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Morita Y, Ohno M, Nishi K, Hiraoka Y, Saijo S, Matsuda S, Kita T, Kimura T, Nishi E. Genome-wide profiling of nardilysin target genes reveals its role in epigenetic regulation and cell cycle progression. Sci Rep 2017; 7:14801. [PMID: 29093577 PMCID: PMC5665917 DOI: 10.1038/s41598-017-14942-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 10/18/2017] [Indexed: 11/28/2022] Open
Abstract
Post-translational histone modifications, such as acetylation and methylation, are prerequisites for transcriptional regulation. The metalloendopeptidase nardilysin (Nrdc) is a H3K4me2-binding protein that controls thermoregulation and β-cell functions through its transcriptional coregulator function. We herein combined high-throughput ChIP-seq and RNA-seq to achieve the first genome-wide identification of Nrdc target genes. A ChIP-seq analysis of immortalized mouse embryo fibroblasts (iMEF) identified 4053 Nrdc-binding sites, most of which were located in proximal promoter sites (2587 Nrdc-binding genes). Global H3K4me2 levels at Nrdc-binding promoters slightly increased, while H3K9ac levels decreased in the absence of Nrdc. Among Nrdc-binding genes, a comparative RNA-seq analysis identified 448 candidates for Nrdc target genes, among which cell cycle-related genes were significantly enriched. We confirmed decreased mRNA and H3K9ac levels at the promoters of individual genes in Nrdc-deficient iMEF, which were restored by the ectopic introduction of Nrdc. Reduced mRNA levels, but not H3K9ac levels were fully restored by the reintroduction of the peptidase-dead mutant of Nrdc. Furthermore, Nrdc promoted cell cycle progression at multiple stages, which enhanced cell proliferation in vivo. Collectively, our integrative studies emphasize the importance of Nrdc for maintaining a proper epigenetic status and cell growth.
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Affiliation(s)
- Yusuke Morita
- Department of Cardiovascular Medicine, Kyoto University Graduate School of Medicine, 54 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Mikiko Ohno
- Department of Cardiovascular Medicine, Kyoto University Graduate School of Medicine, 54 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan.,Department of Pharmacology, Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, 520-2192, Japan
| | - Kiyoto Nishi
- Department of Cardiovascular Medicine, Kyoto University Graduate School of Medicine, 54 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Yoshinori Hiraoka
- Division of Clinical Pharmacy, Faculty of Pharmaceutical Sciences, Kobe Gakuin University, Chuo-ku, Kobe, 650-8586, Japan
| | - Sayaka Saijo
- Department of Cardiovascular Medicine, Kyoto University Graduate School of Medicine, 54 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Shintaro Matsuda
- Department of Cardiovascular Medicine, Kyoto University Graduate School of Medicine, 54 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Toru Kita
- Kobe Home Medical and Nursing Care Promotion Foundation, 14-1 Naka Ichiriyama, Kami Aza, Shimotani, Yamada-cho, Kita-ku, Kobe, 651-1102, Japan
| | - Takeshi Kimura
- Department of Cardiovascular Medicine, Kyoto University Graduate School of Medicine, 54 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Eiichiro Nishi
- Department of Pharmacology, Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, 520-2192, Japan.
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Histone H4 lysine 20 acetylation is associated with gene repression in human cells. Sci Rep 2016; 6:24318. [PMID: 27064113 PMCID: PMC4827026 DOI: 10.1038/srep24318] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 03/24/2016] [Indexed: 01/03/2023] Open
Abstract
Histone acetylation is generally associated with gene activation and chromatin decondensation. Recent mass spectrometry analysis has revealed that histone H4 lysine 20, a major methylation site, can also be acetylated. To understand the function of H4 lysine 20 acetylation (H4K20ac), we have developed a specific monoclonal antibody and performed ChIP-seq analysis using HeLa-S3 cells. H4K20ac was enriched around the transcription start sites (TSSs) of minimally expressed genes and in the gene body of expressed genes, in contrast to most histone acetylation being enriched around the TSSs of expressed genes. The distribution of H4K20ac showed little correlation with known histone modifications, including histone H3 methylations. A motif search in H4K20ac-enriched sequences, together with transcription factor binding profiles based on ENCODE ChIP-seq data, revealed that most transcription activators are excluded from H4K20ac-enriched genes and a transcription repressor NRSF/REST co-localized with H4K20ac. These results suggest that H4K20ac is a unique acetylation mark associated with gene repression.
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Fedchenko VI, Kaloshin AA, Mezhevikina LM, Buneeva OA, Medvedev AE. Construction of the coding sequence of the transcription variant 2 of the human Renalase gene and its expression in the prokaryotic system. Int J Mol Sci 2013; 14:12764-79. [PMID: 23783275 PMCID: PMC3709811 DOI: 10.3390/ijms140612764] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 05/23/2013] [Accepted: 06/05/2013] [Indexed: 01/03/2023] Open
Abstract
Renalase is a recently discovered protein, involved in regulation of blood pressure in humans and animals. Although several splice variants of human renalase mRNA transcripts have been recognized, only one protein product, hRenalase1, has been found so far. In this study, we have used polymerase chain reaction (PCR)-based amplification of individual exons of the renalase gene and their joining for construction of full-length hRenalase2 coding sequence followed by expression of hRenalase2 as a polyHis recombinant protein in Escherichia coli cells. To date this is the first report on synthesis and purification of hRenalase2. Applicability of this approach was verified by constructing hRenalase1 coding sequence, its sequencing and expression in E. coli cells. hRenalase1 was used for generation of polyclonal antiserum in sheep. Western blot analysis has shown that polyclonal anti-renalase1 antibodies effectively interact with the hRenalase2 protein. The latter suggests that some functions and expression patterns of hRenalase1 documented by antibody-based data may be attributed to the presence of hRenalase2. The realized approach may be also used for construction of coding sequences of various (especially weakly expressible) genes, their transcript variants, etc.
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Affiliation(s)
- Valerii I. Fedchenko
- Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, 10 Pogodinskaya Street, Moscow 119121, Russia; E-Mails: (V.I.F.); (A.A.K.); ; (O.A.B.)
| | - Alexei A. Kaloshin
- Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, 10 Pogodinskaya Street, Moscow 119121, Russia; E-Mails: (V.I.F.); (A.A.K.); ; (O.A.B.)
| | - Lyudmila M. Mezhevikina
- Institute Cell Biophysics, Russian Academy of Sciences, 3 Institutskaya Street, Pushchino, Moscow Region, Moscow 142290, Russia; E-Mail:
| | - Olga A. Buneeva
- Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, 10 Pogodinskaya Street, Moscow 119121, Russia; E-Mails: (V.I.F.); (A.A.K.); ; (O.A.B.)
| | - Alexei E. Medvedev
- Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, 10 Pogodinskaya Street, Moscow 119121, Russia; E-Mails: (V.I.F.); (A.A.K.); ; (O.A.B.)
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Russanova VR, Hirai TH, Howard BH. Semirandom sampling to detect differentiation-related and age-related epigenome remodeling. J Gerontol A Biol Sci Med Sci 2005; 59:1221-33. [PMID: 15699521 DOI: 10.1093/gerona/59.12.1221] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
With completion of the human genome project, patterns of higher order chromatin structure can be easily related to other features of genome organization. A well-studied aspect of chromatin, histone H4 acetylation, is examined here on the basis of its role in setting competence for gene activation. Three applications of a new hybrid genome sampling-chromatin immunoprecipitation strategy are described. The first explores aspects of epigenome architecture in human fibroblasts. A second focuses on chromatin from HL-60 promyelocytic leukemia cells before and after differentiation into macrophage-like cells. A third application explores age-related epigenome change. In the latter, acetylation patterns are compared in human skin fibroblast chromatin from donors of various ages. Two sites are reported at which observed histone H4 acetylation differences suggest decreasing acetylation over time. The sites, located in chromosome 4p16.1 and 4q35.2 regions, appear to remodel during late fetal-early child development and from preadolescence through adult life, respectively.
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Affiliation(s)
- Valya R Russanova
- National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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Morrison H, Jeppesen P. Allele-specific underacetylation of histone H4 downstream from promoters is associated with X-inactivation in human cells. Chromosome Res 2003; 10:579-95. [PMID: 12498347 DOI: 10.1023/a:1020966719605] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We have used a novel approach to investigate the histone H4 acetylation status at X-inactivated genes compared with their active counterparts. Immunoprecipitation with a sheep antibody that preferentially binds multiply-acetylated H4 isoforms was used to select hyperacetylated chromatin from a human female lymphoblastoid cell line exhibiting non-random X-inactivation as a result of an X/autosome translocation. The distribution of active and inactive gene sequences between the immunoprecipitated and bulk chromatin was compared at four X-linked loci containing intragenic polymorphic microsatellite repeats to allow identification of individual alleles by polymerase chain reaction. We find that DNA sequences corresponding to transcriptionally silent alleles are consistently under-represented in the hyperacetylated fraction. As the microsatellite repeat sequences used to identify alleles range in distance from 6.5 kb to 25 kb downstream of promoters, we conclude that differential H4 acetylation of active and silent chromatin is not confined to regions involved in the initiation of transcription, contrary to previous reports.
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Affiliation(s)
- Harris Morrison
- MRC Human Genetics Unit, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, Scotland, UK
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Abstract
The transition to malignancy requires an extensive reconfiguration of the genome's expression program that does not result entirely from actual changes in primary DNA sequence-i.e., mutation. Epigenetic-meta-DNA-gene expression states result from an assembly over a given locus of a poorly understood nucleoprotein entity that includes histones and other architectural components of chromatin, nonhistone DNA-bound regulators, and additional chromatin-bound polypeptides. This structure is rapidly reestablished in the wake of the DNA replication fork, thus ensuring its persistence in rapidly proliferating cells and thereby yielding an exceptionally stable mode of gene expression. Chromatin is the perfect vehicle for enabling such genome control. During S phase both covalently modified histones and histone-associated regulatory proteins distribute to the newly synthesized daughter chromatids in a form of "molecular dowry" inherited from the G(1) state of the genome, and impose a specific mode of function on the underlying DNA. An extensively studied example of chromatin-based epigenetic inheritance connects DNA methylation to the targeting of chromatin remodeling and modification. In a broad sense, however, genome reprogramming in cancer is associated with the remodeling of a multitude of regulatory DNA stretches-e.g., promoters, enhancers, locus control regions (LCRs), insulators, etc.-into a specific chromatin architecture. This architectural entity provides a general molecular signature of the cancer epigenome that complements and significantly expands its DNA methylation-based component.
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Affiliation(s)
- Fyodor D Urnov
- Sangamo BioSciences, Inc., Point Richmond Tech Center, 501 Canal Boulevard, Suite A100, Richmond, California 94804, USA.
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Ruminy P, Derambure C, Chandrasegaran S, Salier JP. Long-range identification of hepatocyte nuclear factor-3 (FoxA) high and low-affinity binding sites with a chimeric nuclease. J Mol Biol 2001; 310:523-35. [PMID: 11439020 DOI: 10.1006/jmbi.2001.4788] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Identifying the complete set of transcription factors that bind the promoter and other regulatory regions of a gene of interest is an essential step in functional genomics. We have developed an original assay for the systematic detection of hepatocyte nuclear factor-3 (HNF-3) binding sites within cloned promoters. This assay is based on expression of a recombinant enzyme, HNF-3beta/FN, that is comprised of the rat HNF-3beta DNA-binding domain and the non-specific nuclease domain of the FokI restriction enzyme. Southern analysis of target plasmids with proven HNF-3 binding sites showed that HNF-3beta/FN was able to specifically cut both DNA strands in the vicinity of these binding sites, whereas mutagenized binding sites were no longer cleaved. Likewise, as yet undescribed HNF-3 binding sites were detected easily over a distance spanning several thousand bases. The functionality of such binding sites was confirmed by electromobility shift assay. Furthermore, the extent of cleavage by HNF-3beta/FN at a given binding site was tightly correlated with the affinity of a natural HNF-3beta molecule for this site. This novel approach can be extended to other transcription factors for long-range identification of functional transcription factor binding sites in genes.
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Affiliation(s)
- P Ruminy
- INSERM Unit 519 and Institut Fédératif de Recherches Multidisciplinaires sur les Peptides, Faculté de Médecine-Pharmacie, 22 Boulevard Gambetta, Rouen cedex, 76183, France
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