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Madan V, Cao Z, Teoh WW, Dakle P, Han L, Shyamsunder P, Jeitany M, Zhou S, Li J, Nordin HBM, Shi J, Yu S, Yang H, Hossain MZ, Chng WJ, Koeffler HP. ZRSR1 cooperates with ZRSR2 in regulating splicing of U12-type introns in murine hematopoietic cells. Haematologica 2021; 107:680-689. [PMID: 33691379 PMCID: PMC8883539 DOI: 10.3324/haematol.2020.260562] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Indexed: 12/03/2022] Open
Abstract
Recurrent loss-of-function mutations of spliceosome gene, ZRSR2, occur in myelodysplastic syndromes (MDS). Mutation/loss of ZRSR2 in human myeloid cells primarily causes impaired splicing of the U12-type introns. In order to further investigate the role of this splice factor in RNA splicing and hematopoietic development, we generated mice lacking ZRSR2. Unexpectedly, Zrsr2-deficient mice developed normal hematopoiesis with no abnormalities in myeloid differentiation evident in either young or ≥1-year old knockout mice. Repopulation ability of Zrsr2-deficient hematopoietic stem cells was also unaffected in both competitive and non-competitive reconstitution assays. Myeloid progenitors lacking ZRSR2 exhibited mis-splicing of U12-type introns, however, this phenotype was moderate compared to the ZRSR2-deficient human cells. Our investigations revealed that a closely related homolog, Zrsr1, expressed in the murine hematopoietic cells, but not in human cells contributes to splicing of U12-type introns. Depletion of Zrsr1 in Zrsr2 KO myeloid cells exacerbated retention of the U12-type introns, thus highlighting a collective role of ZRSR1 and ZRSR2 in murine U12-spliceosome. We also demonstrate that aberrant retention of U12-type introns of MAPK9 and MAPK14 leads to their reduced protein expression. Overall, our findings highlight that both ZRSR1 and ZRSR2 are functional components of the murine U12-spliceosome, and depletion of both proteins is required to accurately model ZRSR2-mutant MDS in mice.
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Affiliation(s)
- Vikas Madan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore.
| | - Zeya Cao
- Cancer Science Institute of Singapore, National University of Singapore, Singapore; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Weoi Woon Teoh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Pushkar Dakle
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Lin Han
- Cancer Science Institute of Singapore, National University of Singapore, Singapore; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Pavithra Shyamsunder
- Cancer Science Institute of Singapore, National University of Singapore, Singapore; Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore
| | - Maya Jeitany
- Cancer Science Institute of Singapore, National University of Singapore, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore
| | - Siqin Zhou
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Jia Li
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | | | - JiZhong Shi
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Shuizhou Yu
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Md Zakir Hossain
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Wee Joo Chng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Hematology-Oncology, National University Cancer Institute, NUHS, Singapore
| | - H Phillip Koeffler
- Cancer Science Institute of Singapore, National University of Singapore, Singapore; Cedars-Sinai Medical Center, Division of Hematology/Oncology, UCLA School of Medicine, Los Angeles, USA; National University Cancer Institute, National University Hospital Singapore, Singapore
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Barnett KR, Decato BE, Scott TJ, Hansen TJ, Chen B, Attalla J, Smith AD, Hodges E. ATAC-Me Captures Prolonged DNA Methylation of Dynamic Chromatin Accessibility Loci during Cell Fate Transitions. Mol Cell 2020; 77:1350-1364.e6. [PMID: 31999955 DOI: 10.1016/j.molcel.2020.01.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 11/08/2019] [Accepted: 01/02/2020] [Indexed: 12/16/2022]
Abstract
DNA methylation of enhancers is dynamic, cell-type specific, and vital for cell fate progression. However, current models inadequately define its role within the hierarchy of gene regulation. Analysis of independent datasets shows an unanticipated overlap between DNA methylation and chromatin accessibility at enhancers of steady-state stem cells, suggesting that these two opposing features might exist concurrently. To define their temporal relationship, we developed ATAC-Me, which probes accessibility and methylation from single DNA library preparations. We identified waves of accessibility occurring rapidly across thousands of myeloid enhancers in a monocyte-to-macrophage cell fate model. Prolonged methylation states were observed at a majority of these sites, while transcription of nearby genes tracked closely with accessibility. ATAC-Me uncovers a significant disconnect between chromatin accessibility, DNA methylation status, and gene activity. This unexpected observation highlights the value of ATAC-Me in constructing precise molecular timelines for understanding the role of DNA methylation in gene regulation.
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Affiliation(s)
- Kelly R Barnett
- Department of Biochemistry and Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Benjamin E Decato
- Quantitative and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Timothy J Scott
- Department of Biochemistry and Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Tyler J Hansen
- Department of Biochemistry and Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Bob Chen
- Department of Biochemistry and Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Jonathan Attalla
- Department of Biochemistry and Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Andrew D Smith
- Quantitative and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Emily Hodges
- Department of Biochemistry and Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
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3
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Imprinting evolution and human health. Mamm Genome 2009; 20:563-72. [PMID: 19830403 DOI: 10.1007/s00335-009-9229-y] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2009] [Accepted: 09/16/2009] [Indexed: 01/06/2023]
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La Salle S, Oakes CC, Neaga OR, Bourc'his D, Bestor TH, Trasler JM. Loss of spermatogonia and wide-spread DNA methylation defects in newborn male mice deficient in DNMT3L. BMC DEVELOPMENTAL BIOLOGY 2007; 7:104. [PMID: 17875220 PMCID: PMC2212652 DOI: 10.1186/1471-213x-7-104] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2007] [Accepted: 09/18/2007] [Indexed: 12/13/2022]
Abstract
BACKGROUND Formation of haploid spermatozoa capable of fertilization requires proper programming of epigenetic information. Exactly how DNMT3L (DNA methyltransferase 3-Like), a postulated regulator of DNA methyltransferase activity, contributes to DNA methylation pattern acquisition during gametogenesis remains unclear. Here we report on the role of DNMT3L in male germ cell development. RESULTS A developmental study covering the first 12 days following birth was conducted on a Dnmt3L mutant mouse model; lower germ cell numbers and delayed entry into meiosis were observed in Dnmt3L-/- males, pointing to a mitotic defect. A temporal expression study showed that expression of Dnmt3L is highest in prenatal gonocytes but is also detected and developmentally regulated during spermatogenesis. Using a restriction enzyme qPCR assay (qAMP), DNA methylation analyses were conducted on postnatal primitive type A spermatogonia lacking DNMT3L. Methylation levels along 61 sites across chromosomes 4 and X decreased significantly by approximately 50% compared to the levels observed in Dnmt3L+/+ germ cells, suggesting that many loci throughout the genome are marked for methylation by DNMT3L. More so, hypomethylation was more pronounced in regions of lower GC content than in regions of higher GC content. CONCLUSION Taken together, these data suggest that DNMT3L plays a more global role in genomic methylation patterning than previously believed.
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Affiliation(s)
- Sophie La Salle
- Departments of Pharmacology & Therapeutics, Pediatrics and Human Genetics, McGill University and The Montreal Children's Hospital Research Institute, Montréal, QC, H3H 1P3, Canada
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Christopher C Oakes
- Departments of Pharmacology & Therapeutics, Pediatrics and Human Genetics, McGill University and The Montreal Children's Hospital Research Institute, Montréal, QC, H3H 1P3, Canada
| | - Oana R Neaga
- Departments of Pharmacology & Therapeutics, Pediatrics and Human Genetics, McGill University and The Montreal Children's Hospital Research Institute, Montréal, QC, H3H 1P3, Canada
| | | | - Timothy H Bestor
- Department of Genetics and Development, College of Physicians and Surgeons of Columbia University, New York, NY 10032, USA
| | - Jacquetta M Trasler
- Departments of Pharmacology & Therapeutics, Pediatrics and Human Genetics, McGill University and The Montreal Children's Hospital Research Institute, Montréal, QC, H3H 1P3, Canada
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Zhang Z, Joh K, Yatsuki H, Wang Y, Arai Y, Soejima H, Higashimoto K, Iwasaka T, Mukai T. Comparative analyses of genomic imprinting and CpG island-methylation in mouse Murr1 and human MURR1 loci revealed a putative imprinting control region in mice. Gene 2006; 366:77-86. [PMID: 16305817 DOI: 10.1016/j.gene.2005.08.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2005] [Accepted: 08/13/2005] [Indexed: 01/20/2023]
Abstract
Human MURR1 is an orthologue of mouse Murr1 gene, which was previously reported to be imprinted only in adult brain with a maternal allele-predominant expression and to contain another imprinted gene, U2af1-rs1, in the first intron. Human MURR1 was found not to harbor the U2af1-rs1 orthologue and to be expressed biallelically in tissues, including adult brain. Three genes identified around Murr1 and their orthologues around MURR1 were expressed biallelically. These findings suggest that the mouse imprinting locus is limited to a small region and the introduction of U2af1-rs1 in mouse causes the imprinting of this locus. The CpG island (CGI) at U2af1-rs1 with maternal methylation was the only differentially methylated region among CGIs found in these loci. Detailed methylation analyses of the U2af1-rs1 CGI in germ cells led to identification of a region with oocyte-specific methylation. These results suggest that this region is the imprinting control region of the Murr1/U2af1-rs1 locus in mouse.
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Affiliation(s)
- Zhongming Zhang
- Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga 849-8501, Japan
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Weber M, Hagège H, Aptel N, Brunel C, Cathala G, Forné T. Epigenetic regulation of mammalian imprinted genes: from primary to functional imprints. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2005; 38:207-36. [PMID: 15881897 DOI: 10.1007/3-540-27310-7_9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Parental genomic imprinting was discovered in mammals some 20 years ago. This phenomenon, crucial for normal development, rapidly became a key to understanding epigenetic regulation of mammalian gene expression. In this chapter we present a general overview of the field and describe in detail the 'imprinting cycle'. We provide selected examples that recapitulate our current knowledge of epigenetic regulation at imprinted loci. These epigenetic mechanisms lead to the stable repression of imprinted genes on one parental allele by interfering with 'formatting' for gene expression that usually occurs on expressed alleles. From this perspective, genomic imprinting remarkably illustrates the complexity of the epigenetic mechanisms involved in the control of gene expression in mammals.
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Affiliation(s)
- Michaël Weber
- Institut de Génétique Moléculaire de Montpellier, UMR5535 CNRS-UMII, IFR122, 34293 Montpellier Cedex 5, France
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7
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Davey C, Allan J. Nucleosome positioning signals and potential H-DNA within the DNA sequence of the imprinting control region of the mouse Igf2r gene. ACTA ACUST UNITED AC 2004; 1630:103-16. [PMID: 14654240 DOI: 10.1016/j.bbaexp.2003.09.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The imprinting control region within the second intron of the mouse Igf2r gene contains a CpG island comprising direct repeats, an imprinting box and the Air antisense promoter which is blocked by the methylation imprint on the active maternal allele. We have investigated the structural features of this DNA, including a mapping of all nucleosome positioning signals within the nucleotide sequence. A discrete series of strong positioning signals distinguished the direct repeat region from the much more diverse positioning capacity of the sequence encompassing the known regulatory elements. At only a few locations did CpG methylation modulate the use of this positioning information. Direct effects upon histone-DNA interactions are therefore unlikely to contribute significantly to the means by which the imprint may establish allele-specific chromatin architecture and determine Air expression. A strand-specific obstruction to DNA polymerase was observed between the repeat and regulatory regions. The same region adopts triple-stranded H-DNA structures in supercoiled DNA, according to pH and divalent cation exposure. Methylation did not modulate the occurrence or form of this structure under the conditions tested. This finding nevertheless adds to the repertoire of potential H-DNA structures found in the vicinity of regulatory sequences-here, in an imprinting context.
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Affiliation(s)
- C Davey
- Institute of Cell and Molecular Biology, University of Edinburgh, UK
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8
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Davey C, Fraser R, Smolle M, Simmen MW, Allan J. Nucleosome positioning signals in the DNA sequence of the human and mouse H19 imprinting control regions. J Mol Biol 2003; 325:873-87. [PMID: 12527297 DOI: 10.1016/s0022-2836(02)01340-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We have investigated the sequences of the mouse and human H19 imprinting control regions (ICRs) to see whether they contain nucleosome positioning information pertinent to their function as a methylation-regulated chromatin boundary. Positioning signals were identified by an in vitro approach that employs reconstituted chromatin to comprehensively describe the contribution of the DNA to the most basic, underlying level of chromatin structure. Signals in the DNA sequence of both ICRs directed nucleosomes to flank and encompass the short conserved sequences that constitute the binding sites for the zinc finger protein CTCF, an essential mediator of insulator activity. The repeat structure of the human ICR presented a conserved array of strong positioning signals that would preferentially flank these CTCF binding sites with positioned nucleosomes, a chromatin structure that would tend to maintain their accessibility. Conversely, all four CTCF binding sites in the mouse sequence were located close to the centre of positioning signals that were stronger than those in their flanks; these binding sites might therefore be expected to be more readily incorporated into positioned nucleosomes. We found that CpG methylation did not effect widespread repositioning of nucleosomes on either ICR, indicating that allelic methylation patterns were unlikely to establish allele-specific chromatin structures for H19 by operating directly upon the underlying DNA-histone interactions; instead, epigenetic modulation of ICR chromatin structure is likely to be mediated principally at higher levels of control. DNA methylation did, however, both promote and inhibit nucleosome positioning at several sites in both ICRs and substantially negated one of the strongest nucleosome positioning signals in the human sequence, observations that underline the fact that this epigenetic modification can, nevertheless, directly and decisively modulate core histone-DNA interactions within the nucleosome.
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Affiliation(s)
- C Davey
- Institute of Cell and Molecular Biology, University of Edinburgh, Darwin Building, King's Buildings, West Mains Road, Scotland EH9 3JR, Edinburgh, UK
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9
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Abstract
In mammals, the maternal and paternal genomes are both required for normal embryonic and postnatal development. As a consequence, the majority of genes possess a bi-allelic pattern of expression, with the exception of certain loci where transcription is strictly dependent on parental origin. This alternative, termed genomic imprinting, is an epigenetic form of gene regulation that allows controlled expression of one parental allele. Experimental evidence supports the idea that chromatin organization, DNA methylation, replication timing, genomic domain organization, and more recently methylation-dependent boundary function are key components of imprinting mechanisms. Imprinted genes are mainly required during embryogenesis and development, but loss of controlled imprinting has direct consequences in carcinogenesis. For example, imprinted tumor suppressor genes and proto-oncogenes are highly susceptible to allelic inactivation or in contrast to activation that induces tumorigenic processes. Therefore, genomic imprinting represents one of the more challenging and interesting scientific and medical topics, and especially because a large combinatorial set of possibilities for gene regulation arises from the increasing number of imprinted loci identified.
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Affiliation(s)
- Félix Recillas-Targa
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico.
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Plass C, Soloway PD. DNA methylation, imprinting and cancer. Eur J Hum Genet 2002; 10:6-16. [PMID: 11896451 DOI: 10.1038/sj.ejhg.5200768] [Citation(s) in RCA: 113] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2001] [Revised: 12/05/2001] [Accepted: 12/06/2001] [Indexed: 11/09/2022] Open
Abstract
It is well known that a variety of genetic changes influence the development and progression of cancer. These changes may result from inherited or spontaneous mutations that are not corrected by repair mechanisms prior to DNA replication. It is increasingly clear that so called epigenetic effects that do not affect the primary sequence of the genome also play an important role in tumorigenesis. This was supported initially by observations that cancer genomes undergo changes in their methylation state and that control of parental allele-specific methylation and expression of imprinted loci is lost in several cancers. Many loci acquiring aberrant methylation in cancers have since been identified and shown to be silenced by DNA methylation. In many cases, this mechanism of silencing inactivates tumour suppressors as effectively as frank mutation and is one of the cancer-predisposing hits described in Knudson's two hit hypothesis. In contrast to mutations which are essentially irreversible, methylation changes are reversible, raising the possibility of developing therapeutics based on restoring the normal methylation state to cancer-associated genes. Development of such therapeutics will require identifying loci undergoing methylation changes in cancer, understanding how their methylation influences tumorigenesis and identifying the mechanisms regulating the methylation state of the genome. The purpose of this review is to summarise what is known about these issues.
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Affiliation(s)
- Christoph Plass
- Division of Human Cancer Genetics and the Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA.
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Gregory RI, Randall TE, Johnson CA, Khosla S, Hatada I, O'Neill LP, Turner BM, Feil R. DNA methylation is linked to deacetylation of histone H3, but not H4, on the imprinted genes Snrpn and U2af1-rs1. Mol Cell Biol 2001; 21:5426-36. [PMID: 11463825 PMCID: PMC87265 DOI: 10.1128/mcb.21.16.5426-5436.2001] [Citation(s) in RCA: 106] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The relationship between DNA methylation and histone acetylation at the imprinted mouse genes U2af1-rs1 and Snrpn is explored by chromatin immunoprecipitation (ChIP) and resolution of parental alleles using single-strand conformational polymorphisms. The U2af1-rs1 gene lies within a differentially methylated region (DMR), while Snrpn has a 5' DMR (DMR1) with sequences homologous to the imprinting control center of the Prader-Willi/Angelman region. For both DMR1 of Snrpn and the 5' untranslated region (5'-UTR) and 3'-UTR of U2af1-rs1, the methylated and nonexpressed maternal allele was underacetylated, relative to the paternal allele, at all H3 lysines tested (K14, K9, and K18). For H4, underacetylation of the maternal allele was exclusively (U2af1-rs1) or predominantly (Snrpn) at lysine 5. Essentially the same patterns of differential acetylation were found in embryonic stem (ES) cells, embryo fibroblasts, and adult liver from F1 mice and in ES cells from mice that were dipaternal or dimaternal for U2af1-rs1. In contrast, in a region within Snrpn that has biallelic methylation in the cells and tissues analyzed, the paternal (expressed) allele showed relatively increased acetylation of H4 but not of H3. The methyl-CpG-binding-domain (MBD) protein MeCP2 was found, by ChIP, to be associated exclusively with the maternal U2af1-rs1 allele. To ask whether DNA methylation is associated with histone deacetylation, we produced mice with transgene-induced methylation at the paternal allele of U2af1-rs1. In these mice, H3 was underacetylated across both the parental U2af1-rs1 alleles whereas H4 acetylation was unaltered. Collectively, these data are consistent with the hypothesis that CpG methylation leads to deacetylation of histone H3, but not H4, through a process that involves selective binding of MBD proteins.
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Affiliation(s)
- R I Gregory
- Programme in Developmental Genetics, The Babraham Institute, Cambridge CB2 4AT, United Kingdom
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12
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Sotomaru Y, Kawase Y, Ueda T, Obata Y, Suzuki H, Domeki I, Hatada I, Kono T. Disruption of imprinted expression of U2afbp-rs/U2af1-rs1 gene in mouse parthenogenetic fetuses. J Biol Chem 2001; 276:26694-8. [PMID: 11306578 DOI: 10.1074/jbc.m101367200] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The present study shows that the U2afbp-rs gene, a paternally expressed imprinted gene, is activated and expressed in a biallelic manner from maternal alleles in parthenogenetic mouse fetuses on day 9.5 of gestation. The mean expression was detected to be 88% (31-134%) of that in control biparental fetuses, using real-time quantitative reverse transcription and polymerase chain reaction. This disrupted expression of the gene was associated with changes in the chromatin structure but not with the methylation pattern in the regulation region. The present results show that parental specific expression of imprinted genes is not always maintained in uniparental embryos. This suggests that both parental genomes are necessary to establish parental specific expression of the U2afbp-rs gene.
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Affiliation(s)
- Y Sotomaru
- Department of Animal Science, Tokyo University of Agriculture, 1737, Funako, Atsugi-shi, Kanagawa 243-0034, Japan
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Abstract
Recent studies have focused on the identification of imprinting centers and on the elucidation of the mechanisms by which they control imprinting. These studies begin to shed light on the means by which imprinting marks are established in the gametes and on the various molecular strategies utilized to execute differential expression of the two parental alleles.
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Affiliation(s)
- I Ben-Porath
- Department of Cellular Biochemistry, School of Medicine, The Hebrew University of Jerusalem, 91120, Jerusalem, Israel
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14
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Affiliation(s)
- A P Feinberg
- Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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15
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Sunahara S, Nakamura K, Nakao K, Gondo Y, Nagata Y, Katsuki M. The oocyte-specific methylated region of the U2afbp-rs/U2af1-rs1 gene is dispensable for its imprinted methylation. Biochem Biophys Res Commun 2000; 268:590-5. [PMID: 10679248 DOI: 10.1006/bbrc.2000.2189] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Imprinted genes harbor discrete regions which are differentially methylated in gametes; usually the final differential methylation patterns in adults are established during embryogenesis through modifications of the initial methylation patterns in gametes. Previous reports have shown that a 200-bp region termed region II within the CpG island of the mouse imprinted U2afbp-rs gene is methylated in oocytes but not in sperm, suggesting that this region is a center for the propagation of methylated CpGs on the maternal allele and is also a candidate for an imprinting control element. To determine whether region II is required for the imprinted methylation of this gene at the endogenous locus, we generated mice carrying a deletion of this region. We herein show that parental methylation differences still exist in the CpG island on the region II-deleted allele. These findings suggest that region II is dispensable for the imprinted methylation of the U2afbp-rs gene.
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Affiliation(s)
- S Sunahara
- Division of DNA Biology and Embryo Engineering, CREST, Center for Experimental Medicine, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Tokyo, Minato-ku, 108-8639, Japan
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16
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Schweizer J, Zynger D, Francke U. In vivo nuclease hypersensitivity studies reveal multiple sites of parental origin-dependent differential chromatin conformation in the 150 kb SNRPN transcription unit. Hum Mol Genet 1999; 8:555-66. [PMID: 10072422 DOI: 10.1093/hmg/8.4.555] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Human chromosome region 15q11-q13 contains a cluster of oppositely imprinted genes. Loss of the paternal or the maternal alleles by deletion of the region or by uniparental disomy 15 results in Prader-Willi syndrome (PWS) or Angelman syndrome (AS), respectively. Hence, the two phenotypically distinct neurodevelopmental disorders are caused by the lack of products of imprinted genes. Subsets of PWS and AS patients exhibit 'imprinting mutations', such as small microdeletions within the 5' region of the small nuclear ribonucleoprotein polypeptide N ( SNRPN ) transcription unit which affect the transcriptional activity and methylation status of distant imprinted genes throughout 15q11-q13 in cis. To elucidate the mechanism of these long-range effects, we have analyzed the chromatin structure of the 150 kb SNRPN transcription unit for DNase I- and Msp I-hypersensitive sites. By using an in vivo approach on lymphoblastoid cell lines from PWS and AS individuals, we discovered that the SNRPN exon 1 is flanked by prominent hypersensitive sites on the paternal allele, but is completely inaccessible to nucleases on the maternal allele. In contrast, we identified several regions of increased nuclease hypersensitivity on the maternal allele, one of which coincides with the AS minimal microdeletion region and another lies in intron 1 immediately downstream of the paternal-specific hypersensitive sites. At several sites, parental origin-specific nuclease hypersensitivity was found to be correlated with hypermethylation on the allele contributed by the other parent. The differential parental origin-dependent chromatin conformations might govern access of regulatory protein complexes and/or RNAs which could mediate interaction of the region with other genes.
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Affiliation(s)
- J Schweizer
- Howard Hughes Medical Institute and Department of Genetics, Stanford University School of Medicine, Stanford CA 94305-5323, USA
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17
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Khosla S, Aitchison A, Gregory R, Allen ND, Feil R. Parental allele-specific chromatin configuration in a boundary-imprinting-control element upstream of the mouse H19 gene. Mol Cell Biol 1999; 19:2556-66. [PMID: 10082521 PMCID: PMC84048 DOI: 10.1128/mcb.19.4.2556] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The mouse H19 gene is expressed from the maternal chromosome exclusively. A 2-kb region at 2 to 4 kb upstream of H19 is paternally methylated throughout development, and these sequences are necessary for the imprinted expression of both H19 and the 5'-neighboring Igf2 gene. In particular, on the maternal chromosome this element appears to insulate the Igf2 gene from enhancers located downstream of H19. We analyzed the chromatin organization of this element by assaying its sensitivity to nucleases in nuclei. Six DNase I hypersensitive sites (HS sites) were detected on the unmethylated maternal chromosome exclusively, the two most prominent of which mapped 2.25 and 2.75 kb 5' to the H19 transcription initiation site. Five of the maternal HS sites were present in expressing and nonexpressing tissues and in embryonic stem (ES) cells. They seem, therefore, to reflect the maternal origin of the chromosome rather than the expression of H19. A sixth maternal HS site, at 3.45 kb upstream of H19, was detected in ES cells only. The nucleosomal organization of this element was analyzed in tissues and ES cells by micrococcal nuclease digestion. Specifically on the maternal chromosome, an unusual and strong banding pattern was obtained, suggestive of a nonnucleosomal organization. From our studies, it appears that the unusual chromatin organization with the presence of HS sites (maternal chromosome) and DNA methylation (paternal chromosome) in this element are mutually exclusive and reflect alternate epigenetic states. In addition, our data suggest that nonhistone proteins are associated with the maternal chromosome and that these might be involved in its boundary function.
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Affiliation(s)
- S Khosla
- Programme in Developmental Genetics, The Babraham Institute, Cambridge CB2 4AT, United Kingdom
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18
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Abstract
A number of recent studies have provided new insights into mechanisms that regulate genomic imprinting in the mammalian genome. Regions of allele-specific differential methylation (DMRs) are present in all imprinted genes examined. Differential methylation is erased in germ cells at an early stage of their development, and germ-line-specific methylation imprints in DMRs are reestablished around the time of birth. After fertilization, differential methylation is retained in core DMRs despite genome-wide demethylation and de novo methylation during preimplantation and early postimplantation stages. Direct repeats near CG-rich DMRs may be involved in the establishment and maintenance of allele-specific methylation patterns. Imprinted genes tend to be clustered; one important component of clustering is enhancer competition, whereby promoters of linked imprinted genes compete for access to enhancers. Regional organization and spreading of the epigenotype during development is also important and depends on DMRs and imprinting centers. The mechanism of cis spreading of DNA methylation is not known, but precedent is provided by the Xist RNA, which results in X chromosome inactivation in cis. Reading of the somatic imprints could be carried out by transcription factors that are sensitive to methylation, or by methyl-cytosine-binding proteins that are involved in transcriptional repression through chromatin remodeling.
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Affiliation(s)
- M Constância
- Programme in Developmental Genetics, The Babraham Institute, Cambridge CB2 4AT, UK
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19
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Shibata H, Yoda Y, Kato R, Ueda T, Kamiya M, Hiraiwa N, Yoshiki A, Plass C, Pearsall RS, Held WA, Muramatsu M, Sasaki H, Kusakabe M, Hayashizaki Y. A methylation imprint mark in the mouse imprinted gene Grf1/Cdc25Mm locus shares a common feature with the U2afbp-rs gene: an association with a short tandem repeat and a hypermethylated region. Genomics 1998; 49:30-7. [PMID: 9570946 DOI: 10.1006/geno.1998.5218] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We identified a sperm-specific methylation imprint mark (Site II) associated with a short tandem repeat sequence and a site/region methylated in both gametes (Site I) in the Grf1 locus on mouse chromosome 9, which shared a common feature with the U2afbp-rs gene. Sites or regions of gamete-specific methylation in imprinted genes are strong candidates for carrying information regarding the parental origin of alleles. The gamete-specific methylation pattern of Sites I and II was conserved after fertilization, but attained the somatic cell pattern by the blastocyst stage. In primordial germ cells, Site I was methylated, but Site II was unmethylated in both male and female embryos, suggesting that the sperm-specific methylation imprint mark in Site II was established during spermatogenesis. These common features in methylation imprint regions may be a clue to identifying regions carrying primary information for the imprinting regulation.
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Affiliation(s)
- H Shibata
- Genome Science Laboratory, RIKEN Tsukuba Life Science Center, Ibaraki, Japan
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20
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Affiliation(s)
- R Feil
- Department of Development and Genetics, Babraham Institute, Cambridge, United Kingdom.
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21
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Lefebvre L, Viville S, Barton SC, Ishino F, Surani MA. Genomic structure and parent-of-origin-specific methylation of Peg1. Hum Mol Genet 1997; 6:1907-15. [PMID: 9302270 DOI: 10.1093/hmg/6.11.1907] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
We previously identified Peg1/Mest as a novel paternally expressed gene in the developing mouse embryo. The human PEG1 gene was recently assigned to 7q32 and shown to be imprinted and paternally expressed. Therefore, PEG1 deficiency could participate in the aetiology of pre- and post-natal growth retardation associated with maternal uniparental disomy 7 in humans. We have now initiated the characterization of the Peg1 locus in order to identify and dissect cis-acting elements implicated in its imprinted monoallelic expression. The genomic structure of Peg1 as well as the DNA sequence of the 5'-end of the gene, including 2.4 kb of promoter sequences and covering the first 2 exons, have been determined. Important sequence elements, such as a CpG island spanning exon 1 and direct repeats, are identified and discussed. To address the role of epigenetic modifications in the imprinting of Peg1, a methylation analysis of the Peg1 gene is presented. Partially methylated cytosine residues in 13.5 d.p.c. embryos and undifferentiated ES cells were identified. Using embryos carrying a targetted mutation at the Peg1 locus, we show that this partial promoter methylation pattern reflects a strict parent-of-origin-specific differential methylation: the expressed paternal allele is unmethylated, whereas the silenced maternal allele is fully methylated at the CpG sites studied. That the gametes carry the epigenetic information necessary to lay down this allele-specific methylation pattern is suggested by analysis of DNA isolated from sperm and parthenogenetic embryos.
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Affiliation(s)
- L Lefebvre
- Wellcome/CRC Institute of Cancer and Developmental Biology and Physiological Laboratory, University of Cambridge, UK.
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22
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Shibata H, Ueda T, Kamiya M, Yoshiki A, Kusakabe M, Plass C, Held WA, Sunahara S, Katsuki M, Muramatsu M, Hayashizaki Y. An oocyte-specific methylation imprint center in the mouse U2afbp-rs/U2af1-rs1 gene marks the establishment of allele-specific methylation during preimplantation development. Genomics 1997; 44:171-8. [PMID: 9299233 DOI: 10.1006/geno.1997.4877] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
An oocyte-specific methylation imprint mark region, consisting of approximately 200 bp from the mouse imprinted gene U2afbp-rs, was identified within an area containing a CpG island and a short tandem repeat sequence. The oocyte-specific methylation was preserved in fertilized eggs and then expanded on the repressed maternal allele during preimplantation development until the adult methylation pattern was achieved by 12.5 days of embryonic development. These results indicate that the oocyte-specific imprinting mark region acts as a center in establishing the hypermethylated region on the repressed maternal allele. Furthermore, a region that is hypermethylated in both gametes was identified but its hypermethylation was conserved only on the maternal allele during preimplantation development, suggesting that some factor(s) inherited from oocytes may act to maintain hypermethylation on the maternal allele.
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Affiliation(s)
- H Shibata
- RIKEN Tsukuba Life Science Center, The Institute of Physical and Chemical Research (RIKEN), 3-1-1 Koyadai, Tsukuba, Ibaraki, 305, Japan
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23
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Feil R, Boyano MD, Allen ND, Kelsey G. Parental chromosome-specific chromatin conformation in the imprinted U2af1-rs1 gene in the mouse. J Biol Chem 1997; 272:20893-900. [PMID: 9252416 DOI: 10.1074/jbc.272.33.20893] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The imprinted U2af1-rs1 gene on mouse chromosome 11 is expressed exclusively from the paternal allele. We found that U2af1-rs1 resides in a chromosomal domain that displays marked differences in chromatin conformation and DNA methylation between the parental chromosomes. Chromatin conformation was assayed in brain and liver, in fetuses, and in embryonic stem cells by sensitivity to nucleases in nuclei. In all these tissues, the unmethylated paternal chromosome is sensitive to DNase-I and MspI and has two DNase-I hypersensitive sites in the 5'-untranslated region. In brain and in differentiated stem cells, which display high levels of U2af1-rs1 expression, a paternal DNase-I hypersensitive site is also readily apparent in the promoter region. On the maternal chromosome, in contrast, the entire U2af1-rs1 gene and its promoter are highly resistant to DNase-I and MspI in all tissues analyzed and are fully methylated. No differential MNase sensitivity was detected in this imprinted domain. The parental chromosome-specific DNA methylation and chromatin conformation were also present in parthenogenetic and androgenetic cells and in tissues from animals maternally or paternally disomic for chromosome 11. This demonstrates that these parental chromosome-specific epigenotypes are independently established and maintained and provides no evidence for interallelic trans-sensing and counting mechanisms in U2af1-rs1.
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Affiliation(s)
- R Feil
- Department of Development and Genetics, the Babraham Institute, Cambridge CB2 4AT, United Kingdom.
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24
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Nabetani A, Hatada I, Morisaki H, Oshimura M, Mukai T. Mouse U2af1-rs1 is a neomorphic imprinted gene. Mol Cell Biol 1997; 17:789-98. [PMID: 9001233 PMCID: PMC231805 DOI: 10.1128/mcb.17.2.789] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The mouse U2af1-rs1 gene is an endogenous imprinted gene on the proximal region of chromosome 11. This gene is transcribed exclusively from the unmethylated paternal allele, while the methylated maternal allele is silent. An analysis of genome structure of this gene revealed that the whole gene is located in an intron of the Murr1 gene. Although none of the three human U2af1-related genes have been mapped to chromosome 2, the human homolog of Murr1 is assigned to chromosome 2. The mouse Murr1 gene is transcribed biallelically, and therefore it is not imprinted in neonatal mice. Allele-specific methylation is limited to a region around U2af1-rs1 in an intron of Murr1. These results suggest that in chromosomal homology and genomic imprinting, the U2af1-rs1 gene is distinct from the genome region surrounding it. We have proposed the neomorphic origin of the U2af1-rs1 gene by retrotransposition and the particular mechanism of genomic imprinting of ectopic genes.
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Affiliation(s)
- A Nabetani
- Department of Bioscience, National Cardiovascular Center Research Institute, Suita, Osaka, Japan
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