Genetic Engineering, Seoul National University, Seoul, 08826, Republic of Korea .,Department of Biology Education, Seoul National University, Seoul, 08826, Republic of Korea
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4
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Cheedipudi S, Puri D, Saleh A, Gala HP, Rumman M, Pillai MS, Sreenivas P, Arora R, Sellathurai J, Schrøder HD, Mishra RK, Dhawan J. A fine balance: epigenetic control of cellular quiescence by the tumor suppressor PRDM2/RIZ at a bivalent domain in the cyclin a gene. Nucleic Acids Res 2015; 43:6236-56. [PMID: 26040698 PMCID: PMC4513853 DOI: 10.1093/nar/gkv567] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Accepted: 05/19/2015] [Indexed: 12/20/2022] Open
Abstract
Adult stem cell quiescence is critical to ensure regeneration while minimizing tumorigenesis. Epigenetic regulation contributes to cell cycle control and differentiation, but few regulators of the chromatin state in quiescent cells are known. Here we report that the tumor suppressor PRDM2/RIZ, an H3K9 methyltransferase, is enriched in quiescent muscle stem cells invivo and controls reversible quiescence in cultured myoblasts. We find that PRDM2 associates with >4400 promoters in G0 myoblasts, 55% of which are also marked with H3K9me2 and enriched for myogenic, cell cycle and developmental regulators. Knockdown of PRDM2 alters histone methylation at key promoters such as Myogenin and CyclinA2 (CCNA2), and subverts the quiescence program via global de-repression of myogenesis, and hyper-repression of the cell cycle. Further, PRDM2 acts upstream of the repressive PRC2 complex in G0. We identify a novel G0-specific bivalent chromatin domain in the CCNA2 locus. PRDM2 protein interacts with the PRC2 protein EZH2 and regulates its association with the bivalent domain in the CCNA2 gene. Our results suggest that induction of PRDM2 in G0 ensures that two antagonistic programs—myogenesis and the cell cycle—while stalled, are poised for reactivation. Together, these results indicate that epigenetic regulation by PRDM2 preserves key functions of the quiescent state, with implications for stem cell self-renewal.
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Affiliation(s)
- Sirisha Cheedipudi
- Institute for Stem Cell Biology and Regenerative Medicine, National Center for Biological Sciences, GKVK Post, Bellary Road, Bangalore 560065, India Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology, Hyderabad 500 007, India Max Planck Institute for Heart and Lung Research, Bad Nauheim 61231, Germany
| | - Deepika Puri
- Institute for Stem Cell Biology and Regenerative Medicine, National Center for Biological Sciences, GKVK Post, Bellary Road, Bangalore 560065, India Max Planck Institute of Immunobiology and Epigenetics, Freiburg D-79108, Germany
| | - Amena Saleh
- Institute for Stem Cell Biology and Regenerative Medicine, National Center for Biological Sciences, GKVK Post, Bellary Road, Bangalore 560065, India Manipal University, Manipal 576104 India
| | - Hardik P Gala
- Institute for Stem Cell Biology and Regenerative Medicine, National Center for Biological Sciences, GKVK Post, Bellary Road, Bangalore 560065, India Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology, Hyderabad 500 007, India
| | - Mohammed Rumman
- Institute for Stem Cell Biology and Regenerative Medicine, National Center for Biological Sciences, GKVK Post, Bellary Road, Bangalore 560065, India Manipal University, Manipal 576104 India
| | - Malini S Pillai
- Institute for Stem Cell Biology and Regenerative Medicine, National Center for Biological Sciences, GKVK Post, Bellary Road, Bangalore 560065, India
| | - Prethish Sreenivas
- Institute for Stem Cell Biology and Regenerative Medicine, National Center for Biological Sciences, GKVK Post, Bellary Road, Bangalore 560065, India Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology, Hyderabad 500 007, India
| | - Reety Arora
- Institute for Stem Cell Biology and Regenerative Medicine, National Center for Biological Sciences, GKVK Post, Bellary Road, Bangalore 560065, India
| | - Jeeva Sellathurai
- Institute of Clinical Research, SDU Muscle Research Cluster (SMRC), University of Southern Denmark, Odense 5000 C, Denmark
| | - Henrik Daa Schrøder
- Institute of Clinical Research, SDU Muscle Research Cluster (SMRC), University of Southern Denmark, Odense 5000 C, Denmark
| | - Rakesh K Mishra
- Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology, Hyderabad 500 007, India
| | - Jyotsna Dhawan
- Institute for Stem Cell Biology and Regenerative Medicine, National Center for Biological Sciences, GKVK Post, Bellary Road, Bangalore 560065, India Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology, Hyderabad 500 007, India
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5
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Chang BH, Johnson K, LaTocha D, Rowley JSJ, Bryant J, Burke R, Smith RL, Loriaux M, Müschen M, Mullighan C, Druker BJ, Tyner JW. YM155 potently kills acute lymphoblastic leukemia cells through activation of the DNA damage pathway. J Hematol Oncol 2015; 8:39. [PMID: 25895498 PMCID: PMC4408565 DOI: 10.1186/s13045-015-0132-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 03/26/2015] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Novel-targeted therapies are in rapid development for the treatment of acute lymphoblastic leukemia (ALL) to overcome resistance and decrease toxicity. Survivin, a member of the inhibitor of apoptosis gene family and chromosome passenger complex, is critical in a variety of human cancers, including ALL. A well-established suppressor of survivin has been the small molecule, YM155. Reports are identifying other mechanisms of action for YM155. Therefore, we sought to investigate the mode of action and role of YM155 for therapeutic use in the context of ALL. METHODS Primary ALL samples and ALL cell lines were interrogated with YM155 to identify drug sensitivity. Ph(+)ALL harboring the BCR-ABL1 oncogene were tested for any interaction with YM155 and the multi-kinase inhibitor dasatinib. Representative ALL cell lines were tested to identify the response to YM155 using standard biochemical assays as well as RNA expression and phosphorylation arrays. RESULTS ALL samples exhibited significant sensitivity to YM155, and an additive response was observed with dasatinib in the setting of Ph(+)ALL. ALL cells were more sensitive to YM155 during S phase during DNA replication. YM155 activates the DNA damage pathway leading to phosphorylation of Chk2 and H2AX. Interestingly, screening of primary patient samples identified unique and exquisite YM155 sensitivity in some but not all ALL specimens. CONCLUSION These results are the first to have screened a large number of primary patient leukemic samples to identify individual variations of response to YM155. Our studies further support that YM155 in ALL induces DNA damage leading to S phase arrest. Finally, only subsets of ALL have exquisite sensitivity to YM155 presumably through both suppression of survivin expression and activation of the DNA damage pathway underscoring its potential for therapeutic development.
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Affiliation(s)
- Bill H Chang
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Oregon Health & Science University, Portland, OR, 97239, USA.
- OHSU Knight Cancer Institute, Portland, OR, 97239, USA.
| | - Kara Johnson
- OHSU Knight Cancer Institute, Portland, OR, 97239, USA.
| | | | | | - Jade Bryant
- OHSU Knight Cancer Institute, Portland, OR, 97239, USA.
| | - Russell Burke
- OHSU Knight Cancer Institute, Portland, OR, 97239, USA.
| | | | - Marc Loriaux
- OHSU Knight Cancer Institute, Portland, OR, 97239, USA.
- Department of Pathology, Oregon Health & Science University, Portland, OR, 97239, USA.
| | - Markus Müschen
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.
| | - Charles Mullighan
- Department of Oncology, St Jude Children's Research Hospital and University of Tennessee Health Science Center, Memphis, TN, 38105, USA.
| | - Brian J Druker
- OHSU Knight Cancer Institute, Portland, OR, 97239, USA.
- Howard Hughes Medical Institute, Portland, OR, 97239, USA.
| | - Jeffrey W Tyner
- OHSU Knight Cancer Institute, Portland, OR, 97239, USA.
- Department Cell & Developmental Biology, Oregon Health & Science University, Portland, OR, 97239, USA.
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6
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Calderano SG, Drosopoulos WC, Quaresma MM, Marques CA, Kosiyatrakul S, McCulloch R, Schildkraut CL, Elias MC. Single molecule analysis of Trypanosoma brucei DNA replication dynamics. Nucleic Acids Res 2015; 43:2655-65. [PMID: 25690894 PMCID: PMC4357695 DOI: 10.1093/nar/gku1389] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Eukaryotic genome duplication relies on origins of replication, distributed over multiple chromosomes, to initiate DNA replication. A recent genome-wide analysis of Trypanosoma brucei, the etiological agent of sleeping sickness, localized its replication origins to the boundaries of multigenic transcription units. To better understand genomic replication in this organism, we examined replication by single molecule analysis of replicated DNA. We determined the average speed of replication forks of procyclic and bloodstream form cells and we found that T. brucei DNA replication rate is similar to rates seen in other eukaryotes. We also analyzed the replication dynamics of a central region of chromosome 1 in procyclic forms. We present evidence for replication terminating within the central part of the chromosome and thus emanating from both sides, suggesting a previously unmapped origin toward the 5′ extremity of chromosome 1. Also, termination is not at a fixed location in chromosome 1, but is rather variable. Importantly, we found a replication origin located near an ORC1/CDC6 binding site that is detected after replicative stress induced by hydroxyurea treatment, suggesting it may be a dormant origin activated in response to replicative stress. Collectively, our findings support the existence of more replication origins in T. brucei than previously appreciated.
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Affiliation(s)
- Simone Guedes Calderano
- Laboratório Especial de Ciclo Celular, Instituto Butantan, São Paulo, SP 05503-900, Brasil Center of Toxins, Immune Response and Cell Signaling - CeTICS, Instituto Butantan, São Paulo, SP 05503-900, Brasil
| | - William C Drosopoulos
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Marina Mônaco Quaresma
- Laboratório Especial de Ciclo Celular, Instituto Butantan, São Paulo, SP 05503-900, Brasil Center of Toxins, Immune Response and Cell Signaling - CeTICS, Instituto Butantan, São Paulo, SP 05503-900, Brasil
| | - Catarina A Marques
- The Wellcome Trust Centre for Molecular Parasitology, College of Medical, Veterinary and Life Sciences, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G128TA, UK
| | | | - Richard McCulloch
- The Wellcome Trust Centre for Molecular Parasitology, College of Medical, Veterinary and Life Sciences, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G128TA, UK
| | - Carl L Schildkraut
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Maria Carolina Elias
- Laboratório Especial de Ciclo Celular, Instituto Butantan, São Paulo, SP 05503-900, Brasil Center of Toxins, Immune Response and Cell Signaling - CeTICS, Instituto Butantan, São Paulo, SP 05503-900, Brasil
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7
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Roukos V, Pegoraro G, Voss TC, Misteli T. Cell cycle staging of individual cells by fluorescence microscopy. Nat Protoc 2015; 10:334-48. [PMID: 25633629 PMCID: PMC6318798 DOI: 10.1038/nprot.2015.016] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Progression through the cell cycle is one of the most fundamental features of cells. Studies of the cell cycle have traditionally relied on the analysis of populations, and they often require specific markers or the use of genetically modified systems, making it difficult to determine the cell cycle stage of individual, unperturbed cells. We describe a protocol, suitable for use in high-resolution imaging approaches, for determining cell cycle staging of individual cells by measuring their DNA content by fluorescence microscopy. The approach is based on the accurate quantification by image analysis of the integrated nuclear intensity of cells stained with a DNA dye, and it can be used in combination with several histochemical methods. We describe and provide the algorithms for two automated image analysis pipelines and the derivation of cell cycle profiles with both commercial and open-source software. This 1-2-d protocol is applicable to adherent cells, and it is adaptable for use with several DNA dyes.
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Affiliation(s)
- Vassilis Roukos
- National Cancer Institute, National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Gianluca Pegoraro
- 1] National Cancer Institute, National Institutes of Health (NIH), Bethesda, Maryland, USA. [2] High-Throughput Imaging Facility, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Ty C Voss
- 1] National Cancer Institute, National Institutes of Health (NIH), Bethesda, Maryland, USA. [2] PerkinElmer Health Sciences Inc., Waltham, Maryland, USA
| | - Tom Misteli
- National Cancer Institute, National Institutes of Health (NIH), Bethesda, Maryland, USA
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8
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Minocherhomji S, Hansen C, Kim HG, Mang Y, Bak M, Guldberg P, Papadopoulos N, Eiberg H, Doh GD, Møllgård K, Hertz JM, Nielsen JE, Ropers HH, Tümer Z, Tommerup N, Kalscheuer VM, Silahtaroglu A. Epigenetic remodelling and dysregulation of DLGAP4 is linked with early-onset cerebellar ataxia. Hum Mol Genet 2014; 23:6163-76. [PMID: 24986922 PMCID: PMC4222360 DOI: 10.1093/hmg/ddu337] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Genome instability, epigenetic remodelling and structural chromosomal rearrangements are hallmarks of cancer. However, the coordinated epigenetic effects of constitutional chromosomal rearrangements that disrupt genes associated with congenital neurodevelopmental diseases are poorly understood. To understand the genetic-epigenetic interplay at breakpoints of chromosomal translocations disrupting CG-rich loci, we quantified epigenetic modifications at DLGAP4 (SAPAP4), a key post-synaptic density 95 (PSD95) associated gene, truncated by the chromosome translocation t(8;20)(p12;q11.23), co-segregating with cerebellar ataxia in a five-generation family. We report significant epigenetic remodelling of the DLGAP4 locus triggered by the t(8;20)(p12;q11.23) translocation and leading to dysregulation of DLGAP4 expression in affected carriers. Disruption of DLGAP4 results in monoallelic hypermethylation of the truncated DLGAP4 promoter CpG island. This induced hypermethylation is maintained in somatic cells of carriers across several generations in a t(8;20) dependent-manner however, is erased in the germ cells of the translocation carriers. Subsequently, chromatin remodelling of the locus-perturbed monoallelic expression of DLGAP4 mRNAs and non-coding RNAs in haploid cells having the translocation. Our results provide new mechanistic insight into the way a balanced chromosomal rearrangement associated with a neurodevelopmental disorder perturbs allele-specific epigenetic mechanisms at breakpoints leading to the deregulation of the truncated locus.
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Affiliation(s)
- Sheroy Minocherhomji
- Wilhelm Johannsen Centre for Functional Genome Research, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen N DK-2200, Denmark
| | - Claus Hansen
- Wilhelm Johannsen Centre for Functional Genome Research, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen N DK-2200, Denmark
| | - Hyung-Goo Kim
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin 14195, Germany
| | - Yuan Mang
- Wilhelm Johannsen Centre for Functional Genome Research, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen N DK-2200, Denmark
| | - Mads Bak
- Wilhelm Johannsen Centre for Functional Genome Research, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen N DK-2200, Denmark
| | - Per Guldberg
- Danish Cancer Society, Institute of Cancer Biology, Copenhagen DK-2100, Denmark
| | - Nickolas Papadopoulos
- Ludwig Center for Cancer Genetics, Johns Hopkins Kimmel Cancer Center, Baltimore, MD 21231, USA
| | - Hans Eiberg
- Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen N DK-2200, Denmark
| | - Gerald Dayebga Doh
- Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen N DK-2200, Denmark
| | - Kjeld Møllgård
- Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen N DK-2200, Denmark
| | - Jens Michael Hertz
- Department of Clinical Genetics, Odense University Hospital, Odense C DK-5000, Denmark
| | - Jørgen E Nielsen
- Section for Neurogenetics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen N 2200, Denmark, Danish Dementia Research Centre, Neurogenetics Clinic, Department of Neurology, Rigshospitalet, Copenhagen University Hospital, Copenhagen Ø 2100, Denmark and
| | - Hans-Hilger Ropers
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin 14195, Germany
| | - Zeynep Tümer
- Wilhelm Johannsen Centre for Functional Genome Research, Applied Human Molecular Genetics, Kennedy Center, Copenhagen University Hospital, Rigshospitalet, Glostrup DK-2600, Denmark
| | - Niels Tommerup
- Wilhelm Johannsen Centre for Functional Genome Research, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen N DK-2200, Denmark
| | - Vera M Kalscheuer
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin 14195, Germany
| | - Asli Silahtaroglu
- Wilhelm Johannsen Centre for Functional Genome Research, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen N DK-2200, Denmark,
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9
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Li B, Su T, Ferrari R, Li JY, Kurdistani SK. A unique epigenetic signature is associated with active DNA replication loci in human embryonic stem cells. Epigenetics 2013; 9:257-67. [PMID: 24172870 DOI: 10.4161/epi.26870] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The cellular epigenetic landscape changes as pluripotent stem cells differentiate to somatic cells or when differentiated cells transform to a cancerous state. These epigenetic changes are commonly correlated with differences in gene expression. Whether active DNA replication is also associated with distinct chromatin environments in these developmentally and phenotypically diverse cell types has not been known. Here, we used BrdU-seq to map active DNA replication loci in human embryonic stem cells (hESCs), normal primary fibroblasts and a cancer cell line, and correlated these maps to the epigenome. In all cell lines, the majority of BrdU peaks were enriched in euchromatin and at DNA repetitive elements, especially at microsatellite repeats, and coincided with previously determined replication origins. The most prominent BrdU peaks were shared between all cells but a sizable fraction of the peaks were specific to each cell type and associated with cell type-specific genes. Surprisingly, the BrdU peaks that were common to all cell lines were associated with H3K18ac, H3K56ac, and H4K20me1 histone marks only in hESCs but not in normal fibroblasts or cancer cells. Depletion of the histone acetyltransferases for H3K18 and H3K56 dramatically decreased the number and intensity of BrdU peaks in hESCs. Our data reveal a unique epigenetic signature that distinguishes active replication loci in hESCs from normal somatic or malignant cells.
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Affiliation(s)
- Bing Li
- Department of Biological Chemistry; University of California; Los Angeles, CA USA
| | - Trent Su
- Department of Biological Chemistry; University of California; Los Angeles, CA USA; Division of Oral Biology and Medicine; School of Dentistry; University of California; Los Angeles, CA USA
| | - Roberto Ferrari
- Department of Biological Chemistry; University of California; Los Angeles, CA USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research; David Geffen School of Medicine; University of California; Los Angeles, CA USA
| | - Jing-Yu Li
- Department of Biological Chemistry; University of California; Los Angeles, CA USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research; David Geffen School of Medicine; University of California; Los Angeles, CA USA
| | - Siavash K Kurdistani
- Department of Biological Chemistry; University of California; Los Angeles, CA USA; Molecular Biology Institute; University of California; Los Angeles, CA USA; Department of Pathology and Laboratory Medicine; University of California; Los Angeles, CA USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research; David Geffen School of Medicine; University of California; Los Angeles, CA USA
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10
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A mechanistic role for DNA methylation in endothelial cell (EC)-enriched gene expression: relationship with DNA replication timing. Blood 2013; 121:3531-40. [PMID: 23449636 DOI: 10.1182/blood-2013-01-479170] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Proximal promoter DNA methylation has been shown to be important for regulating gene expression. However, its relative contribution to the cell-specific expression of endothelial cell (EC)-enriched genes has not been defined. We used methyl-DNA immunoprecipitation and bisulfite conversion to analyze the DNA methylation profile of EC-enriched genes in ECs vs nonexpressing cell types, both in vitro and in vivo. We show that prototypic EC-enriched genes exhibit functional differential patterns of DNA methylation in proximal promoter regions of most (eg, CD31, von Willebrand factor [vWF], VE-cadherin, and intercellular adhesion molecule-2), but not all (eg, VEGFR-1 and VEGFR-2), EC-enriched genes. Comparable findings were evident in cultured ECs, human blood origin ECs, and murine aortic ECs. Promoter-reporter episomal transfection assays for endothelial nitric oxide synthase, VE-cadherin, and vWF indicated functional promoter activity in cell types where the native gene was not active. Inhibition of DNA methyltransferase activity indicated important functional relevance. Importantly, profiling DNA replication timing patterns indicated that EC-enriched gene promoters with differentially methylated regions replicate early in S-phase in both expressing and nonexpressing cell types. Collectively, these studies highlight the functional importance of promoter DNA methylation in controlling vascular EC gene expression.
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Lo Sardo F, Lanzuolo C, Comoglio F, De Bardi M, Paro R, Orlando V. PcG-mediated higher-order chromatin structures modulate replication programs at the Drosophila BX-C. PLoS Genet 2013; 9:e1003283. [PMID: 23437006 PMCID: PMC3578750 DOI: 10.1371/journal.pgen.1003283] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Accepted: 12/14/2012] [Indexed: 12/03/2022] Open
Abstract
Polycomb group proteins (PcG) exert conserved epigenetic functions that convey maintenance of repressed transcriptional states, via post-translational histone modifications and high order structure formation. During S-phase, in order to preserve cell identity, in addition to DNA information, PcG-chromatin-mediated epigenetic signatures need to be duplicated requiring a tight coordination between PcG proteins and replication programs. However, the interconnection between replication timing control and PcG functions remains unknown. Using Drosophila embryonic cell lines, we find that, while presence of specific PcG complexes and underlying transcription state are not the sole determinants of cellular replication timing, PcG-mediated higher-order structures appear to dictate the timing of replication and maintenance of the silenced state. Using published datasets we show that PRC1, PRC2, and PhoRC complexes differently correlate with replication timing of their targets. In the fully repressed BX-C, loss of function experiments revealed a synergistic role for PcG proteins in the maintenance of replication programs through the mediation of higher-order structures. Accordingly, replication timing analysis performed on two Drosophila cell lines differing for BX-C gene expression states, PcG distribution, and chromatin domain conformation revealed a cell-type-specific replication program that mirrors lineage-specific BX-C higher-order structures. Our work suggests that PcG complexes, by regulating higher-order chromatin structure at their target sites, contribute to the definition and the maintenance of genomic structural domains where genes showing the same epigenetic state replicate at the same time. DNA replication is a tightly orchestrated process that precisely duplicates the entire genome during cell division to ensure that daughter cells inherit the same genetic information. The genome is replicated following a specific temporal program, where different segments replicate in distinct moments of the S phase correlating with active (early) and repressed (late) transcriptional state of resident genes. Moreover, replicating chromosomal domains are organized in the nuclear space, perhaps to guarantee the conservation of the same topological order in daughter cells. Epigenetic mechanisms, acting via chromatin organization, determine transcriptional states and must be maintained through cell division. Here, we analyzed in detail the link between Polycomb Group (PcG) proteins, higher-order chromatin structure, and replication timing in Drosophila. By using bioinformatic analyses combined with functional experiments, we show that Polycomb Repressive Complex 1 (PRC1), PRC2, and PhoRC differently correlate with replication timing of their targets and that transcription per se does not determine replication timing. Strikingly, by analyzing the PcG-regulated Bithorax Complex, where PRC1, PRC2, and PhoRC complexes are bound to repressed targets, we provide evidence for a synergistic role of PcG proteins in the modulation and maintenance of replication timing through the definition of specific, topologically distinct genomic domains.
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Affiliation(s)
- Federica Lo Sardo
- Dulbecco Telethon Institute, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Chiara Lanzuolo
- Dulbecco Telethon Institute, IRCCS Santa Lucia Foundation, Rome, Italy
- CNR Institute of Cellular Biology and Neurobiology, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Federico Comoglio
- Department of Biosystems Science and Engineering, Swiss Federal Institute of Technology Zürich, Basel, Switzerland
| | - Marco De Bardi
- Neuroimmunology Unit, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Renato Paro
- Department of Biosystems Science and Engineering, Swiss Federal Institute of Technology Zürich, Basel, Switzerland
- Faculty of Science, University of Basel, Basel, Switzerland
| | - Valerio Orlando
- Dulbecco Telethon Institute, IRCCS Santa Lucia Foundation, Rome, Italy
- Neuroimmunology Unit, IRCCS Santa Lucia Foundation, Rome, Italy
- * E-mail:
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Petruk S, Sedkov Y, Johnston DM, Hodgson JW, Black KL, Kovermann SK, Beck S, Canaani E, Brock HW, Mazo A. TrxG and PcG proteins but not methylated histones remain associated with DNA through replication. Cell 2012; 150:922-33. [PMID: 22921915 DOI: 10.1016/j.cell.2012.06.046] [Citation(s) in RCA: 192] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Revised: 05/08/2012] [Accepted: 06/26/2012] [Indexed: 12/01/2022]
Abstract
Propagation of gene-expression patterns through the cell cycle requires the existence of an epigenetic mark that re-establishes the chromatin architecture of the parental cell in the daughter cells. We devised assays to determine which potential epigenetic marks associate with epigenetic maintenance elements during DNA replication in Drosophila embryos. Histone H3 trimethylated at lysines 4 or 27 is present during transcription but, surprisingly, is replaced by nonmethylated H3 following DNA replication. Methylated H3 is detected on DNA only in nuclei not in S phase. In contrast, the TrxG and PcG proteins Trithorax and Enhancer-of-Zeste, which are H3K4 and H3K27 methylases, and Polycomb continuously associate with their response elements on the newly replicated DNA. We suggest that histone modification enzymes may re-establish the histone code on newly assembled unmethylated histones and thus may act as epigenetic marks.
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Affiliation(s)
- Svetlana Petruk
- Department of Biochemistry and Molecular Biology and Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
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13
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Global mapping of H3K4me3 and H3K27me3 reveals chromatin state-based regulation of human monocyte-derived dendritic cells in different environments. Genes Immun 2012; 13:311-20. [PMID: 22278394 DOI: 10.1038/gene.2011.87] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Depending on the environment, dendritic cells (DCs) may become active or tolerogenic, but little is known about whether heritable epigenetic modifications are involved in these processes. Here, we have found that epigenetic histone modifications can regulate the differentiation of human monocyte-derived DCs (moDCs) into either activated or tolerized DCs. The inhibition or silencing of methyltransferases or methylation-associated factors affects the expression of multiple genes. Genome mapping of transforming growth factor (TGF-β)- or lipopolysaccharide (LPS)-associated H3K4 trimethylation (H3K4me3) and H3K27 trimethylation (H3K27me3) demonstrated the presence of histone modification of gene expression in human TGF-β- or LPS-conditioned moDCs. Although the upregulated or downregulated genes were not always associated with H3K4me3 and/or H3K27me3 modifications in TGF-β-conditioned (tolerized) or LPS-conditioned (activated) moDCs, some of these genes may be regulated by the increased and/or decreased H3K4me3 or H3K27me3 levels or by the alteration of these epigenetic marks, especially in TGF-β-conditioned moDCs. Thus, our results suggested that the differentiation and function of moDCs in tumor and inflammation environments are associated with the modification of the H3K4me3 and K3K27me3 epigenetic marks.
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Interaction of HTLV-1 Tax with minichromosome maintenance proteins accelerates the replication timing program. Blood 2011; 119:151-60. [PMID: 22058115 DOI: 10.1182/blood-2011-05-356790] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Tax oncoprotein encoded by the human T-cell leukemia virus type 1 plays a pivotal role in viral persistence and pathogenesis. Human T-cell leukemia virus type 1-infected cells proliferate faster than normal lymphocytes, expand through mitotic division, and accumulate genomic lesions. Here, we show that Tax associates with the minichromosome maintenance MCM2-7 helicase complex and localizes to origins of replication. Tax modulates the spatiotemporal program of origin activation and fires supplementary origins at the onset of S phase. Thereby, Tax increases the DNA replication rate, accelerates S phase progression, but also generates a replicative stress characterized by the presence of genomic lesions. Mechanistically, Tax favors p300 recruitment and histone hyperacetylation at late replication domains, advancing their replication timing in early S phase.
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15
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Abstract
Despite advances in treatment and outcomes for patients with pediatric acute lymphoblastic leukemia (ALL), there continue to be subsets of patients who are refractory to standard chemotherapy and hematopoietic stem cell transplant. Therefore, novel gene targets for therapy are needed to further advance treatment for this disease. RNA interference technology has identified survivin as a potential therapeutic target. Survivin, a member of the inhibitor of apoptosis (IAP) proteins and chromosome passenger complex, is expressed in hematologic malignancies and overexpressed in relapsed pediatric ALL. Our studies show that survivin is uniformly expressed at high levels in multiple pediatric ALL cell lines. Furthermore, silencing of survivin expression in pediatric ALL cell lines as well as primary leukemic blasts reduces viability of these cells. This includes cell lines derived from patients with relapsed disease featuring cytogenetic anomalies such as t(12;21), Philadelphia chromosome t(9;22), t(1;19) as well as a cell line carrying t(17;19) from a patient with de novo ALL. Furthermore, inhibition of survivin increases p53-dependent apoptosis that can be rescued by inhibition of p53. Finally, a screen of randomly selected primary patient samples confirms that survivin-specific small interfering RNA and survivin-targeted drug, YM155, effectively reduce viability of leukemic blasts.
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Massirer KB, Carromeu C, Griesi-Oliveira K, Muotri AR. Maintenance and differentiation of neural stem cells. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2011; 3:107-14. [PMID: 21061307 DOI: 10.1002/wsbm.100] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The adult mammalian brain contains self-renewable, multipotent neural stem cells (NSCs) that are responsible for neurogenesis and plasticity in specific regions of the adult brain. Extracellular matrix, vasculature, glial cells, and other neurons are components of the niche where NSCs are located. This surrounding environment is the source of extrinsic signals that instruct NSCs to either self-renew or differentiate. Additionally, factors such as the intracellular epigenetics state and retrotransposition events can influence the decision of NSC's fate into neurons or glia. Extrinsic and intrinsic factors form an intricate signaling network, which is not completely understood. These factors altogether reflect a few of the key players characterized so far in the new field of NSC research and are covered in this review.
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Affiliation(s)
- Katlin B Massirer
- Department of Pediatrics/Rady Children's Hospital San Diego, Department of Cellular and Molecular Medicine, University of California San Diego, San Diego, CA, USA
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O’Sullivan RJ, Kubicek S, Schreiber SL, Karlseder J. Reduced histone biosynthesis and chromatin changes arising from a damage signal at telomeres. Nat Struct Mol Biol 2010; 17:1218-25. [PMID: 20890289 PMCID: PMC2951278 DOI: 10.1038/nsmb.1897] [Citation(s) in RCA: 320] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2010] [Accepted: 07/29/2010] [Indexed: 11/09/2022]
Abstract
During replicative aging of primary cells morphological transformations occur, the expression pattern is altered and chromatin changes globally. Here we show that chronic damage signals, probably caused by telomere processing, affect expression of histones and lead to their depletion. We investigated the abundance and cell cycle expression of histones and histone chaperones and found defects in histone biosynthesis during replicative aging. Simultaneously, epigenetic marks were redistributed across the phases of the cell cycle and the DNA damage response (DDR) machinery was activated. The age-dependent reprogramming affected telomeric chromatin itself, which was progressively destabilized, leading to a boost of the telomere-associated DDR with each successive cell cycle. We propose a mechanism in which changes in the structural and epigenetic integrity of telomeres affect core histones and their chaperones, enforcing a self-perpetuating pathway of global epigenetic changes that ultimately leads to senescence.
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Affiliation(s)
- Roderick J. O’Sullivan
- The Salk Institute for Biological Studies, Molecular and Cellular Biology Department, 10010 North Torrey Pines Rd., La Jolla, CA92037, USA
| | - Stefan Kubicek
- The Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA02142, USA
| | - Stuart L. Schreiber
- The Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA02142, USA
- Howard Hughes Medical Institute, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA
- Department of Chemistry and Chemical Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA
| | - Jan Karlseder
- The Salk Institute for Biological Studies, Molecular and Cellular Biology Department, 10010 North Torrey Pines Rd., La Jolla, CA92037, USA
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Episomal replication timing of gamma-herpesviruses in latently infected cells. Virology 2010; 400:207-14. [PMID: 20172574 DOI: 10.1016/j.virol.2010.01.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2009] [Revised: 11/24/2009] [Accepted: 01/21/2010] [Indexed: 02/08/2023]
Abstract
This study addresses the timing of gammaherpesviral episomal DNA replication with respect to the cell cycle. For the first time we analyzed a rhadinovirus, the prototype Herpesvirus saimiri (HVS), and compared it to the lymphocryptovirus Epstein-Barr virus (EBV). Newly synthesized DNA of latently infected B- or T-cells was first BrdU-labeled; then we sorted the cells corresponding to cell cycle phases G(0/1), G(2/M), and S (4 fractions S(1)-S(4)) and performed anti-BrdU chromatin immunoprecipitation. Next, DNA of different viral gene loci was quantitatively detected together with cellular control genes of known replication time. The sensitive technique is further enhanced by an internal coprecipitation standard for increased precision. Both gammaherpesviruses replicated very early in S-phase, together with cellular euchromatin. Our work suggests that early S-phase DNA replication is a general characteristic of episomal herpesviral genomes.
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Chen CL, Rappailles A, Duquenne L, Huvet M, Guilbaud G, Farinelli L, Audit B, d'Aubenton-Carafa Y, Arneodo A, Hyrien O, Thermes C. Impact of replication timing on non-CpG and CpG substitution rates in mammalian genomes. Genome Res 2010; 20:447-57. [PMID: 20103589 DOI: 10.1101/gr.098947.109] [Citation(s) in RCA: 162] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Neutral nucleotide substitutions occur at varying rates along genomes, and it remains a major issue to unravel the mechanisms that cause these variations and to analyze their evolutionary consequences. Here, we study the role of replication in the neutral substitution pattern. We obtained a high-resolution replication timing profile of the whole human genome by massively parallel sequencing of nascent BrdU-labeled replicating DNA. These data were compared to the neutral substitution rates along the human genome, obtained by aligning human and chimpanzee genomes using macaque and orangutan as outgroups. All substitution rates increase monotonously with replication timing even after controlling for local or regional nucleotide composition, crossover rate, distance to telomeres, and chromatin compaction. The increase in non-CpG substitution rates might result from several mechanisms including the increase in mutation-prone activities or the decrease in efficiency of DNA repair during the S phase. In contrast, the rate of C --> T transitions in CpG dinucleotides increases in later-replicating regions due to increasing DNA methylation level that reflects a negative correlation between timing and gene expression. Similar results are observed in the mouse, which indicates that replication timing is a main factor affecting nucleotide substitution dynamics at non-CpG sites and constitutes a major neutral process driving mammalian genome evolution.
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Affiliation(s)
- Chun-Long Chen
- Centre de Génétique Moléculaire, Allée de la Terrasse, 91198 Gif-sur-Yvette, France
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Polycomb mediated epigenetic silencing and replication timing at the INK4a/ARF locus during senescence. PLoS One 2009; 4:e5622. [PMID: 19462008 PMCID: PMC2680618 DOI: 10.1371/journal.pone.0005622] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2009] [Accepted: 04/18/2009] [Indexed: 11/28/2022] Open
Abstract
Background The INK4/ARF locus encodes three tumor suppressor genes (p15Ink4b, Arf and p16Ink4a) and is frequently inactivated in a large number of human cancers. Mechanisms regulating INK4/ARF expression are not fully characterized. Principal Findings Here we show that in young proliferating embryonic fibroblasts (MEFs) the Polycomb Repressive Complex 2 (PRC2) member EZH2 together with PRC1 members BMI1 and M33 are strongly expressed and localized at the INK4/ARF regulatory domain (RD) identified as a DNA replication origin. When cells enter senescence the binding to RD of both PRC1 and PRC2 complexes is lost leading to a decreased level of histone H3K27 trimethylation (H3K27me3). This loss is accompanied with an increased expression of the histone demethylase Jmjd3 and with the recruitment of the MLL1 protein, and correlates with the expression of the Ink4a/Arf genes. Moreover, we show that the Polycomb protein BMI1 interacts with CDC6, an essential regulator of DNA replication in eukaryotic cells. Finally, we demonstrate that Polycomb proteins and associated epigenetic marks are crucial for the control of the replication timing of the INK4a/ARF locus during senescence. Conclusions We identified the replication licencing factor CDC6 as a new partner of the Polycomb group member BMI1. Our results suggest that in young cells Polycomb proteins are recruited to the INK4/ARF locus through CDC6 and the resulting silent locus is replicated during late S-phase. Upon senescence, Jmjd3 is overexpressed and the MLL1 protein is recruited to the locus provoking the dissociation of Polycomb from the INK4/ARF locus, its transcriptional activation and its replication during early S-phase. Together, these results provide a unified model that integrates replication, transcription and epigenetics at the INK4/ARF locus.
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Francis NJ, Follmer NE, Simon MD, Aghia G, Butler JD. Polycomb proteins remain bound to chromatin and DNA during DNA replication in vitro. Cell 2009; 137:110-22. [PMID: 19303136 PMCID: PMC2667909 DOI: 10.1016/j.cell.2009.02.017] [Citation(s) in RCA: 136] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2008] [Revised: 10/22/2008] [Accepted: 02/02/2009] [Indexed: 01/11/2023]
Abstract
The transcriptional status of a gene can be maintained through multiple rounds of cell division during development. This epigenetic effect is believed to reflect heritable changes in chromatin folding and histone modifications or variants at target genes, but little is known about how these chromatin features are inherited through cell division. A particular challenge for maintaining transcription states is DNA replication, which disrupts or dilutes chromatin-associated proteins and histone modifications. PRC1-class Polycomb group protein complexes are essential for development and are thought to heritably silence transcription by altering chromatin folding and histone modifications. It is not known whether these complexes and their effects are maintained during DNA replication or subsequently re-established. We find that when PRC1-class Polycomb complex-bound chromatin or DNA is replicated in vitro, Polycomb complexes remain bound to replicated templates. Retention of Polycomb proteins through DNA replication may contribute to maintenance of transcriptional silencing through cell division.
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Affiliation(s)
- Nicole J Francis
- Department of Molecular and Cellular Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA.
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22
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Jørgensen HF, Terry A, Beretta C, Pereira CF, Leleu M, Chen ZF, Kelly C, Merkenschlager M, Fisher AG. REST selectively represses a subset of RE1-containing neuronal genes in mouse embryonic stem cells. Development 2009; 136:715-21. [PMID: 19201947 PMCID: PMC2685939 DOI: 10.1242/dev.028548] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/05/2009] [Indexed: 12/19/2022]
Abstract
REST is a transcriptional repressor that targets a group of neuronal genes in non-neuronal cells. In embryonic stem (ES) cells, REST has been implicated in controlling the expression of transcription factor genes that are crucial for lineage determination and for maintaining ES cell potential. Here, we asked whether REST directly regulates neural-specifying genes in mouse ES cells using siRNA-mediated REST knockdown and ES cells that lack functional REST protein as a result of gene targeting. Loss of REST did not affect the expression of any of ten transcription factor genes known to promote neural commitment and did not affect the expression of several microRNAs, including miR-21, a putative REST target in ES cells. REST-deficient ES cells retained the ability to self-renew and to undergo appropriate differentiation towards mesoderm, endoderm and ectoderm lineages upon LIF withdrawal. Genome-wide expression profiling showed that genes that were deregulated in the absence of REST were preferentially expressed in the brain and highly enriched for the presence of canonical REST binding sites (RE1). Chromatin immunoprecipitation studies confirmed these genes as direct targets of REST in ES cells. Collectively, these data show that REST selectively silences a cohort of neuronal genes in ES cells.
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Affiliation(s)
- Helle F. Jørgensen
- MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Anna Terry
- MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Chiara Beretta
- MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - C. Filipe Pereira
- MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Marion Leleu
- MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Zhou-Feng Chen
- Departments of Anesthesiology, Psychiatry, Developmental Biology, Washington University School of Medicine Pain Center, St Louis, MO 63110, USA
| | - Claire Kelly
- MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Matthias Merkenschlager
- MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Amanda G. Fisher
- MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
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