1
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Noë M, Mathios D, Annapragada AV, Koul S, Foda ZH, Medina JE, Cristiano S, Cherry C, Bruhm DC, Niknafs N, Adleff V, Ferreira L, Easwaran H, Baylin S, Phallen J, Scharpf RB, Velculescu VE. DNA methylation and gene expression as determinants of genome-wide cell-free DNA fragmentation. Nat Commun 2024; 15:6690. [PMID: 39107309 PMCID: PMC11303779 DOI: 10.1038/s41467-024-50850-8] [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: 07/24/2023] [Accepted: 07/23/2024] [Indexed: 08/10/2024] Open
Abstract
Circulating cell-free DNA (cfDNA) is emerging as an avenue for cancer detection, but the characteristics of cfDNA fragmentation in the blood are poorly understood. We evaluate the effect of DNA methylation and gene expression on genome-wide cfDNA fragmentation through analysis of 969 individuals. cfDNA fragment ends more frequently contained CCs or CGs, and fragments ending with CGs or CCGs are enriched or depleted, respectively, at methylated CpG positions. Higher levels and larger sizes of cfDNA fragments are associated with CpG methylation and reduced gene expression. These effects are validated in mice with isogenic tumors with or without the mutant IDH1, and are associated with genome-wide changes in cfDNA fragmentation in patients with cancer. Tumor-related hypomethylation and increased gene expression are associated with decrease in cfDNA fragment size that may explain smaller cfDNA fragments in human cancers. These results provide a connection between epigenetic changes and cfDNA fragmentation with implications for disease detection.
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Grants
- T32 GM136577 NIGMS NIH HHS
- U01 CA271896 NCI NIH HHS
- R01 CA121113 NCI NIH HHS
- UG1 CA233259 NCI NIH HHS
- P50 CA062924 NCI NIH HHS
- P30 CA006973 NCI NIH HHS
- Dr. Miriam and Sheldon G. Adelson Medical Research Foundation (Dr. Miriam & Sheldon G. Adelson Medical Research Foundation)
- U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)
- EIF | Stand Up To Cancer (SU2C)
- This work was supported in part by the Dr. Miriam and Sheldon G. Adelson Medical Research Foundation, SU2C in-Time Lung Cancer Interception Dream Team Grant, Stand Up to Cancer-Dutch Cancer Society International Translational Cancer Research Dream Team Grant (SU2C-AACR-DT1415), the Gray Foundation, the Commonwealth Foundation, the Mark Foundation for Cancer Research, the Cole Foundation, a research grant from Delfi Diagnostics, and US National Institutes of Health grants CA121113, CA006973, CA233259, CA062924, and 1T32GM136577. Stand Up To Cancer is a program of the Entertainment Industry Foundation administered by the American Association for Cancer Research.
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Affiliation(s)
- Michaël Noë
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Dimitrios Mathios
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Akshaya V Annapragada
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Shashikant Koul
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Zacharia H Foda
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jamie E Medina
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Stephen Cristiano
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Christopher Cherry
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Daniel C Bruhm
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Noushin Niknafs
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Vilmos Adleff
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Leonardo Ferreira
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hari Easwaran
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Stephen Baylin
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jillian Phallen
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Robert B Scharpf
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Victor E Velculescu
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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2
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Forsyth KS, Jiwrajka N, Lovell CD, Toothacre NE, Anguera MC. The conneXion between sex and immune responses. Nat Rev Immunol 2024; 24:487-502. [PMID: 38383754 PMCID: PMC11216897 DOI: 10.1038/s41577-024-00996-9] [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] [Accepted: 01/18/2024] [Indexed: 02/23/2024]
Abstract
There are notable sex-based differences in immune responses to pathogens and self-antigens, with female individuals exhibiting increased susceptibility to various autoimmune diseases, and male individuals displaying preferential susceptibility to some viral, bacterial, parasitic and fungal infections. Although sex hormones clearly contribute to sex differences in immune cell composition and function, the presence of two X chromosomes in female individuals suggests that differential gene expression of numerous X chromosome-linked immune-related genes may also influence sex-biased innate and adaptive immune cell function in health and disease. Here, we review the sex differences in immune system composition and function, examining how hormones and genetics influence the immune system. We focus on the genetic and epigenetic contributions responsible for altered X chromosome-linked gene expression, and how this impacts sex-biased immune responses in the context of pathogen infection and systemic autoimmunity.
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Affiliation(s)
- Katherine S Forsyth
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Nikhil Jiwrajka
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Rheumatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Claudia D Lovell
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Natalie E Toothacre
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Montserrat C Anguera
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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3
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Keniry A, Blewitt ME. Chromatin-mediated silencing on the inactive X chromosome. Development 2023; 150:dev201742. [PMID: 37991053 DOI: 10.1242/dev.201742] [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: 11/23/2023]
Abstract
In mammals, the second X chromosome in females is silenced to enable dosage compensation between XX females and XY males. This essential process involves the formation of a dense chromatin state on the inactive X (Xi) chromosome. There is a wealth of information about the hallmarks of Xi chromatin and the contribution each makes to silencing, leaving the tantalising possibility of learning from this knowledge to potentially remove silencing to treat X-linked diseases in females. Here, we discuss the role of each chromatin feature in the establishment and maintenance of the silent state, which is of crucial relevance for such a goal.
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Affiliation(s)
- Andrew Keniry
- Epigenetics and Development Division, The Walter and Eliza Hall Institute for Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
- The Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Marnie E Blewitt
- Epigenetics and Development Division, The Walter and Eliza Hall Institute for Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
- The Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
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4
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Gene regulation in time and space during X-chromosome inactivation. Nat Rev Mol Cell Biol 2022; 23:231-249. [PMID: 35013589 DOI: 10.1038/s41580-021-00438-7] [Citation(s) in RCA: 85] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/18/2021] [Indexed: 12/21/2022]
Abstract
X-chromosome inactivation (XCI) is the epigenetic mechanism that ensures X-linked dosage compensation between cells of females (XX karyotype) and males (XY). XCI is essential for female embryos to survive through development and requires the accurate spatiotemporal regulation of many different factors to achieve remarkable chromosome-wide gene silencing. As a result of XCI, the active and inactive X chromosomes are functionally and structurally different, with the inactive X chromosome undergoing a major conformational reorganization within the nucleus. In this Review, we discuss the multiple layers of genetic and epigenetic regulation that underlie initiation of XCI during development and then maintain it throughout life, in light of the most recent findings in this rapidly advancing field. We discuss exciting new insights into the regulation of X inactive-specific transcript (XIST), the trigger and master regulator of XCI, and into the mechanisms and dynamics that underlie the silencing of nearly all X-linked genes. Finally, given the increasing interest in understanding the impact of chromosome organization on gene regulation, we provide an overview of the factors that are thought to reshape the 3D structure of the inactive X chromosome and of the relevance of such structural changes for XCI establishment and maintenance.
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5
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de Sena Brandine G, Smith AD. Fast and memory-efficient mapping of short bisulfite sequencing reads using a two-letter alphabet. NAR Genom Bioinform 2022; 3:lqab115. [PMID: 34988438 PMCID: PMC8693577 DOI: 10.1093/nargab/lqab115] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 10/25/2021] [Accepted: 11/29/2021] [Indexed: 01/03/2023] Open
Abstract
DNA cytosine methylation is an important epigenomic mark with a wide range of functions in many organisms. Whole genome bisulfite sequencing is the gold standard to interrogate cytosine methylation genome-wide. Algorithms used to map bisulfite-converted reads often encode the four-base DNA alphabet with three letters by reducing two bases to a common letter. This encoding substantially reduces the entropy of nucleotide frequencies in the resulting reference genome. Within the paradigm of read mapping by first filtering possible candidate alignments, reduced entropy in the sequence space can increase the required computing effort. We introduce another bisulfite mapping algorithm (abismal), based on the idea of encoding a four-letter DNA sequence as only two letters, one for purines and one for pyrimidines. We show that this encoding can lead to greater specificity compared to existing encodings used to map bisulfite sequencing reads. Through the two-letter encoding, the abismal software tool maps reads in less time and using less memory than most bisulfite sequencing read mapping software tools, while attaining similar accuracy. This allows in silico methylation analysis to be performed in a wider range of computing machines with limited hardware settings.
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Affiliation(s)
- Guilherme de Sena Brandine
- Quantitative and Computational Biology, University of Southern California. 1050 Child's way, Los Angeles, CA 90007, USA
| | - Andrew D Smith
- Quantitative and Computational Biology, University of Southern California. 1050 Child's way, Los Angeles, CA 90007, USA
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6
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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: 4] [Impact Index Per Article: 1.3] [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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7
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Boeren J, Gribnau J. Xist-mediated chromatin changes that establish silencing of an entire X chromosome in mammals. Curr Opin Cell Biol 2020; 70:44-50. [PMID: 33360102 DOI: 10.1016/j.ceb.2020.11.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/17/2020] [Accepted: 11/22/2020] [Indexed: 12/19/2022]
Abstract
X chromosome inactivation (XCI) ensures an equal gene dosage between the sexes in placental mammals. Xist, a modular multi-domain X-encoded long non-coding RNA coats the X chromosome in cis during XCI. Xist recruits chromatin remodelers and repressor complexes ensuring silencing of the inactive X (Xi). Here, we review the recent work focused on the role of Xist functional repeats and interacting RNA-binding factors in the establishment of the silent state. Xist orchestrates recruitment of remodelers and repressors that first facilitate removal of the active chromatin landscape and subsequently direct the transition into a repressive heterochromatic environment. Some of these factors affect silencing on a chromosome-wide scale, while others display gene-specific silencing defects. The temporal order of recruitment shows each silencing step is party dependent on one another. After the Xi is established, many of the factors are dispensable, and a different repertoire of proteins ensure the silenced Xi is maintained and propagated.
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Affiliation(s)
- Jeffrey Boeren
- Department of Developmental Biology, Erasmus University Medical Center, the Netherlands; Oncode Institute, Erasmus University Medical Center, the Netherlands
| | - Joost Gribnau
- Department of Developmental Biology, Erasmus University Medical Center, the Netherlands; Oncode Institute, Erasmus University Medical Center, the Netherlands.
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8
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Panda A, Zylicz JJ, Pasque V. New Insights into X-Chromosome Reactivation during Reprogramming to Pluripotency. Cells 2020; 9:E2706. [PMID: 33348832 PMCID: PMC7766869 DOI: 10.3390/cells9122706] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 12/08/2020] [Accepted: 12/10/2020] [Indexed: 02/06/2023] Open
Abstract
Dosage compensation between the sexes results in one X chromosome being inactivated during female mammalian development. Chromosome-wide transcriptional silencing from the inactive X chromosome (Xi) in mammalian cells is erased in a process termed X-chromosome reactivation (XCR), which has emerged as a paradigm for studying the reversal of chromatin silencing. XCR is linked with germline development and induction of naive pluripotency in the epiblast, and also takes place upon reprogramming somatic cells to induced pluripotency. XCR depends on silencing of the long non-coding RNA (lncRNA) X inactive specific transcript (Xist) and is linked with the erasure of chromatin silencing. Over the past years, the advent of transcriptomics and epigenomics has provided new insights into the transcriptional and chromatin dynamics with which XCR takes place. However, multiple questions remain unanswered about how chromatin and transcription related processes enable XCR. Here, we review recent work on establishing the transcriptional and chromatin kinetics of XCR, as well as discuss a model by which transcription factors mediate XCR not only via Xist repression, but also by direct targeting of X-linked genes.
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Affiliation(s)
- Amitesh Panda
- Laboratory of Cellular Reprogramming and Epigenetic Regulation, Department of Development and Regeneration, Leuven Stem Cell Institute, KU Leuven-University of Leuven, 3000 Leuven, Belgium;
| | - Jan J. Zylicz
- The Novo Nordisk Foundation Center for Stem Cell Biology, University of Copenhagen, 2200 Copenhagen, Denmark;
| | - Vincent Pasque
- Laboratory of Cellular Reprogramming and Epigenetic Regulation, Department of Development and Regeneration, Leuven Stem Cell Institute, KU Leuven-University of Leuven, 3000 Leuven, Belgium;
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9
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Żylicz JJ, Heard E. Molecular Mechanisms of Facultative Heterochromatin Formation: An X-Chromosome Perspective. Annu Rev Biochem 2020; 89:255-282. [PMID: 32259458 DOI: 10.1146/annurev-biochem-062917-012655] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Facultative heterochromatin (fHC) concerns the developmentally regulated heterochromatinization of different regions of the genome and, in the case of the mammalian X chromosome and imprinted loci, of only one allele of a homologous pair. The formation of fHC participates in the timely repression of genes, by resisting strong trans activators. In this review, we discuss the molecular mechanisms underlying the establishment and maintenance of fHC in mammals using a mouse model. We focus on X-chromosome inactivation (XCI) as a paradigm for fHC but also relate it to genomic imprinting and homeobox (Hox) gene cluster repression. A vital role for noncoding transcription and/or transcripts emerges as the general principle of triggering XCI and canonical imprinting. However, other types of fHC are established through an unknown mechanism, independent of noncoding transcription (Hox clusters and noncanonical imprinting). We also extensively discuss polycomb-group repressive complexes (PRCs), which frequently play a vital role in fHC maintenance.
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Affiliation(s)
- Jan J Żylicz
- Mammalian Developmental Epigenetics Group, Institut Curie, CNRS UMR 3215, INSERM U934, PSL University, 75248 Paris Cedex 05, France.,Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EL, United Kingdom
| | - Edith Heard
- Directors' Research, EMBL Heidelberg, 69117 Heidelberg, Germany;
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10
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Strehle M, Guttman M. Xist drives spatial compartmentalization of DNA and protein to orchestrate initiation and maintenance of X inactivation. Curr Opin Cell Biol 2020; 64:139-147. [PMID: 32535328 DOI: 10.1016/j.ceb.2020.04.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 04/13/2020] [Accepted: 04/23/2020] [Indexed: 12/15/2022]
Abstract
X chromosome inactivation (XCI) is the process whereby one of the X chromosomes in female mammalian cells is silenced to equalize X-linked gene expression with males. XCI depends on the long noncoding RNA Xist, which coats the inactive X chromosome in cis and triggers a cascade of events that ultimately lead to chromosome-wide transcriptional silencing that is stable for the lifetime of an organism. In recent years, the discovery of proteins that interact with Xist have led to new insights into how the initiation of XCI occurs. Nevertheless, there are still various unknowns about the mechanisms by which Xist orchestrates and maintains stable X-linked silencing. Here, we review recent work elucidating the role of Xist and its protein partners in mediating chromosome-wide transcriptional repression, as well as discuss a model by which Xist may compartmentalize proteins across the inactive X chromosome to enable both the initiation and maintenance of XCI.
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Affiliation(s)
- Mackenzie Strehle
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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11
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The influence of DNA methylation on monoallelic expression. Essays Biochem 2020; 63:663-676. [PMID: 31782494 PMCID: PMC6923323 DOI: 10.1042/ebc20190034] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 11/10/2019] [Accepted: 11/11/2019] [Indexed: 01/02/2023]
Abstract
Monoallelic gene expression occurs in diploid cells when only one of the two alleles of a gene is active. There are three main classes of genes that display monoallelic expression in mammalian genomes: (1) imprinted genes that are monoallelically expressed in a parent-of-origin dependent manner; (2) X-linked genes that undergo random X-chromosome inactivation in female cells; (3) random monoallelically expressed single and clustered genes located on autosomes. The heritability of monoallelic expression patterns during cell divisions implies that epigenetic mechanisms are involved in the cellular memory of these expression states. Among these, methylation of CpG sites on DNA is one of the best described modification to explain somatic inheritance. Here, we discuss the relevance of DNA methylation for the establishment and maintenance of monoallelic expression patterns among these three groups of genes, and how this is intrinsically linked to development and cellular states.
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12
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Pacini CE, Bradshaw CR, Garrett NJ, Koziol MJ. Characteristics and homogeneity of N6-methylation in human genomes. Sci Rep 2019; 9:5185. [PMID: 30914725 PMCID: PMC6435722 DOI: 10.1038/s41598-019-41601-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 03/13/2019] [Indexed: 12/31/2022] Open
Abstract
A novel DNA modification, N-6 methylated deoxyadenosine (m6dA), has recently been discovered in eukaryotic genomes. Despite its low abundance in eukaryotes, m6dA is implicated in human diseases such as cancer. It is therefore important to precisely identify and characterize m6dA in the human genome. Here, we identify m6dA sites at nucleotide level, in different human cells, genome wide. We compare m6dA features between distinct human cells and identify m6dA characteristics in human genomes. Our data demonstrates for the first time that despite low m6dA abundance, the m6dA mark does often occur consistently at the same genomic location within a given human cell type, demonstrating m6dA homogeneity. We further show, for the first time, higher levels of m6dA homogeneity within one chromosome. Most m6dA are found on a single chromosome from a diploid sample, suggesting inheritance. Our transcriptome analysis not only indicates that human genes with m6dA are associated with higher RNA transcript levels but identifies allele-specific gene transcripts showing haplotype-specific m6dA methylation, which are implicated in different biological functions. Our analyses demonstrate the precision and consistency by which the m6dA mark occurs within the human genome, suggesting that m6dA marks are precisely inherited in humans.
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Affiliation(s)
- Clare E Pacini
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, UK
- Department of Zoology, University of Cambridge, Cambridge, CB3 3EJ, UK
| | - Charles R Bradshaw
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, UK
| | - Nigel J Garrett
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, UK
- Department of Zoology, University of Cambridge, Cambridge, CB3 3EJ, UK
| | - Magdalena J Koziol
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, UK.
- Department of Zoology, University of Cambridge, Cambridge, CB3 3EJ, UK.
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13
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Abstract
Fundamental differences exist between males and females, encompassing anatomy, physiology, behaviour, and genetics. Such differences undoubtedly play a part in the well documented, yet poorly understood, disparity in disease susceptibility between the sexes. Although traditionally attributed to gonadal sex hormone effects, recent work has begun to shed more light on the contribution of genetics - and in particular the sex chromosomes - to these sexual dimorphisms. Here, we explore the accumulating evidence for a significant genetic component to mammalian sexual dimorphism through the paradigm of sex chromosome evolution. The differences between the extant X and Y chromosomes, at both a sequence and regulatory level, arose across 166 million years. A functional result of these differences is cell autonomous sexual dimorphism. By understanding the process that changed a pair of homologous ancestral autosomes into the extant mammalian X and Y, we believe it easier to consider the mechanisms that may contribute to hormone-independent male-female differences. We highlight key roles for genes with homologues present on both sex chromosomes, where the X-linked copy escapes X chromosome inactivation. Finally, we summarise current experimental paradigms and suggest areas for developments to further increase our understanding of cell autonomous sexual dimorphism in the context of health and disease.
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Affiliation(s)
- Daniel M Snell
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - James M A Turner
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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14
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Galupa R, Heard E. X-Chromosome Inactivation: A Crossroads Between Chromosome Architecture and Gene Regulation. Annu Rev Genet 2018; 52:535-566. [PMID: 30256677 DOI: 10.1146/annurev-genet-120116-024611] [Citation(s) in RCA: 144] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In somatic nuclei of female therian mammals, the two X chromosomes display very different chromatin states: One X is typically euchromatic and transcriptionally active, and the other is mostly silent and forms a cytologically detectable heterochromatic structure termed the Barr body. These differences, which arise during female development as a result of X-chromosome inactivation (XCI), have been the focus of research for many decades. Initial approaches to define the structure of the inactive X chromosome (Xi) and its relationship to gene expression mainly involved microscopy-based approaches. More recently, with the advent of genomic techniques such as chromosome conformation capture, molecular details of the structure and expression of the Xi have been revealed. Here, we review our current knowledge of the 3D organization of the mammalian X-chromosome chromatin and discuss its relationship with gene activity in light of the initiation, spreading, and maintenance of XCI, as well as escape from gene silencing.
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Affiliation(s)
- Rafael Galupa
- Genetics and Developmental Biology Unit and Mammalian Developmental Epigenetics Group, Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, 75248 Paris, France; .,Current affiliation: Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Edith Heard
- Genetics and Developmental Biology Unit and Mammalian Developmental Epigenetics Group, Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, 75248 Paris, France; .,Collège de France, 75231 Paris, France
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15
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16
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Alvarez-Ponce D, Torres-Sánchez M, Feyertag F, Kulkarni A, Nappi T. Molecular evolution of DNMT1 in vertebrates: Duplications in marsupials followed by positive selection. PLoS One 2018; 13:e0195162. [PMID: 29621315 PMCID: PMC5886458 DOI: 10.1371/journal.pone.0195162] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 03/16/2018] [Indexed: 01/01/2023] Open
Abstract
DNA methylation is mediated by a conserved family of DNA methyltransferases (Dnmts). The human genome encodes three active Dnmts (Dnmt1, Dnmt3a and Dnmt3b), the tRNA methyltransferase Dnmt2, and the regulatory protein Dnmt3L. Despite their high degree of conservation among different species, genes encoding Dnmts have been duplicated and/or lost in multiple lineages throughout evolution, indicating that the DNA methylation machinery has some potential to undergo evolutionary change. However, little is known about the extent to which this machinery, or the methylome, varies among vertebrates. Here, we study the molecular evolution of Dnmt1, the enzyme responsible for maintenance of DNA methylation patterns after replication, in 79 vertebrate species. Our analyses show that all studied species exhibit a single copy of the DNMT1 gene, with the exception of tilapia and marsupials (tammar wallaby, koala, Tasmanian devil and opossum), each of which displays two apparently functional DNMT1 copies. Our phylogenetic analyses indicate that DNMT1 duplicated before the radiation of major marsupial groups (i.e., at least ~75 million years ago), thus giving rise to two DNMT1 copies in marsupials (copy 1 and copy 2). In the opossum lineage, copy 2 was lost, and copy 1 recently duplicated again, generating three DNMT1 copies: two putatively functional genes (copy 1a and 1b) and one pseudogene (copy 1ψ). Both marsupial copies (DNMT1 copies 1 and 2) are under purifying selection, and copy 2 exhibits elevated rates of evolution and signatures of positive selection, suggesting a scenario of neofunctionalization. This gene duplication might have resulted in modifications in marsupial methylomes and their dynamics.
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Affiliation(s)
- David Alvarez-Ponce
- Department of Biology, University of Nevada, Reno, Nevada, United States of America
- * E-mail:
| | - María Torres-Sánchez
- Department of Biology, University of Nevada, Reno, Nevada, United States of America
- Department of Biodiversity, Ecology and Evolution, Complutense University of Madrid, Madrid, Spain
| | - Felix Feyertag
- Department of Biology, University of Nevada, Reno, Nevada, United States of America
| | - Asmita Kulkarni
- Department of Biology, University of Nevada, Reno, Nevada, United States of America
| | - Taylen Nappi
- Department of Biology, University of Nevada, Reno, Nevada, United States of America
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17
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Waters SA, Livernois AM, Patel H, O’Meally D, Craig JM, Marshall Graves JA, Suter CM, Waters PD. Landscape of DNA Methylation on the Marsupial X. Mol Biol Evol 2017; 35:431-439. [DOI: 10.1093/molbev/msx297] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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18
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Abstract
X-chromosome inactivation, which was discovered by Mary Lyon in 1961 results in random silencing of one X chromosome in female mammals. This review is dedicated to Mary Lyon, who passed away last year. She predicted many of the features of X inactivation, for e.g., the existence of an X inactivation center, the role of L1 elements in spreading of silencing and the existence of genes that escape X inactivation. Starting from her published work here we summarize advances in the field.
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19
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Baronchelli S, La Spada A, Conforti P, Redaelli S, Dalprà L, De Blasio P, Cattaneo E, Biunno I. Investigating DNA Methylation Dynamics and Safety of Human Embryonic Stem Cell Differentiation Toward Striatal Neurons. Stem Cells Dev 2015; 24:2366-77. [DOI: 10.1089/scd.2015.0057] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Simona Baronchelli
- Institute of Genetic and Biomedical Research, National Research Council (UOS IRGB-CNR), Milan, Italy
| | - Alberto La Spada
- Institute of Genetic and Biomedical Research, National Research Council (UOS IRGB-CNR), Milan, Italy
| | - Paola Conforti
- Department of Biosciences, Center for Stem Cell Research, University of Milan, Milan, Italy
| | - Serena Redaelli
- Department of Surgery and Translational Medicine, University of Milan-Bicocca, Monza, Italy
| | - Leda Dalprà
- Department of Surgery and Translational Medicine, University of Milan-Bicocca, Monza, Italy
| | | | - Elena Cattaneo
- Department of Biosciences, Center for Stem Cell Research, University of Milan, Milan, Italy
| | - Ida Biunno
- Institute of Genetic and Biomedical Research, National Research Council (UOS IRGB-CNR), Milan, Italy
- IRCCS Multimedica, Milan, Italy
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20
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Zhang J, Xing Y, Li Y, Yin C, Ge C, Li F. DNA methyltransferases have an essential role in female fecundity in brown planthopper, Nilaparvata lugens. Biochem Biophys Res Commun 2015; 464:83-8. [DOI: 10.1016/j.bbrc.2015.05.114] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 05/30/2015] [Indexed: 12/19/2022]
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21
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Pells S, Koutsouraki E, Morfopoulou S, Valencia-Cadavid S, Tomlinson SR, Kalathur R, Futschik ME, De Sousa PA. Novel Human Embryonic Stem Cell Regulators Identified by Conserved and Distinct CpG Island Methylation State. PLoS One 2015; 10:e0131102. [PMID: 26151932 PMCID: PMC4495055 DOI: 10.1371/journal.pone.0131102] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 05/27/2015] [Indexed: 12/21/2022] Open
Abstract
Human embryonic stem cells (hESCs) undergo epigenetic changes in vitro which may compromise function, so an epigenetic pluripotency “signature” would be invaluable for line validation. We assessed Cytosine-phosphate-Guanine Island (CGI) methylation in hESCs by genomic DNA hybridisation to a CGI array, and saw substantial variation in CGI methylation between lines. Comparison of hESC CGI methylation profiles to corresponding somatic tissue data and hESC mRNA expression profiles identified a conserved hESC-specific methylation pattern associated with expressed genes. Transcriptional repressors and activators were over-represented amongst genes whose associated CGIs were methylated or unmethylated specifically in hESCs, respectively. Knockdown of candidate transcriptional regulators (HMGA1, GLIS2, PFDN5) induced differentiation in hESCs, whereas ectopic expression in fibroblasts modulated iPSC colony formation. Chromatin immunoprecipitation confirmed interaction between the candidates and the core pluripotency transcription factor network. We thus identify novel pluripotency genes on the basis of a conserved and distinct epigenetic configuration in human stem cells.
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Affiliation(s)
- Steve Pells
- MRC Centre for Regenerative Medicine, School of Clinical Studies, University of Edinburgh, Edinburgh, EH16 4SB, United Kingdom
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, EH16 4SB, United Kingdom
- * E-mail: (PDS); (SP)
| | - Eirini Koutsouraki
- MRC Centre for Regenerative Medicine, School of Clinical Studies, University of Edinburgh, Edinburgh, EH16 4SB, United Kingdom
| | - Sofia Morfopoulou
- MRC Centre for Regenerative Medicine, School of Clinical Studies, University of Edinburgh, Edinburgh, EH16 4SB, United Kingdom
| | - Sara Valencia-Cadavid
- MRC Centre for Regenerative Medicine, School of Clinical Studies, University of Edinburgh, Edinburgh, EH16 4SB, United Kingdom
| | - Simon R. Tomlinson
- MRC Centre for Regenerative Medicine, School of Clinical Studies, University of Edinburgh, Edinburgh, EH16 4SB, United Kingdom
| | - Ravi Kalathur
- Centre for Molecular and Structural Biomedicine, University of Algarve, 8005–139, Faro, Portugal
| | - Matthias E. Futschik
- Centre for Molecular and Structural Biomedicine, University of Algarve, 8005–139, Faro, Portugal
| | - Paul A. De Sousa
- MRC Centre for Regenerative Medicine, School of Clinical Studies, University of Edinburgh, Edinburgh, EH16 4SB, United Kingdom
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, EH16 4SB, United Kingdom
- * E-mail: (PDS); (SP)
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Jensen TJ, Kim SK, Zhu Z, Chin C, Gebhard C, Lu T, Deciu C, van den Boom D, Ehrich M. Whole genome bisulfite sequencing of cell-free DNA and its cellular contributors uncovers placenta hypomethylated domains. Genome Biol 2015; 16:78. [PMID: 25886572 PMCID: PMC4427941 DOI: 10.1186/s13059-015-0645-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 03/27/2015] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Circulating cell-free fetal DNA has enabled non-invasive prenatal fetal aneuploidy testing without direct discrimination of the maternal and fetal DNA. Testing may be improved by specifically enriching the sample material for fetal DNA. DNA methylation may allow for such a separation of DNA; however, this depends on knowledge of the methylomes of circulating cell-free DNA and its cellular contributors. RESULTS We perform whole genome bisulfite sequencing on a set of unmatched samples including circulating cell-free DNA from non-pregnant and pregnant female donors and genomic DNA from maternal buffy coat and placenta samples. We find CpG cytosines within longer fragments are more likely to be methylated. Comparison of the methylomes of placenta and non-pregnant circulating cell-free DNA reveal many of the 51,259 identified differentially methylated regions are located in domains exhibiting consistent placenta hypomethylation across millions of consecutive bases. We find these placenta hypomethylated domains are consistently located within regions exhibiting low CpG and gene density. Differentially methylated regions identified when comparing placenta to non-pregnant circulating cell-free DNA are recapitulated in pregnant circulating cell-free DNA, confirming the ability to detect differential methylation in circulating cell-free DNA mixtures. CONCLUSIONS We generate methylome maps for four sample types at single-base resolution, identify a link between DNA methylation and fragment length in circulating cell-free DNA, identify differentially methylated regions between sample groups, and uncover the presence of megabase-size placenta hypomethylated domains.
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Affiliation(s)
- Taylor J Jensen
- Sequenom Laboratories, 3595 John Hopkins Ct, San Diego, CA, 92121, USA.
| | - Sung K Kim
- Sequenom Laboratories, 3595 John Hopkins Ct, San Diego, CA, 92121, USA.
| | - Zhanyang Zhu
- Sequenom Laboratories, 3595 John Hopkins Ct, San Diego, CA, 92121, USA.
| | - Christine Chin
- Sequenom Laboratories, 3595 John Hopkins Ct, San Diego, CA, 92121, USA.
| | - Claudia Gebhard
- Sequenom Laboratories, 3595 John Hopkins Ct, San Diego, CA, 92121, USA.
| | - Tim Lu
- Sequenom Laboratories, 3595 John Hopkins Ct, San Diego, CA, 92121, USA.
| | - Cosmin Deciu
- Sequenom Laboratories, 3595 John Hopkins Ct, San Diego, CA, 92121, USA.
| | | | - Mathias Ehrich
- Sequenom Inc., 3595 John Hopkins Ct, San Diego, CA, 92121, USA.
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Brancaleoni V, Balwani M, Granata F, Graziadei G, Missineo P, Fiorentino V, Fustinoni S, Cappellini MD, Naik H, Desnick RJ, Di Pierro E. X-chromosomal inactivation directly influences the phenotypic manifestation of X-linked protoporphyria. Clin Genet 2015; 89:20-6. [PMID: 25615817 DOI: 10.1111/cge.12562] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 01/09/2015] [Accepted: 01/20/2015] [Indexed: 11/29/2022]
Abstract
X-linked protoporphyria (XLP), a rare erythropoietic porphyria, results from terminal exon gain-of-function mutations in the ALAS2 gene causing increased ALAS2 activity and markedly increased erythrocyte protoporphyrin levels. Patients present with severe cutaneous photosensitivity and may develop liver dysfunction. XLP was originally reported as X-linked dominant with 100% penetrance in males and females. We characterized 11 heterozygous females from six unrelated XLP families and show markedly varying phenotypic and biochemical heterogeneity, reflecting the degree of X-chromosomal inactivation of the mutant gene. ALAS2 sequencing identified the specific mutation and confirmed heterozygosity among the females. Clinical history, plasma and erythrocyte protoporphyrin levels were determined. Methylation assays of the androgen receptor and zinc-finger MYM type 3 short tandem repeat polymorphisms estimated each heterozygotes X-chromosomal inactivation pattern. Heterozygotes with equal or increased skewing, favoring expression of the wild-type allele had no clinical symptoms and only slightly increased erythrocyte protoporphyrin concentrations and/or frequency of protoporphyrin-containing peripheral blood fluorocytes. When the wild-type allele was preferentially inactivated, heterozygous females manifested the disease phenotype and had both higher erythrocyte protoporphyrin levels and circulating fluorocytes. These findings confirm that the previous dominant classification of XLP is inappropriate and genetically misleading, as the disorder is more appropriately designated XLP.
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Affiliation(s)
- V Brancaleoni
- Fondazione IRCCS "Cà-Granda" Ospedale Maggiore Policlinico, U.O. di Medicina Interna, Milano, Italy
| | - M Balwani
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - F Granata
- Fondazione IRCCS "Cà-Granda" Ospedale Maggiore Policlinico, U.O. di Medicina Interna, Milano, Italy
| | - G Graziadei
- Fondazione IRCCS "Cà-Granda" Ospedale Maggiore Policlinico, U.O. di Medicina Interna, Milano, Italy
| | - P Missineo
- Dipartimento di Scienze Cliniche e di Comunità, Università degli Studi di Milano, Milano, Italy
| | - V Fiorentino
- Fondazione IRCCS "Cà-Granda" Ospedale Maggiore Policlinico, U.O. di Medicina Interna, Milano, Italy
| | - S Fustinoni
- Dipartimento di Scienze Cliniche e di Comunità, Università degli Studi di Milano, Milano, Italy
| | - M D Cappellini
- Fondazione IRCCS "Cà-Granda" Ospedale Maggiore Policlinico, U.O. di Medicina Interna, Milano, Italy.,Dipartimento di Scienze Cliniche e di Comunità, Università degli Studi di Milano, Milano, Italy
| | - H Naik
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - R J Desnick
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - E Di Pierro
- Fondazione IRCCS "Cà-Granda" Ospedale Maggiore Policlinico, U.O. di Medicina Interna, Milano, Italy
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24
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Richard JLC, Ogawa Y. Understanding the Complex Circuitry of lncRNAs at the X-inactivation Center and Its Implications in Disease Conditions. Curr Top Microbiol Immunol 2015; 394:1-27. [PMID: 25982976 DOI: 10.1007/82_2015_443] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Balanced gene expression is a high priority in order to maintain optimal functioning since alterations and variations could result in acute consequences. X chromosome inactivation (X-inactivation) is one such strategy utilized by mammalian species to silence the extra X chromosome in females to uphold a similar level of expression between the two sexes. A functionally versatile class of molecules called long noncoding RNA (lncRNA) has emerged as key regulators of gene expression and plays important roles during development. An lncRNA that is indispensable for X-inactivation is X-inactive specific transcript (Xist), which induces a repressive epigenetic landscape and creates the inactive X chromosome (Xi). With recent advents in the field of X-inactivation, novel positive and negative lncRNA regulators of Xist such as Jpx and Tsix, respectively, have broadened the regulatory network of X-inactivation. Xist expression failure or dysregulation has been implicated in producing developmental anomalies and disease states. Subsequently, reactivation of the Xi at a later stage of development has also been associated with certain tumors. With the recent influx of information about lncRNA biology and advancements in methods to probe lncRNA, we can now attempt to understand this complex network of Xist regulation in development and disease. It has become clear that the presence of an extra set of genes could be fatal for the organism. Only by understanding the precise ways in which lncRNAs function can treatments be developed to bring aberrations under control. This chapter summarizes our current understanding and knowledge with regard to how lncRNAs are orchestrated at the X-inactivation center (Xic), with a special focus on how genetic diseases come about as a consequence of lncRNA dysregulation.
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Affiliation(s)
- John Lalith Charles Richard
- Division of Reproductive Sciences, Cincinnati Children's Hospital Medical Center; Department of Pediatrics, University of Cincinnati College of Medicine, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA
| | - Yuya Ogawa
- Division of Reproductive Sciences, Cincinnati Children's Hospital Medical Center; Department of Pediatrics, University of Cincinnati College of Medicine, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA.
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25
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Zemlyanskaya EV, Degtyarev SK. Substrate specificity and properties of methyl-directed site-specific DNA endonucleases. Mol Biol 2013. [DOI: 10.1134/s0026893313060186] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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26
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Wang X, Wheeler D, Avery A, Rago A, Choi JH, Colbourne JK, Clark AG, Werren JH. Function and evolution of DNA methylation in Nasonia vitripennis. PLoS Genet 2013; 9:e1003872. [PMID: 24130511 PMCID: PMC3794928 DOI: 10.1371/journal.pgen.1003872] [Citation(s) in RCA: 118] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 08/27/2013] [Indexed: 12/22/2022] Open
Abstract
The parasitoid wasp Nasonia vitripennis is an emerging genetic model for functional analysis of DNA methylation. Here, we characterize genome-wide methylation at a base-pair resolution, and compare these results to gene expression across five developmental stages and to methylation patterns reported in other insects. An accurate assessment of DNA methylation across the genome is accomplished using bisulfite sequencing of adult females from a highly inbred line. One-third of genes show extensive methylation over the gene body, yet methylated DNA is not found in non-coding regions and rarely in transposons. Methylated genes occur in small clusters across the genome. Methylation demarcates exon-intron boundaries, with elevated levels over exons, primarily in the 5′ regions of genes. It is also elevated near the sites of translational initiation and termination, with reduced levels in 5′ and 3′ UTRs. Methylated genes have higher median expression levels and lower expression variation across development stages than non-methylated genes. There is no difference in frequency of differential splicing between methylated and non-methylated genes, and as yet no established role for methylation in regulating alternative splicing in Nasonia. Phylogenetic comparisons indicate that many genes maintain methylation status across long evolutionary time scales. Nasonia methylated genes are more likely to be conserved in insects, but even those that are not conserved show broader expression across development than comparable non-methylated genes. Finally, examination of duplicated genes shows that those paralogs that have lost methylation in the Nasonia lineage following gene duplication evolve more rapidly, show decreased median expression levels, and increased specialization in expression across development. Methylation of Nasonia genes signals constitutive transcription across developmental stages, whereas non-methylated genes show more dynamic developmental expression patterns. We speculate that loss of methylation may result in increased developmental specialization in evolution and acquisition of methylation may lead to broader constitutive expression. Insects use methylation to modulate genome function in a different manner from vertebrates. Here, we quantified the global methylation profile in a parasitic wasp species, Nasonia vitripennis, a model with some advantages over ant and honeybee for functional and genetic analyses of methylation, such as short generation time, inbred lines, and inter-fertile species. Using a highly inbred line permitted us to precisely characterize DNA methylation, which is compared to gene expression variation across developmental stages, and contrasted to other insect species. DNA methylation is almost exclusively on the 5′-most 1 kbp coding exons, and ∼1/3 of protein coding genes are methylated. Methylated genes tend to occur in small clusters in the genome. Unlike many organisms, Nasonia leaves nearly all transposable element genes non-methylated. Methylated genes exhibit more uniform expression across developmental stages for both moderately and highly expressed genes, suggesting that DNA methylation is marking the genes for constitutive expression. Among pairs of differentially methylated duplicated genes, the paralogs that lose DNA methylation after duplication in the Nasonia lineage show lower expression and greater specialization of expression. Finally, by comparative analysis, we show that methylated genes are more conserved at three different time scales during evolution.
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Affiliation(s)
- Xu Wang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
- Cornell Center for Comparative and Population Genomics, Cornell University, Ithaca, New York, United States of America
| | - David Wheeler
- Department of Biology, University of Rochester, Rochester, New York, United States of America
| | - Amanda Avery
- Department of Biology, University of Rochester, Rochester, New York, United States of America
| | - Alfredo Rago
- School of Biosciences, The University of Birmingham, Birmingham, United Kingdom
| | - Jeong-Hyeon Choi
- Cancer Center, Department of Biostatistics and Epidemiology, Georgia Regents University, Augusta, Georgia, United States of America
| | - John K. Colbourne
- School of Biosciences, The University of Birmingham, Birmingham, United Kingdom
| | - Andrew G. Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
- Cornell Center for Comparative and Population Genomics, Cornell University, Ithaca, New York, United States of America
- * E-mail: (AGC); (JHW)
| | - John H. Werren
- Department of Biology, University of Rochester, Rochester, New York, United States of America
- * E-mail: (AGC); (JHW)
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Lessing D, Anguera MC, Lee JT. X chromosome inactivation and epigenetic responses to cellular reprogramming. Annu Rev Genomics Hum Genet 2013; 14:85-110. [PMID: 23662665 DOI: 10.1146/annurev-genom-091212-153530] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Reprogramming somatic cells to derive induced pluripotent stem cells (iPSCs) has provided a new method to model disease and holds great promise for regenerative medicine. Although genetically identical to their donor somatic cells, iPSCs undergo substantial changes in the epigenetic landscape during reprogramming. One such epigenetic process, X chromosome inactivation (XCI), has recently been shown to vary widely in human female iPSCs and embryonic stem cells (ESCs). XCI is a form of dosage compensation whose chief regulator is the noncoding RNA Xist. In mouse iPSCs and ESCs, Xist expression and XCI strictly correlate with the pluripotent state, but no such correlation exists in humans. Lack of XIST expression in human cells is linked to reduced developmental potential and an altered transcriptional profile, including upregulation of genes associated with cancer, which has therefore led to concerns about the safety of pluripotent stem cells for use in regenerative medicine. In this review, we describe how different states of XIST expression define three classes of female human pluripotent stem cells and explore progress in discovering the reasons for these variations and how they might be countered.
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Affiliation(s)
- Derek Lessing
- Howard Hughes Medical Institute, Department of Molecular Biology, and Department of Genetics, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114; , ,
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28
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Smchd1-dependent and -independent pathways determine developmental dynamics of CpG island methylation on the inactive X chromosome. Dev Cell 2012; 23:265-79. [PMID: 22841499 PMCID: PMC3437444 DOI: 10.1016/j.devcel.2012.06.011] [Citation(s) in RCA: 133] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2010] [Revised: 04/12/2012] [Accepted: 06/20/2012] [Indexed: 11/30/2022]
Abstract
X chromosome inactivation involves multiple levels of chromatin modification, established progressively and in a stepwise manner during early development. The chromosomal protein Smchd1 was recently shown to play an important role in DNA methylation of CpG islands (CGIs), a late step in the X inactivation pathway that is required for long-term maintenance of gene silencing. Here we show that inactive X chromosome (Xi) CGI methylation can occur via either Smchd1-dependent or -independent pathways. Smchd1-dependent CGI methylation, the primary pathway, is acquired gradually over an extended period, whereas Smchd1-independent CGI methylation occurs rapidly after the onset of X inactivation. The de novo methyltransferase Dnmt3b is required for methylation of both classes of CGI, whereas Dnmt3a and Dnmt3L are dispensable. Xi CGIs methylated by these distinct pathways differ with respect to their sequence characteristics and immediate chromosomal environment. We discuss the implications of these results for understanding CGI methylation during development.
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29
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Thapar M, Covault J, Hesselbrock V, Bonkovsky HL. DNA methylation patterns in alcoholics and family controls. World J Gastrointest Oncol 2012; 4:138-44. [PMID: 22737275 PMCID: PMC3382660 DOI: 10.4251/wjgo.v4.i6.138] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Revised: 05/16/2012] [Accepted: 05/21/2012] [Indexed: 02/05/2023] Open
Abstract
AIM: To assess whether DNA methylation patterns in chronic alcoholics are different from non-alcoholic sibling controls.
METHODS: We examined the methylation patterns in DNA samples from 25 chronic alcoholics and 22 matched siblings as controls (one per family). DNA was extracted from peripheral blood and analyzed for differences in the methylation patterns after bisulfite-conversion. We used the Illumina GoldenGate Methylation Cancer Panel I (Illumina, San Diego, CA), which probes the methylation profile at 1505 CpG sites from 807 cancer related genes. We excluded the 84 X-chromosome CpG sites and 134 autosomal CpG sites that failed to show a within sample reliability score of at least 95% for all samples, leaving 1287 autosomal CpG sites (associated with 743 autosomal genes) with reliable signals for all samples. A methylation score was calculated as the average methylation for the 1287 CpG sites examined. Differences were assessed by a two-sample t-test. We also examined the average sib pair differences in methylation scores at each of the 1287 sites. All analyses were performed using SPSS, version 9.0, P < 0.05 was considered significant.
RESULTS: Methylation levels at the 1287 CpG sites averaged 28.2% for both alcoholics and controls. The mean difference in methylation scores between alcoholic and non-alcoholic sibs by CpG site was < 1% with small inter-individual variances; and only 5 CpG sites had an average sib difference > 5%. Subgroup analysis showed that methylation scores were significantly lower for the alcoholic-dependent subjects who smoked compared to their non-smoking unaffected siblings. Specifically, among smokers who are alcoholic, global methylation indices were significantly lower than in non-alcoholic sib controls, whereas among non-smoking alcoholics, the global indices were significantly higher (P = 0.008).
CONCLUSION: Although we observed no effect of alcoholism alone on DNA methylation, there is a decrease in alcoholics who smoke, suggesting a mechanism for alcohol-tobacco synergy for carcinogenesis.
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Affiliation(s)
- Manish Thapar
- Manish Thapar, Herbert L Bonkovsky, Department of Medicine, The University of Connecticut Health Center, Farmington, CT 06030, United States
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30
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Phenotypic diversity and epigenomic variation – The utility of mass spectrometric analysis of DNA methylation. J Proteomics 2012; 75:3400-9. [DOI: 10.1016/j.jprot.2012.01.036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Revised: 01/09/2012] [Accepted: 01/30/2012] [Indexed: 01/10/2023]
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31
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Gertz J, Varley KE, Reddy TE, Bowling KM, Pauli F, Parker SL, Kucera KS, Willard HF, Myers RM. Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation. PLoS Genet 2011; 7:e1002228. [PMID: 21852959 PMCID: PMC3154961 DOI: 10.1371/journal.pgen.1002228] [Citation(s) in RCA: 236] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Accepted: 06/21/2011] [Indexed: 12/17/2022] Open
Abstract
The methylation of cytosines in CpG dinucleotides is essential for cellular differentiation and the progression of many cancers, and it plays an important role in gametic imprinting. To assess variation and inheritance of genome-wide patterns of DNA methylation simultaneously in humans, we applied reduced representation bisulfite sequencing (RRBS) to somatic DNA from six members of a three-generation family. We observed that 8.1% of heterozygous SNPs are associated with differential methylation in cis, which provides a robust signature for Mendelian transmission and relatedness. The vast majority of differential methylation between homologous chromosomes (>92%) occurs on a particular haplotype as opposed to being associated with the gender of the parent of origin, indicating that genotype affects DNA methylation of far more loci than does gametic imprinting. We found that 75% of genotype-dependent differential methylation events in the family are also seen in unrelated individuals and that overall genotype can explain 80% of the variation in DNA methylation. These events are under-represented in CpG islands, enriched in intergenic regions, and located in regions of low evolutionary conservation. Even though they are generally not in functionally constrained regions, 22% (twice as many as expected by chance) of genes harboring genotype-dependent DNA methylation exhibited allele-specific gene expression as measured by RNA-seq of a lymphoblastoid cell line, indicating that some of these events are associated with gene expression differences. Overall, our results demonstrate that the influence of genotype on patterns of DNA methylation is widespread in the genome and greatly exceeds the influence of imprinting on genome-wide methylation patterns. DNA methylation is a dynamic epigenetic mark that is essential for mammalian organismal development. DNA methylation levels can be influenced by environment, a chromosome's parental origin, and genome sequence. In this study, we evaluated the impact that DNA sequence has on DNA methylation by analyzing methylation levels in a three-generation family as well as unrelated individuals. By following DNA methylation patterns through the family along with nearby SNPs, we found that allelic differences between chromosomes play a much larger role in determining DNA methylation than the parental origin of the chromosome, indicating that DNA sequence has a larger impact on DNA methylation than gametic imprinting. We also found that allelic differences in DNA methylation found in the family can also be observed in unrelated individuals. In fact, the majority of variation in DNA methylation can be explained by genotype. Our results emphasize the importance of genome sequence in setting patterns of DNA methylation and indicate that genotype will need to be taken into account when assessing DNA methylation in the context of disease.
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Affiliation(s)
- Jason Gertz
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - Katherine E. Varley
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - Timothy E. Reddy
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - Kevin M. Bowling
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - Florencia Pauli
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - Stephanie L. Parker
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - Katerina S. Kucera
- Duke Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina, United States of America
| | - Huntington F. Willard
- Duke Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina, United States of America
| | - Richard M. Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
- * E-mail:
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Casas-Delucchi CS, Brero A, Rahn HP, Solovei I, Wutz A, Cremer T, Leonhardt H, Cardoso MC. Histone acetylation controls the inactive X chromosome replication dynamics. Nat Commun 2011; 2:222. [PMID: 21364561 PMCID: PMC3072080 DOI: 10.1038/ncomms1218] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2010] [Accepted: 01/27/2011] [Indexed: 12/20/2022] Open
Abstract
In mammals, dosage compensation between male and female cells is achieved by inactivating one female X chromosome (Xi). Late replication of Xi was proposed to be involved in the maintenance of its silenced state. Here, we show a highly synchronous replication of the Xi within 1 to 2 h during early-mid S-phase by following DNA replication in living mammalian cells with green fluorescent protein-tagged replication proteins. The Xi was replicated before or concomitant with perinuclear or perinucleolar facultative heterochromatin and before constitutive heterochromatin. Ectopic expression of the X-inactive-specific transcript (Xist) gene from an autosome imposed the same synchronous replication pattern. We used mutations and chemical inhibition affecting different epigenetic marks as well as inducible Xist expression and we demonstrate that histone hypoacetylation has a key role in controlling Xi replication. The epigenetically controlled, highly coordinated replication of the Xi is reminiscent of embryonic genome replication in flies and frogs before genome activation and might be a common feature of transcriptionally silent chromatin.
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Abstract
In humans, sexual dimorphism is associated with the presence of two X chromosomes in the female, whereas males possess only one X and a small and largely degenerate Y chromosome. How do men cope with having only a single X chromosome given that virtually all other chromosomal monosomies are lethal? Ironically, or even typically many might say, women and more generally female mammals contribute most to the job by shutting down one of their two X chromosomes at random. This phenomenon, called X-inactivation, was originally described some 50 years ago by Mary Lyon and has captivated an increasing number of scientists ever since. The fascination arose in part from the realisation that the inactive X corresponded to a dense heterochromatin mass called the “Barr body” whose number varied with the number of Xs within the nucleus and from the many intellectual questions that this raised: How does the cell count the X chromosomes in the nucleus and inactivate all Xs except one? What kind of molecular mechanisms are able to trigger such a profound, chromosome-wide metamorphosis? When is X-inactivation initiated? How is it transmitted to daughter cells and how is it reset during gametogenesis? This review retraces some of the crucial findings, which have led to our current understanding of a biological process that was initially considered as an exception completely distinct from conventional regulatory systems but is now viewed as a paradigm “par excellence” for epigenetic regulation.
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Affiliation(s)
- Céline Morey
- Institut Pasteur, Unité de Génétique Moléculaire Murine, CNRS, URA2578, Paris, France
- * E-mail:
| | - Philip Avner
- Institut Pasteur, Unité de Génétique Moléculaire Murine, CNRS, URA2578, Paris, France
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34
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Evolutionary diversity and developmental regulation of X-chromosome inactivation. Hum Genet 2011; 130:307-27. [PMID: 21687993 PMCID: PMC3132430 DOI: 10.1007/s00439-011-1029-2] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2011] [Accepted: 05/31/2011] [Indexed: 12/26/2022]
Abstract
X-chromosome inactivation (XCI) results in the transcriptional silencing of one X-chromosome in females to attain gene dosage parity between XX female and XY male mammals. Mammals appear to have developed rather diverse strategies to initiate XCI in early development. In placental mammals XCI depends on the regulatory noncoding RNA X-inactive specific transcript (Xist), which is absent in marsupials and monotremes. Surprisingly, even placental mammals show differences in the initiation of XCI in terms of Xist regulation and the timing to acquire dosage compensation. Despite this, all placental mammals achieve chromosome-wide gene silencing at some point in development, and this is maintained by epigenetic marks such as chromatin modifications and DNA methylation. In this review, we will summarise recent findings concerning the events that occur downstream of Xist RNA coating of the inactive X-chromosome (Xi) to ensure its heterochromatinization and the maintenance of the inactive state in the mouse and highlight similarities and differences between mammals.
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35
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Abstract
X chromosome inactivation (XCI) is a process in mammals that ensures equal transcript levels between males and females by genetic inactivation of one of the two X chromosomes in females. Central to XCI is the long non-coding RNA Xist, which is highly and specifically expressed from the inactive X chromosome. Xist covers the X chromosome in cis and triggers genetic silencing, but its working mechanism remains elusive. Here, we review current knowledge about Xist regulation, structure, function and conservation and speculate on possible mechanisms by which its action is restricted in cis. We also discuss dosage compensation mechanisms other than XCI and how knowledge from invertebrate species may help to provide a better understanding of the mechanisms of mammalian XCI.
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Affiliation(s)
- Daphne B. Pontier
- Department of Reproduction and Development, Erasmus MC, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands
| | - Joost Gribnau
- Department of Reproduction and Development, Erasmus MC, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands
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36
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Senner CE. The role of DNA methylation in mammalian development. Reprod Biomed Online 2011; 22:529-35. [PMID: 21498123 DOI: 10.1016/j.rbmo.2011.02.016] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Revised: 02/25/2011] [Accepted: 02/28/2011] [Indexed: 01/12/2023]
Abstract
DNA methylation is involved in a number of important processes such as maintaining genome stability, silencing of retrotransposons, co-ordinating mono-alleleic expression of parentally imprinted genes and ensuring transcriptional repression of genes on the inactive X chromosome. Further, correct DNA methylation patterns are necessary for normal development and lineage commitment. DNA methylation provides a stable and heritable epigenetic mark. However, it can be removed, either actively or passively, during periods of reprogramming in primordial germ cells and preimplantation embryos. By combining immunofluorescence data with recent insights from genome-wide studies utilizing techniques such as Bisulphite-seq and MeDIP-ChIP, a clearer picture of the dynamic patterns of DNA methylation throughout gametogenesis, preimplantation development and early lineage commitment is beginning to emerge. The continuing use of these next-generation technologies to elucidate genome-wide methylation patterns in a variety of cellular contexts will further understanding of how this epigenetic mark contributes to lineage commitment, differentiation and pluripotency and, ultimately, to human health and disease.
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Affiliation(s)
- Claire E Senner
- Laboratory of Epigenetics, The Babraham Institute, Babraham Research Campus, Cambridge, UK.
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37
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Senner CE, Nesterova TB, Norton S, Dewchand H, Godwin J, Mak W, Brockdorff N. Disruption of a conserved region of Xist exon 1 impairs Xist RNA localisation and X-linked gene silencing during random and imprinted X chromosome inactivation. Development 2011; 138:1541-50. [PMID: 21389056 DOI: 10.1242/dev.056812] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In XX female mammals a single X chromosome is inactivated early in embryonic development, a process that is required to equalise X-linked gene dosage relative to XY males. X inactivation is regulated by a cis-acting master switch, the Xist locus, the product of which is a large non-coding RNA that coats the chromosome from which it is transcribed, triggering recruitment of chromatin modifying factors that establish and maintain gene silencing chromosome wide. Chromosome coating and Xist RNA-mediated silencing remain poorly understood, both at the level of RNA sequence determinants and interacting factors. Here, we describe analysis of a novel targeted mutation, Xist(INV), designed to test the function of a conserved region located in exon 1 of Xist RNA during X inactivation in mouse. We show that Xist(INV) is a strong hypomorphic allele that is appropriately regulated but compromised in its ability to silence X-linked loci in cis. Inheritance of Xist(INV) on the paternal X chromosome results in embryonic lethality due to failure of imprinted X inactivation in extra-embryonic lineages. Female embryos inheriting Xist(INV) on the maternal X chromosome undergo extreme secondary non-random X inactivation, eliminating the majority of cells that express the Xist(INV) allele. Analysis of cells that express Xist(INV) RNA demonstrates reduced association of the mutant RNA to the X chromosome, suggesting that conserved sequences in the inverted region are important for Xist RNA localisation.
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Affiliation(s)
- Claire E Senner
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK
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38
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Gontan C, Jonkers I, Gribnau J. Long Noncoding RNAs and X Chromosome Inactivation. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2011; 51:43-64. [PMID: 21287133 DOI: 10.1007/978-3-642-16502-3_3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
In female somatic cells, one of the two X chromosomes is inactivated to equalize the dose of sex-linked gene products between female and male cells. X chromosome inactivation X chromosome inactivation (XCI) is initiated very early during development and requires Xist Xist , which is a noncoding X-linked gene. Upon initiation of XCI, Xist-RNA spreads along the X chromosome in cis, and Xist spreading is required for the recruitment of different chromatin remodeling complexes involved in the establishment and maintenance of the inactive X chromosome. Because XCI acts chromosomewise, Xist-mediated silencing has served as an important paradigm to study the function of noncoding RNAs (ncRNA) in gene silencing. In this chapter, we describe the current knowledge about the structure and function of Xist. We also discuss the important cis- and trans-regulatory elements and proteins in the initiation, establishment, and maintenance of XCI. In addition, we highlight new findings with other ncRNAs involved in gene repression and discuss these findings in relation to Xist-mediated gene silencing.
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Affiliation(s)
- Cristina Gontan
- Department of Reproduction and Development, Erasmus MC, University Medical Center, Room Ee 09-71, 2040, 3000, CA, Rotterdam, The Netherlands
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39
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Barzily-Rokni M, Friedman N, Ron-Bigger S, Isaac S, Michlin D, Eden A. Synergism between DNA methylation and macroH2A1 occupancy in epigenetic silencing of the tumor suppressor gene p16(CDKN2A). Nucleic Acids Res 2010; 39:1326-35. [PMID: 21030442 PMCID: PMC3045621 DOI: 10.1093/nar/gkq994] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Promoter hypermethylation and heterochromatinization is a frequent event leading to gene inactivation and tumorigenesis. At the molecular level, inactivation of tumor suppressor genes in cancer has many similarities to the inactive X chromosome in female cells and is defined and maintained by DNA methylation and characteristic histone modifications. In addition, the inactive-X is marked by the histone macroH2A, a variant of H2A with a large non-histone region of unknown function. Studying tumor suppressor genes (TSGs) silenced in cancer cell lines, we find that when active, these promoters are associated with H2A.Z but become enriched for macroH2A1 once silenced. Knockdown of macroH2A1 was not sufficient for reactivation of silenced genes. However, when combined with DNA demethylation, macroH2A1 deficiency significantly enhanced reactivation of the tumor suppressor genes p16, MLH1 and Timp3 and inhibited cell proliferation. Our findings link macroH2A1 to heterochromatin of epigenetically silenced cancer genes and indicate synergism between macroH2A1 and DNA methylation in maintenance of the silenced state.
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Affiliation(s)
- Michal Barzily-Rokni
- Department of Cell & Developmental Biology, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
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40
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Epigenetic modifications on X chromosomes in marsupial and monotreme mammals and implications for evolution of dosage compensation. Proc Natl Acad Sci U S A 2010; 107:17657-62. [PMID: 20861449 DOI: 10.1073/pnas.0910322107] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
X chromosome dosage compensation in female eutherian mammals is regulated by the noncoding Xist RNA and is associated with the differential acquisition of active and repressive histone modifications, resulting in repression of most genes on one of the two X chromosome homologs. Marsupial mammals exhibit dosage compensation; however, they lack Xist, and the mechanisms conferring epigenetic control of X chromosome dosage compensation remain elusive. Oviparous mammals, the monotremes, have multiple X chromosomes, and it is not clear whether they undergo dosage compensation and whether there is epigenetic dimorphism between homologous pairs in female monotremes. Here, using antibodies against DNA methylation, eight different histone modifications, and HP1, we conduct immunofluorescence on somatic cells of the female Australian marsupial possum Trichosurus vulpecula, the female platypus Ornithorhynchus anatinus, and control mouse cells. The two marsupial X's were different for all epigenetic features tested. In particular, unlike in the mouse, both repressive modifications, H3K9me3 and H4K20Me3, are enriched on one of the X chromosomes, and this is associated with the presence of HP1 and hypomethylation of DNA. Using sequential labeling, we determine that this DNA hypomethylated X correlates with histone marks of inactivity. These results suggest that female marsupials use a repressive histone-mediated inactivation mechanism and that this may represent an ancestral dosage compensation process that differs from eutherians that require Xist transcription and DNA methylation. In comparison to the marsupial, the monotreme exhibited no epigenetic differences between homologous X chromosomes, suggesting the absence of a dosage compensation process comparable to that in therians.
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41
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Barakat TS, Gribnau J. X chromosome inactivation and embryonic stem cells. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2010; 695:132-54. [PMID: 21222204 DOI: 10.1007/978-1-4419-7037-4_10] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
X chromosome inactivation (XCI) is a process required to equalize the dosage of X-encoded genes between female and male cells. XCI is initiated very early during female embryonic development or upon differentiation of female embryonic stem (ES) cells and results in inactivation of one X chromosome in every female somatic cell. The regulation of XCI involves factors that also play a crucial role in ES cell maintenance and differentiation and the XCI process therefore provides a beautiful paradigm to study ES cell biology. In this chapter we describe the important cis and trans acting regulators of XCI and introduce the models that have been postulated to explain initiation of XCI in female cells only. We also discuss the proteins involved in the establishment of the inactive X chromosome and describe the different chromatin modifications associated with the inactivation process. Finally, we describe the potential of mouse and human ES and induced pluripotent stem (iPS) cells as model systems to study the XCI process.
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Affiliation(s)
- Tahsin Stefan Barakat
- Department of Reproduction and Development, University Medical Center, Room Ee 09-71, Erasmus MC, 3015 GE, Rotterdam, Netherlands
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42
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Deakin JE, Chaumeil J, Hore TA, Marshall Graves JA. Unravelling the evolutionary origins of X chromosome inactivation in mammals: insights from marsupials and monotremes. Chromosome Res 2009; 17:671-85. [DOI: 10.1007/s10577-009-9058-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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43
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De Sario A. Clinical and molecular overview of inherited disorders resulting from epigenomic dysregulation. Eur J Med Genet 2009; 52:363-72. [PMID: 19632366 DOI: 10.1016/j.ejmg.2009.07.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2009] [Accepted: 07/21/2009] [Indexed: 01/23/2023]
Abstract
Epigenetics is the study of heritable changes in gene expression that occur without a change in the DNA sequence. Most constitutional defects in genes encoding components of the machinery that regulates the epigenome lead to embryonic death. Hypomorphic mutations may be compatible with life, but lead to severe developmental disorders. Their study is of great importance to our understanding of epigenetics and may clarify the interplay between different epigenetic mechanisms. This review will briefly introduce DNA methylation, post-translational histone modifications, and non-coding small RNA transcription, which are the best known epigenetic mechanisms. Then it will describe five human disorders (RETT, ATRX, ICF, Coffin-Lowry, and Rubinstein-Taybi) resulting from mutations in genes responsible for DNA methylation and in genes involved in chromatin remodeling. Finally, it will discuss how research in medical genetics can elucidate fundamental epigenetic processes.
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Affiliation(s)
- Albertina De Sario
- Institut de Génétique Humaine, CNRS UPR 1142, 141 rue de la Cardonille, 34396 Montpellier, France.
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44
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Sawalha AH, Harley JB, Scofield RH. Autoimmunity and Klinefelter's syndrome: when men have two X chromosomes. J Autoimmun 2009; 33:31-4. [PMID: 19464849 DOI: 10.1016/j.jaut.2009.03.006] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2009] [Accepted: 03/03/2009] [Indexed: 11/19/2022]
Abstract
Similar to other autoimmune diseases, systemic lupus erythematosus (SLE) predominately affects women. Recent reports demonstrate excess Klinefelter's among men with SLE and a possible under-representation of Turner's syndrome among women with SLE as well as a case report of a 46,XX boy with SLE. These data suggest that risk of SLE is related to a gene dose effect for the X chromosome. Such an effect could be mediated by abnormal inactivation of genes on the X chromosome as has been demonstrated for CD40L, or by genetic polymorphism as has been demonstrated for Xq28. On the other hand, a gene dose effect could also be mediated by a gene without an SLE-associated polymorphism in that a gene that avoids X inactivation will have a higher level of expression in persons with two X chromosomes.
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Affiliation(s)
- Amr H Sawalha
- Arthritis and Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
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45
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Koina E, Chaumeil J, Greaves IK, Tremethick DJ, Graves JAM. Specific patterns of histone marks accompany X chromosome inactivation in a marsupial. Chromosome Res 2009; 17:115-26. [PMID: 19214764 DOI: 10.1007/s10577-009-9020-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2008] [Revised: 11/25/2008] [Accepted: 11/25/2008] [Indexed: 02/03/2023]
Abstract
The inactivation of one of the two X chromosomes in female placental mammals represents a remarkable example of epigenetic silencing. X inactivation occurs also in marsupial mammals, but is phenotypically different, being incomplete, tissue-specific and paternal. Paternal X inactivation occurs also in the extraembryonic cells of rodents, suggesting that imprinted X inactivation represents a simpler ancestral mechanism. This evolved into a complex and random process in placental mammals under the control of the XIST gene, involving notably variant and modified histones. Molecular mechanisms of X inactivation in marsupials are poorly known, but occur in the absence of an XIST homologue. We analysed the specific pattern of histone modifications using immunofluorescence on metaphasic chromosomes of a model kangaroo, the tammar wallaby. We found that all active marks are excluded from the inactive X in marsupials, as in placental mammals, so this represents a common feature of X inactivation throughout mammals. However, we were unable to demonstrate the accumulation of inactive histone marks, suggesting some fundamental differences in the molecular mechanism of X inactivation between marsupial and placental mammals. A better understanding of the epigenetic mechanisms underlying X inactivation in marsupials will provide important insights into the evolution of this complex process.
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Affiliation(s)
- Edda Koina
- Research School of Biological Sciences, The Australian National University, Canberra, ACT, 0200, Australia
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46
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Schneider R, Grosschedl R. Dynamics and interplay of nuclear architecture, genome organization, and gene expression. Genes Dev 2008; 21:3027-43. [PMID: 18056419 DOI: 10.1101/gad.1604607] [Citation(s) in RCA: 314] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The organization of the genome in the nucleus of a eukaryotic cell is fairly complex and dynamic. Various features of the nuclear architecture, including compartmentalization of molecular machines and the spatial arrangement of genomic sequences, help to carry out and regulate nuclear processes, such as DNA replication, DNA repair, gene transcription, RNA processing, and mRNA transport. Compartmentalized multiprotein complexes undergo extensive modifications or exchange of protein subunits, allowing for an exquisite dynamics of structural components and functional processes of the nucleus. The architecture of the interphase nucleus is linked to the spatial arrangement of genes and gene clusters, the structure of chromatin, and the accessibility of regulatory DNA elements. In this review, we discuss recent studies that have provided exciting insight into the interplay between nuclear architecture, genome organization, and gene expression.
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47
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Latham T, Gilbert N, Ramsahoye B. DNA methylation in mouse embryonic stem cells and development. Cell Tissue Res 2007; 331:31-55. [PMID: 18060563 DOI: 10.1007/s00441-007-0537-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2007] [Accepted: 10/17/2007] [Indexed: 01/01/2023]
Abstract
Mammalian development is associated with considerable changes in global DNA methylation levels at times of genomic reprogramming. Normal DNA methylation is essential for development but, despite considerable advances in our understanding of the DNA methyltransferases, the reason that development fails when DNA methylation is deficient remains unclear. Furthermore, although much is known about the enzymes that cause DNA methylation, comparatively little is known about the mechanisms or significance of active demethylation in early development. In this review, we discuss the roles of the various DNA methyltransferases and their likely functions in development.
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Affiliation(s)
- Tom Latham
- Cancer Research Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
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48
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Ohgane J, Yagi S, Shiota K. Epigenetics: the DNA methylation profile of tissue-dependent and differentially methylated regions in cells. Placenta 2007; 29 Suppl A:S29-35. [PMID: 18031808 DOI: 10.1016/j.placenta.2007.09.011] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2007] [Revised: 09/25/2007] [Accepted: 09/26/2007] [Indexed: 10/22/2022]
Abstract
Methylation of DNA, which occurs at cytosines of CpG sequences, is a unique chemical modification of the vertebrate genome. Methylation patterns can be copied to daughter DNA after mitosis; thus DNA methylation has been suggested to act as a "cellular memory of the genome function". Genome-wide analysis of DNA methylation revealed that there are numerous tissue-dependent differentially methylated regions (T-DMRs) in unique sequences of the mammalian genome. There are T-DMRs in both CpG-rich and -poor sequences. Methylation of T-DMRs is responsible for gene-silencing and chromatin structure change. Each tissue/cell type has a unique DNA methylation profile that consists of methylation patterns of numerous loci in the genome. DNA methylation profiles are not associated with bulk DNA, which is mainly comprised of repetitive sequences. Disruption of DNA methylation profiles putatively produce abnormal cells and tissues. Cloned mice produced by somatic nuclear transfer are associated with aberrant DNA methylation profiles. Tissue/cell type-specific DNA methylation profiles can provide a novel viewpoint for understanding normal and aberrant development, in terms of both differentiation and reproduction.
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Affiliation(s)
- J Ohgane
- Laboratory of Cellular Biochemistry, Animal Resource Sciences/Veterinary Medical Sciences, Graduate School of Agriculture and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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49
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El-Maarri O, Becker T, Junen J, Manzoor SS, Diaz-Lacava A, Schwaab R, Wienker T, Oldenburg J. Gender specific differences in levels of DNA methylation at selected loci from human total blood: a tendency toward higher methylation levels in males. Hum Genet 2007; 122:505-14. [PMID: 17851693 DOI: 10.1007/s00439-007-0430-3] [Citation(s) in RCA: 213] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2007] [Accepted: 08/30/2007] [Indexed: 01/05/2023]
Abstract
Abnormal patterns of DNA methylation are observed in many diseases such as tumors and imprinting disorders. Little is known about inter-individual and gender specific variations. Here, we report on accurate and sensitive quantitative measurements of methylation in DNA from total blood in 96 healthy human males and 96 healthy human females. Global methylation was estimated by studying two repetitive DNA elements, namely Line-1 and Alu repeats, while single loci were investigated for three differentially methylated regions (DMRs) at PEG3, NESP55 and H19 imprinted genes and two additional loci at Xq28 (F8 gene) and at 19q13.4 (locus between PEG3 and ubiquitin specific protease 29). We observed inter-individual correlations in the degree of methylation between Alu and Line-1 repeats. Moreover, all studied CpGs showed slightly higher methylation in males (P < 0.0003-0.0381), with the exception of DMRs at imprinted genes (P = 0.0342-0.9616) which were almost equally methylated in both sexes with only a small tendency towards higher methylation in males. This observed difference could be due to the process of X chromosome inactivation or merely to the presence of an additional X chromosome in female cells or could be a result of downstream effects of sex determination.
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Affiliation(s)
- Osman El-Maarri
- Institute of Experimental Hematology and Transfusion Medicine, University of Bonn, Sigmund-Freud-Str. 25, 53127, Bonn, Germany.
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Salstrom JL. X-inactivation and the dynamic maintenance of gene silencing. Mol Genet Metab 2007; 92:56-62. [PMID: 17604203 DOI: 10.1016/j.ymgme.2007.05.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2007] [Revised: 05/23/2007] [Accepted: 05/23/2007] [Indexed: 01/25/2023]
Abstract
X-inactivation has long been a topic of fascination for educators, researchers, and clinicians alike. From complex patterns of inheritance to phenotypic variation among females with X-linked traits, a myriad of hypothesis and interpretations exist. Once thought to be random yet complete, X-inactivation has proven itself the poster child of the exception rather than the rule. Indeed, patterns of X-inactivation are all too often non-random, and many X-linked genes are capable of escaping X-inactivation. Similarly, X-inactivation is well-known for being stably maintained for life, but some previously inactivated X-linked genes reactivate with increasing age. Moreover, recent papers illustrate that X-inactivation can be challenged in other ways, thereby rendering the stability of X-inactivation compromised. This review describes factors involved in the maintenance of X-inactivation as we know it and discusses these emerging data that suggest a more dynamic model of the maintenance of X-inactivation may be in order.
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Affiliation(s)
- Jennifer L Salstrom
- Department of Human Genetics, David Geffen School of Medicine at UCLA, 6505 Gonda Center-Mail Code 708822, 695 Charles E Young Drive South, Los Angeles, CA 90095-708822, USA.
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