1
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van Breugel ME, Gerber A, van Leeuwen F. The choreography of chromatin in RNA polymerase III regulation. Biochem Soc Trans 2024; 52:1173-1189. [PMID: 38666598 DOI: 10.1042/bst20230770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/17/2024] [Accepted: 04/18/2024] [Indexed: 06/27/2024]
Abstract
Regulation of eukaryotic gene expression involves a dynamic interplay between the core transcriptional machinery, transcription factors, and chromatin organization and modification. While this applies to transcription by all RNA polymerase complexes, RNA polymerase III (RNAPIII) seems to be atypical with respect to its mechanisms of regulation. One distinctive feature of most RNAPIII transcribed genes is that they are devoid of nucleosomes, which relates to the high levels of transcription. Moreover, most of the regulatory sequences are not outside but within the transcribed open chromatin regions. Yet, several lines of evidence suggest that chromatin factors affect RNAPIII dynamics and activity and that gene sequence alone does not explain the observed regulation of RNAPIII. Here we discuss the role of chromatin modification and organization of RNAPIII transcribed genes and how they interact with the core transcriptional RNAPIII machinery and regulatory DNA elements in and around the transcribed genes.
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Affiliation(s)
- Maria Elize van Breugel
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam 1066 CX, The Netherlands
| | - Alan Gerber
- Department of Neurosurgery, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam 1081HV, The Netherlands
- Cancer Center Amsterdam, Cancer Biology, Amsterdam 1081HV, The Netherlands
| | - Fred van Leeuwen
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam 1066 CX, The Netherlands
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam 1105 AZ, The Netherlands
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2
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Sizer RE, Butterfield SP, Hancocks LA, Gato De Sousa L, White RJ. Selective Occupation by E2F and RB of Loci Expressed by RNA Polymerase III. Cancers (Basel) 2024; 16:481. [PMID: 38339234 PMCID: PMC10854548 DOI: 10.3390/cancers16030481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/15/2024] [Accepted: 01/15/2024] [Indexed: 02/12/2024] Open
Abstract
In all cases tested, TFIIIB is responsible for recruiting pol III to its genetic templates. In mammalian cells, RB binds TFIIIB and prevents its interactions with both promoter DNA and pol III, thereby suppressing transcription. As TFIIIB is not recruited to its target genes when bound by RB, the mechanism predicts that pol III-dependent templates will not be occupied by RB; this contrasts with the situation at most genes controlled by RB, where it can be tethered by promoter-bound sequence-specific DNA-binding factors such as E2F. Contrary to this prediction, however, ChIP-seq data reveal the presence of RB in multiple cell types and the related protein p130 at many loci that rely on pol III for their expression, including RMRP, RN7SL, and a variety of tRNA genes. The sets of genes targeted varies according to cell type and growth state. In such cases, recruitment of RB and p130 can be explained by binding of E2F1, E2F4 and/or E2F5. Genes transcribed by pol III had not previously been identified as common targets of E2F family members. The data provide evidence that E2F may allow for the selective regulation of specific non-coding RNAs by RB, in addition to its influence on overall pol III output through its interaction with TFIIIB.
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Affiliation(s)
| | | | | | | | - Robert J. White
- Department of Biology, University of York, York YO10 5DD, UK; (R.E.S.)
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3
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Zuzina AB, Vinarskaya AK, Balaban PM. DNA Methylation Inhibition Reversibly Impairs the Long-Term Context Memory Maintenance in Helix. Int J Mol Sci 2023; 24:14068. [PMID: 37762369 PMCID: PMC10531757 DOI: 10.3390/ijms241814068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/08/2023] [Accepted: 09/10/2023] [Indexed: 09/29/2023] Open
Abstract
This work aims to study the epigenetic mechanisms of regulating long-term context memory in the gastropod mollusk: Helix. We have shown that RG108, an inhibitor of DNA methyltransferase (DNMT), impaired long-term context memory in snails, and this impairment can be reversed within a limited time window: no more than 48 h. Research on the mechanisms through which the long-term context memory impaired by DNMT inhibition could be reinstated demonstrated that this effect depends on several biochemical mechanisms: nitric oxide synthesis, protein synthesis, and activity of the serotonergic system. Memory recovery did not occur if at least one of these mechanisms was impaired. The need for the joint synergic activity of several biochemical systems for a successful memory rescue confirms the assumption that the memory recovery process depends on the process of active reconsolidation, and is not simply a passive weakening of the effect of RG108 over time. Finally, we showed that the reactivation of the impaired memory by RG108, followed by administration of histone deacetylase inhibitor sodium butyrate, led to memory recovery only within a narrow time window: no more than 48 h after memory disruption.
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Affiliation(s)
| | | | - Pavel M. Balaban
- Cellular Neurobiology of Learning Lab, Institute of Higher Nervous Activity and Neurophysiology, Russian Academy of Sciences, 5A Butlerova St., Moscow 117485, Russia; (A.B.Z.); (A.K.V.)
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4
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Qian S, Shi C, Huang S, Yang C, Luo Y. DNA methyltransferase activity in the basolateral amygdala is critical for reconsolidation of a heroin reward memory. Front Mol Neurosci 2022; 15:1002139. [PMID: 36176958 PMCID: PMC9513049 DOI: 10.3389/fnmol.2022.1002139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 08/18/2022] [Indexed: 11/17/2022] Open
Abstract
The persistence of drug memory contributes to relapse to drug seeking. The association between repeated drug exposure and drug-related cues leads to cravings triggered by drug-paired cues. The erasure of drug memories has been considered a promising way to inhibit cravings and prevent relapse. The re-exposure to drug-related cues destabilizes well-consolidated drug memories, during which a de novo protein synthesis-dependent process termed “reconsolidation” occurs to restabilize the reactivated drug memory. Disrupting reconsolidation of drug memories leads to the attenuation of drug-seeking behavior in both animal models and people with addictions. Additionally, epigenetic mechanisms regulated by DNA methyltransferase (DNMT) are involved in the reconsolidation of fear and cocaine reward memory. In the present study, we investigated the role of DNMT in the reconsolidation of heroin reward memory. In the heroin self-administration model in rats, we tested the effects of DNMT inhibition during the reconsolidation process on cue-induced reinstatement, heroin-priming-induced reinstatement, and spontaneous recovery of heroin-seeking behavior. We found that the bilateral infusion of 5-azacytidine (5-AZA) inhibiting DNMT into the basolateral amygdala (BLA) immediately after heroin reward memory retrieval, but not delayed 6 h after retrieval or without retrieval, decreased subsequent cue-induced and heroin-priming-induced reinstatement of heroin-seeking behavior. These findings demonstrate that inhibiting the activity of DNMT in BLA during the reconsolidation of heroin reward memory attenuates heroin-seeking behavior, which may provide a potential strategy for the therapeutic of heroin addiction.
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Affiliation(s)
- Shuyi Qian
- Department of Nephrology and Laboratory of Kidney Disease, Hunan Provincial People’s Hospital, Hunan Normal University, Changsha, China
| | - Cuijie Shi
- Hunan Province People’s Hospital, The First-Affiliated Hospital of Hunan Normal University, Changsha, China
| | - Shihao Huang
- National Institute on Drug Dependence, Beijing Key Laboratory of Drug Dependence, Peking University, Beijing, China
| | - Chang Yang
- Hunan Province People’s Hospital, The First-Affiliated Hospital of Hunan Normal University, Changsha, China
| | - Yixiao Luo
- Hunan Province People’s Hospital, The First-Affiliated Hospital of Hunan Normal University, Changsha, China
- *Correspondence: Yixiao Luo,
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5
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Epigenetic regulation of human non-coding RNA gene transcription. Biochem Soc Trans 2022; 50:723-736. [PMID: 35285478 DOI: 10.1042/bst20210860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/18/2022] [Accepted: 02/21/2022] [Indexed: 12/12/2022]
Abstract
Recent investigations on the non-protein-coding transcriptome of human cells have revealed previously hidden layers of gene regulation relying on regulatory non-protein-coding (nc) RNAs, including the widespread ncRNA-dependent regulation of epigenetic chromatin states and of mRNA translation and stability. However, despite its centrality, the epigenetic regulation of ncRNA genes has received relatively little attention. In this mini-review, we attempt to provide a synthetic account of recent literature suggesting an unexpected complexity in chromatin-dependent regulation of ncRNA gene transcription by the three human nuclear RNA polymerases. Emerging common features, like the heterogeneity of chromatin states within ncRNA multigene families and their influence on 3D genome organization, point to unexplored issues whose investigation could lead to a better understanding of the whole human epigenomic network.
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6
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Park JL, Lee YS, Kunkeaw N, Kim SY, Kim IH, Lee YS. Epigenetic regulation of noncoding RNA transcription by mammalian RNA polymerase III. Epigenomics 2017; 9:171-187. [PMID: 28112569 DOI: 10.2217/epi-2016-0108] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
RNA polymerase III (Pol III) synthesizes a range of medium-sized noncoding RNAs (collectively 'Pol III genes') whose early established biological roles were so essential that they were considered 'housekeeping genes'. Besides these fundamental functions, diverse unconventional roles of mammalian Pol III genes have recently been recognized and their expression must be exquisitely controlled. In this review, we summarize the epigenetic regulation of Pol III genes by chromatin structure, histone modification and CpG DNA methylation. We also recapitulate the association between dysregulation of Pol III genes and diseases such as cancer and neurological disorders. Additionally, we will discuss why in-depth molecular studies of Pol III genes have not been attempted and how nc886, a Pol III gene, may resolve this issue.
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Affiliation(s)
- Jong-Lyul Park
- Personalized Genomic Medicine Research Center, KRIBB, Daejeon 305-806, Korea.,Department of Functional Genomics, University of Science & Technology, Daejeon 305-806, Korea
| | - Yeon-Su Lee
- Cancer Genomics Branch, Research Institute, National Cancer Center, Goyang 10408, Korea
| | - Nawapol Kunkeaw
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555-1072, USA.,Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - Seon-Young Kim
- Personalized Genomic Medicine Research Center, KRIBB, Daejeon 305-806, Korea.,Department of Functional Genomics, University of Science & Technology, Daejeon 305-806, Korea
| | - In-Hoo Kim
- Graduate School of Cancer Science & Policy, National Cancer Center, Goyang 10408, Korea
| | - Yong Sun Lee
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555-1072, USA.,Graduate School of Cancer Science & Policy, National Cancer Center, Goyang 10408, Korea
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7
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Park JL, Lee YS, Song MJ, Hong SH, Ahn JH, Seo EH, Shin SP, Lee SJ, Johnson BH, Stampfer MR, Kim HP, Kim SY, Lee YS. Epigenetic regulation of RNA polymerase III transcription in early breast tumorigenesis. Oncogene 2017; 36:6793-6804. [PMID: 28846112 DOI: 10.1038/onc.2017.285] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Revised: 06/13/2017] [Accepted: 07/03/2017] [Indexed: 02/07/2023]
Abstract
RNA polymerase III (Pol III) transcribes medium-sized non-coding RNAs (collectively termed Pol III genes). Emerging diverse roles of Pol III genes suggest that individual Pol III genes are exquisitely regulated by transcription and epigenetic factors. Here we report global Pol III expression/methylation profiles and molecular mechanisms of Pol III regulation that have not been as extensively studied, using nc886 as a representative Pol III gene. In a human mammary epithelial cell system that recapitulates early breast tumorigenesis, the fraction of actively transcribed Pol III genes increases reaching a plateau during immortalization. Hyper-methylation of Pol III genes inhibits Pol III binding to DNA via inducing repressed chromatin and is a determinant for the Pol III repertoire. When Pol III genes are hypo-methylated, MYC amplifies their transcription, regardless of its recognition DNA motif. Thus, Pol III expression during tumorigenesis is delineated by methylation and magnified by MYC.
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Affiliation(s)
- J-L Park
- Personalized Genomic Medicine Research Center, KRIBB, Daejeon, Korea.,Department of Functional Genomics, University of Science and Technology, Daejeon, Korea
| | - Y-S Lee
- Rare Cancer Branch, Research Institute, National Cancer Center, Goyang-si, Korea
| | - M-J Song
- Department of Environmental Medical Biology, Yonsei University College of Medicine, Seoul, Korea
| | - S-H Hong
- Rare Cancer Branch, Research Institute, National Cancer Center, Goyang-si, Korea
| | - J-H Ahn
- Department of Life and Nanopharmaceutical Sciences and Department of Oriental Pharmacy, Kyung Hee University, Seoul, Korea
| | - E-H Seo
- Personalized Genomic Medicine Research Center, KRIBB, Daejeon, Korea.,Department of Functional Genomics, University of Science and Technology, Daejeon, Korea
| | - S-P Shin
- Immunotherapeutics Branch, Research Institute, National Cancer Center, Goyang-si, Korea
| | - S-J Lee
- Immunotherapeutics Branch, Research Institute, National Cancer Center, Goyang-si, Korea
| | - B H Johnson
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, USA
| | - M R Stampfer
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - H-P Kim
- Department of Environmental Medical Biology, Yonsei University College of Medicine, Seoul, Korea.,Institute of Tropical Medicine, Yonsei University College of Medicine, Seoul, Korea.,Brain Korea 21 Plus Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - S-Y Kim
- Personalized Genomic Medicine Research Center, KRIBB, Daejeon, Korea.,Department of Functional Genomics, University of Science and Technology, Daejeon, Korea
| | - Y S Lee
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, USA.,Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
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8
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Interplay between epigenetics and metabolism in oncogenesis: mechanisms and therapeutic approaches. Oncogene 2017; 36:3359-3374. [PMID: 28092669 PMCID: PMC5485177 DOI: 10.1038/onc.2016.485] [Citation(s) in RCA: 181] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 11/07/2016] [Accepted: 11/07/2016] [Indexed: 02/06/2023]
Abstract
Epigenetic and metabolic alterations in cancer cells are highly intertwined. Oncogene-driven metabolic rewiring modifies the epigenetic landscape via modulating the activities of DNA and histone modification enzymes at the metabolite level. Conversely, epigenetic mechanisms regulate the expression of metabolic genes, thereby altering the metabolome. Epigenetic-metabolomic interplay has a critical role in tumourigenesis by coordinately sustaining cell proliferation, metastasis and pluripotency. Understanding the link between epigenetics and metabolism could unravel novel molecular targets, whose intervention may lead to improvements in cancer treatment. In this review, we summarized the recent discoveries linking epigenetics and metabolism and their underlying roles in tumorigenesis; and highlighted the promising molecular targets, with an update on the development of small molecule or biologic inhibitors against these abnormalities in cancer.
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9
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Diette N, Koo J, Cabarcas-Petroski S, Schramm L. Gender Specific Differences in RNA Polymerase III Transcription. ACTA ACUST UNITED AC 2016; 7. [PMID: 27158556 DOI: 10.4172/2157-2518.1000251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
BACKGROUND RNA polymerase (pol) III transcribes a variety of untranslated RNAs responsible for regulating cellular growth and is deregulated in a variety of cancers. In this study, we examined gender differences in RNA pol III transcription in vitro and in vivo. METHODS Expression levels of U6 snRNA, tMet, and known modulators of RNA pol III transcription were assayed in male and female derived adenocarcinoma (AC) lung cancer cell lines and male and female C57BL/6J mice using real time quantitative PCR. Methylation status of the U6 snRNA promoter was determined for lung and liver tissue isolated from male and female C57BL/6J mice by digesting genomic DNA with methylation sensitive restriction enzymes and digestion profiles were analyzed by qPCR using primers spanning the U6 promoter. RESULTS Here, we demonstrate that RNA pol III transcription is differentially regulated by EGCG in male and female derived AC lung cancer cell lines. Basal RNA pol III transcript levels are significantly different in male and female derived AC lung cancer cell lines. These data prompted an investigation of gender specific differences in RNA pol III transcription in vivo in lung and liver tissue. Herein, we report that U6 snRNA RNA pol III transcription is significantly stimulated in the liver tissue of male C57BL/6J mice. Further, the increase in U6 transcription correlates with a significant inhibition in the expression of p53, a negative regulator of RNA pol III transcription, and demethylation of the U6 promoter in the liver tissue of male C57BL/6J mice. CONCLUSIONS To the best of our knowledge, this is the first study demonstrating gender specific differences in RNA pol III transcription both in vivo and in vitro and further highlights the need to include both male and female cell lines and animals in experimental design.
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Affiliation(s)
- N Diette
- Department of Biological Sciences, St. John's University, Queens, New York, 11439, USA
| | - J Koo
- Department of Biological Sciences, St. John's University, Queens, New York, 11439, USA
| | - S Cabarcas-Petroski
- Pennsylvania State University, Beaver Campus, Monaca, Pennsylvania, 15061 USA
| | - L Schramm
- Department of Biological Sciences, St. John's University, Queens, New York, 11439, USA
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10
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Inhibition of DNA methyltransferase as a novel therapeutic strategy to overcome acquired resistance to dual PI3K/mTOR inhibitors. Oncotarget 2016; 6:5134-46. [PMID: 25762617 PMCID: PMC4467138 DOI: 10.18632/oncotarget.3016] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 12/31/2014] [Indexed: 12/24/2022] Open
Abstract
Dual PI3K/mTOR(phosphatidylinositol 3-kinase/mammalian target of rapamycin) inhibitors are being evaluated clinically for the treatment of tumors with a hyperactivated PI3K/mTOR pathway. However, unexpected outcomes were obtained in clinical studies of cancer patients with an aberrant PI3K pathway. In clinical trials, applicable combination regimens are not yet available. In this study, using an integrated analysis of acquired BEZ235-resistant nasopharyngeal carcinoma cells, we demonstrate that DNA methyltransferase is a key modulator and a common node upstream of the AKT/mTOR and PDK1/MYC pathways, which are activated in cancer cells with acquired BEZ235 resistance. DNA methyltransferases were upregulated and induced PTEN and PPP2R2B gene hypermethylation, which downregulated their expression in BEZ235-resistant cancer cells. Reduced PTEN and PPP2R2B expression correlated with activated AKT/mTOR and PDK1/MYC pathways and conferred considerable BEZ235 resistance in nasopharyngeal carcinoma. Targeting methyltransferases in combination with BEZ235 sensitized BEZ235-resistant cells to BEZ235 in vitro and in vivo, suggesting the potential clinical application of this strategy to overcome BEZ235 resistance.
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11
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Arya D, Kapoor S, Kapoor M. Physcomitrella patens DNA methyltransferase 2is required for recovery from salt and osmotic stress. FEBS J 2016; 283:556-70. [DOI: 10.1111/febs.13611] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 11/06/2015] [Accepted: 11/25/2015] [Indexed: 01/22/2023]
Affiliation(s)
- Deepshikha Arya
- University School of Biotechnology; Guru Gobind Singh Indraprastha University; New Delhi India
| | - Sanjay Kapoor
- Department of Plant Molecular Biology; Interdisciplinary Centre for Plant Genomics; University of Delhi; India
| | - Meenu Kapoor
- University School of Biotechnology; Guru Gobind Singh Indraprastha University; New Delhi India
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12
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Dumay-Odelot H, Durrieu-Gaillard S, El Ayoubi L, Parrot C, Teichmann M. Contributions of in vitro transcription to the understanding of human RNA polymerase III transcription. Transcription 2015; 5:e27526. [PMID: 25764111 DOI: 10.4161/trns.27526] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Human RNA polymerase III transcribes small untranslated RNAs that contribute to the regulation of essential cellular processes, including transcription, RNA processing and translation. Analysis of this transcription system by in vitro transcription techniques has largely contributed to the discovery of its transcription factors and to the understanding of the regulation of human RNA polymerase III transcription. Here we review some of the key steps that led to the identification of transcription factors and to the definition of minimal promoter sequences for human RNA polymerase III transcription.
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Affiliation(s)
- Hélène Dumay-Odelot
- a INSERM U869; University of Bordeaux; Institut Européen de Chimie et Biologie (IECB); 33607 Pessac, France
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13
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Lou G, Ma N, Xu Y, Jiang L, Yang J, Wang C, Jiao Y, Gao X. Differential distribution of U6 (RNU6-1) expression in human carcinoma tissues demonstrates the requirement for caution in the internal control gene selection for microRNA quantification. Int J Mol Med 2015; 36:1400-8. [PMID: 26352225 DOI: 10.3892/ijmm.2015.2338] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Accepted: 08/24/2015] [Indexed: 11/06/2022] Open
Abstract
Alterations in microRNA (miRNA) expression patterns have been associated with a number of human diseases. Accurate quantitation of miRNA levels is important for their use as biomarkers and in determining their functions. Although the issue of proper miRNA detection was solved with the introduction of standard reverse transcription‑quantitative polymerase chain reaction (RT‑qPCR) assays, numerous issues with the selection of appropriate internal control genes remain. U6 (RNU6‑1) snRNA, the most commonly used internal control gene in miRNA RT‑qPCR assays, was shown to be unstable in clinical samples, particularly cancer tissues. Identification of the distribution of U6 in different tissues is the premise of more accurate quantification of miRNAs. However, the distribution of U6 in human carcinoma tissues and corresponding normal tissues is unknown. In the present study, U6 levels were significantly higher in human breast carcinoma tissues compared with the corresponding normal tissues by RT‑qPCR. In the carcinoma or corresponding adjacent normal tissues, the expression levels of U6 in epithelial cells were higher than those in the mesenchymal cells. Furthermore, the expression levels of U6 in the carcinoma tissues of the liver and intrahepatic bile ducts were higher than those in the adjacent normal tissues. These results suggest that the expression and distribution of U6 exhibits a high degree of variability among several types of human cells. Therefore, caution is required when selecting U6 as an internal control gene for evaluating expression profiles of miRNAs in patients with carcinoma, particularly carcinoma of the liver and intrahepatic bile ducts.
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Affiliation(s)
- Ge Lou
- Department of Pathology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, P.R. China
| | - Ning Ma
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin 150081, P.R. China
| | - Ya Xu
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin 150081, P.R. China
| | - Lei Jiang
- Department of Pathology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, P.R. China
| | - Jing Yang
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin 150081, P.R. China
| | - Chuxuan Wang
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin 150081, P.R. China
| | - Yufei Jiao
- Department of Pathology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, P.R. China
| | - Xu Gao
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin 150081, P.R. China
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14
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Shi HS, Luo YX, Yin X, Wu HH, Xue G, Geng XH, Hou YN. Reconsolidation of a cocaine associated memory requires DNA methyltransferase activity in the basolateral amygdala. Sci Rep 2015; 5:13327. [PMID: 26289919 PMCID: PMC4542613 DOI: 10.1038/srep13327] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 07/22/2015] [Indexed: 11/14/2022] Open
Abstract
Drug addiction is considered an aberrant form of learning, and drug-associated memories evoked by the presence of associated stimuli (drug context or drug-related cues) contribute to recurrent craving and reinstatement. Epigenetic changes mediated by DNA methyltransferase (DNMT) have been implicated in the reconsolidation of fear memory. Here, we investigated the role of DNMT activity in the reconsolidation of cocaine-associated memories. Rats were trained over 10 days to intravenously self-administer cocaine by nosepokes. Each injection was paired with a light/tone conditioned stimulus (CS). After acquisition of stable self-administration behaviour, rats underwent nosepoke extinction (10 d) followed by cue-induced reactivation and subsequent cue-induced and cocaine-priming + cue-induced reinstatement tests or subsequently tested to assess the strength of the cocaine-associated cue as a conditioned reinforcer to drive cocaine seeking behaviour. Bilateral intra-basolateral amygdala (BLA) infusion of the DNMT inhibitor5-azacytidine (5-AZA, 1 μg per side) immediately following reactivation decreased subsequent reinstatement induced by cues or cocaine priming as well as cue-maintained cocaine-seeking behaviour. In contrast, delayed intra-BLA infusion of 5-AZA 6 h after reactivation or 5-AZA infusion without reactivation had no effect on subsequent cue-induced reinstatement. These findings indicate that memory reconsolidation for a cocaine-paired stimulus depends critically on DNMT activity in the BLA.
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Affiliation(s)
- Hai-Shui Shi
- Department of Pharmacy, Bethune International Peace Hospital of PLA, Shijiazhuang 050082, China
- Department of Biochemistry and Molecular Biology, Basic Medical College, Hebei Medical University, Shijiazhuang 050017, China
| | - Yi-Xiao Luo
- Department of Pharmacology, Medical College of Hunan Normal University, Changsha 410013, China
| | - Xi Yin
- Department of Diagnosis Region of Function, Hebei Medical University Fourth Hospital, Hebei Medical University, Shijiazhuang, Hebei province, 050011
| | - Hong-Hai Wu
- Department of Pharmacy, Bethune International Peace Hospital of PLA, Shijiazhuang 050082, China
| | - Gai Xue
- Department of Pharmacy, Bethune International Peace Hospital of PLA, Shijiazhuang 050082, China
| | - Xu-Hong Geng
- Department of Diagnosis Region of Function, Hebei Medical University Fourth Hospital, Hebei Medical University, Shijiazhuang, Hebei province, 050011
| | - Yan-Ning Hou
- Department of Pharmacy, Bethune International Peace Hospital of PLA, Shijiazhuang 050082, China
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15
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Sadeghifar F, Böhm S, Vintermist A, Östlund Farrants AK. The B-WICH chromatin-remodelling complex regulates RNA polymerase III transcription by promoting Max-dependent c-Myc binding. Nucleic Acids Res 2015; 43:4477-90. [PMID: 25883140 PMCID: PMC4482074 DOI: 10.1093/nar/gkv312] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Accepted: 03/27/2015] [Indexed: 01/11/2023] Open
Abstract
The chromatin-remodelling complex B-WICH, comprised of William syndrome transcription factor, the ATPase SNF2h and nuclear myosin, specifically activates RNA polymerase III transcription of the 5S rRNA and 7SL genes. However, the underlying mechanism is unknown. Using high-resolution MN walking we demonstrate here that B-WICH changes the chromatin structure in the vicinity of the 5S rRNA and 7SL RNA genes during RNA polymerase III transcription. The action of B-WICH is required for the binding of the RNA polymerase machinery and the regulatory factors c-Myc at the 5S rRNA and 7SL RNA genes. In addition to the c-Myc binding site at the 5S genes, we have revealed a novel c-Myc and Max binding site in the intergenic spacer of the 5S rDNA. This region also contains a region remodelled by B-WICH. We demonstrate that c-Myc binds to both sites in a Max-dependent way, and thereby activate transcription by acetylating histone H3. The novel binding patterns of c-Myc and Max link transcription of 5S rRNA to the Myc/Max/Mxd network. Since B-WICH acts prior to c-Myc and other factors, we propose a model in which the B-WICH complex is required to maintain an open chromatin structure at these RNA polymerase III genes. This is a prerequisite for the binding of additional regulatory factors.
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Affiliation(s)
- Fatemeh Sadeghifar
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Sweden
| | - Stefanie Böhm
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Sweden
| | - Anna Vintermist
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Sweden
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16
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SINE transcription by RNA polymerase III is suppressed by histone methylation but not by DNA methylation. Nat Commun 2015; 6:6569. [PMID: 25798578 PMCID: PMC4382998 DOI: 10.1038/ncomms7569] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 02/03/2015] [Indexed: 12/31/2022] Open
Abstract
Short interspersed nuclear elements (SINEs), such as Alu, spread by retrotransposition, which requires their transcripts to be copied into DNA and then inserted into new chromosomal sites. This can lead to genetic damage through insertional mutagenesis and chromosomal rearrangements between non-allelic SINEs at distinct loci. SINE DNA is heavily methylated and this was thought to suppress its accessibility and transcription, thereby protecting against retrotransposition. Here we provide several lines of evidence that methylated SINE DNA is occupied by RNA polymerase III, including the use of high-throughput bisulphite sequencing of ChIP DNA. We find that loss of DNA methylation has little effect on accessibility of SINEs to transcription machinery or their expression in vivo. In contrast, a histone methyltransferase inhibitor selectively promotes SINE expression and occupancy by RNA polymerase III. The data suggest that methylation of histones rather than DNA plays a dominant role in suppressing SINE transcription.
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17
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Cao J. The functional role of long non-coding RNAs and epigenetics. Biol Proced Online 2014; 16:11. [PMID: 25276098 PMCID: PMC4177375 DOI: 10.1186/1480-9222-16-11] [Citation(s) in RCA: 249] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 09/06/2014] [Indexed: 02/07/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are non-protein coding transcripts longer than 200 nucleotides. The post-transcriptional regulation is influenced by these lncRNAs by interfering with the microRNA pathways, involving in diverse cellular processes. The regulation of gene expression by lncRNAs at the epigenetic level, transcriptional and post-transcriptional level have been well known and widely studied. Recent recognition that lncRNAs make effects in many biological and pathological processes such as stem cell pluripotency, neurogenesis, oncogenesis and etc. This review will focus on the functional roles of lncRNAs in epigenetics and related research progress will be summarized.
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Affiliation(s)
- Jinneng Cao
- Department of respiratory medicine, Fuyong People's Hospital, Baoan District, Shenzhen 518103, Guangdong, People's Republic of China
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18
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Lee KS, Park JL, Lee K, Richardson LE, Johnson BH, Lee HS, Lee JS, Kim SB, Kwon OH, Song KS, Kim YS, Ashktorab H, Smoot DT, Jeon SH, Kim SY, Lee YS. nc886, a non-coding RNA of anti-proliferative role, is suppressed by CpG DNA methylation in human gastric cancer. Oncotarget 2014; 5:3944-55. [PMID: 25003254 PMCID: PMC4116533 DOI: 10.18632/oncotarget.2047] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 05/30/2014] [Indexed: 02/07/2023] Open
Abstract
nc886 is a 101 nucleotide long non-coding RNA that has been designated as a precursor microRNA or a vault RNA based upon it sequence. nc886 has also been suggested to be a tumor suppressor, mainly inferred by its expression pattern as well as its genomic location at human chromosome 5q31, a locus for a tumor suppressor gene(s). However, legitimate data based on nc886's correct identity for its functional cellular roles as a tumor suppressor have not been provided yet. Here we have investigated nc886 in gastric cancer where its expression is suppressed due to CpG DNA hypermethylation at its promoter region in a cohort of paired tumor/normal tissues from 88 gastric cancer patients. CpG hypermethylation of nc886 and thus its diminished expression is significantly associated with poor survival in these cancer patients. nc886 inhibits cell proliferation when ectopically expressed in gastric cancer cells. nc886's tumor suppressive role is corroborated by the induction of well-known oncogenes such as FOS, NF-κB, and MYC upon its knockdown. All these activities of nc886 are undoubtedly independent of mature microRNA or vault RNA. Our data indicate that nc886 is a putative tumor suppressor and could potentially be used as a diagnostic marker in gastric cancer.
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Affiliation(s)
- Kwang-Soo Lee
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
- Department of Life Science and Center for Aging and Health Care, Hallym University, Chuncheon, Korea
- co-first authors
| | - Jong-Lyul Park
- Medical Genomics Research Center, KRIBB, Daejeon, Korea
- Department of Functional Genomics, University of Science and Technology, Daejeon, Korea
- co-first authors
| | - Kwanbok Lee
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Lauren E. Richardson
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
- Lamar University, Beaumont, TX77710, USA
| | - Betty H. Johnson
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Hyun-Sung Lee
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ju-Seog Lee
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sang-Bae Kim
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Oh-Hyung Kwon
- Medical Genomics Research Center, KRIBB, Daejeon, Korea
| | - Kyu Sang Song
- Department of Pathology, College of Medicine, Chungnam National University, Daejeon, Korea
| | - Yong Sung Kim
- Medical Genomics Research Center, KRIBB, Daejeon, Korea
- Department of Functional Genomics, University of Science and Technology, Daejeon, Korea
| | - Hassan Ashktorab
- Departments of Medicine, Howard University, Washington, D. C., USA
| | - Duane T. Smoot
- Departments of Medicine, Howard University, Washington, D. C., USA
| | - Sung Ho Jeon
- Department of Life Science and Center for Aging and Health Care, Hallym University, Chuncheon, Korea
| | - Seon-Young Kim
- Medical Genomics Research Center, KRIBB, Daejeon, Korea
- Department of Functional Genomics, University of Science and Technology, Daejeon, Korea
| | - Yong Sun Lee
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
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19
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Epigenetic regulation of transcription by RNA polymerase III. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1829:1015-25. [DOI: 10.1016/j.bbagrm.2013.05.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 05/11/2013] [Accepted: 05/15/2013] [Indexed: 01/11/2023]
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20
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Perez P, Jang SI, Alevizos I. Emerging landscape of non-coding RNAs in oral health and disease. Oral Dis 2013; 20:226-35. [PMID: 23781896 DOI: 10.1111/odi.12142] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 05/08/2013] [Accepted: 05/09/2013] [Indexed: 12/20/2022]
Abstract
The world of non-coding RNAs has only recently started being discovered. For the past 40 years, coding genes, mRNA, and proteins have been the center of cellular and molecular biology, and pathologic alterations were attributed to either the aberration of gene sequence or altered promoter activity. It was only after the completion of the human genome sequence that the scientific community started seriously wondering why only a very small portion of the genome corresponded to protein-coding genes. New technologies such as the whole-genome and whole-transcriptome sequencing demonstrated that at least 90% of the genome is actively transcribed. The identification and cataloguing of multiple kinds of non-coding RNA (ncRNA) have exponentially increased, and it is now widely accepted that ncRNAs play major biological roles in cellular physiology, development, metabolism, and are also implicated in a variety of diseases. The aim of this review is to describe the two major classes (long and short forms) of non-coding RNAs and describe their subclasses in terms of function and their relevance and potential in oral diseases.
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Affiliation(s)
- P Perez
- Sjögren's Clinic, Molecular Physiology & Therapeutics, National Institute of Dental and Craniofacial Research, Bethesda, MD, USA
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21
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Mroczek S, Dziembowski A. U6 RNA biogenesis and disease association. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 4:581-92. [PMID: 23776162 DOI: 10.1002/wrna.1181] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 05/14/2013] [Accepted: 05/15/2013] [Indexed: 12/15/2022]
Abstract
U6 snRNA is one of five uridine-rich noncoding RNAs that form the major spliceosome complex. Unlike other U-snRNAs, it reveals many distinctive aspects of biogenesis such as transcription by RNA polymerase III, transcript nuclear retention and particular features of transcript ends: monomethylated 5'-guanosine triphosphate as cap structure and a 2',3'-cyclic phosphate moiety (>P) at the 3' termini. U6-snRNA plays a central role in splicing and thus its transcription, maturation, snRNP formation, and recycling are essential for cellular homeostasis. U6 snRNA enters the splicing cycle as part of the tri-U4/U6.U5snRNP complex, and after significant structural arrangements forms the catalytic site of the spliceosome together with U2 snRNA and Prp8. U6 snRNA also contributes to the splicing reaction by coordinating metal cations required for catalysis. Many human diseases are associated with altered splicing processes. Disruptions of the basal splicing machinery can be lethal or lead to severe diseases such as spinal muscular atrophy, amyotrophic lateral sclerosis, or retinitis pigmentosa. Recent studies have identified a new U6 snRNA biogenesis factor Usb1, the absence of which leads to poikiloderma with neutropenia (PN) (OMIM 604173), an autosomal recessive skin disease. Usb1 is an evolutionarily conserved 3'→5' exoribonuclease that is responsible for removing 3'-terminal uridines from U6 snRNA transcripts, which leads to the formation of a 2',3' cyclic phosphate moiety (>P). This maturation step is fundamental for U6 snRNP assembly and recycling. Usb1 represents the first example of a direct association between a spliceosomal U6 snRNA biogenesis factor and human genetic disease.
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Affiliation(s)
- Seweryn Mroczek
- Department of Biophysics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
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22
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Gjidoda A, Henry RW. RNA polymerase III repression by the retinoblastoma tumor suppressor protein. BIOCHIMICA ET BIOPHYSICA ACTA 2013; 1829:385-92. [PMID: 23063750 PMCID: PMC3549324 DOI: 10.1016/j.bbagrm.2012.09.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 09/28/2012] [Accepted: 09/30/2012] [Indexed: 12/29/2022]
Abstract
The retinoblastoma (RB) tumor suppressor protein regulates multiple pathways that influence cell growth, and as a key regulatory node, its function is inactivated in most cancer cells. In addition to its canonical roles in cell cycle control, RB functions as a global repressor of RNA polymerase (Pol) III transcription. Indeed, Pol III transcripts accumulate in cancer cells and their heightened levels are implicated in accelerated growth associated with RB dysfunction. Herein we review the mechanisms of RB repression for the different types of Pol III genes. For type 1 and type 2 genes, RB represses transcription through direct contacts with the core transcription machinery, notably Brf1-TFIIIB, and inhibits preinitiation complex formation and Pol III recruitment. A contrasting model for type 3 gene repression indicates that RB regulation involves stable and simultaneous promoter association by RB, the general transcription machinery including SNAPc, and Pol III, suggesting that RB may impede Pol III promoter escape or elongation. Interestingly, analysis of published genomic association data for RB and Pol III revealed added regulatory complexity for Pol III genes both during active growth and during arrested growth associated with quiescence and senescence. This article is part of a Special Issue entitled: Transcription by Odd Pols.
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Affiliation(s)
- Alison Gjidoda
- Department of Biochemistry & Molecular Biology, Michigan State University, 603 Wilson Road, East Lansing, MI 48824
| | - R. William Henry
- Department of Biochemistry & Molecular Biology, Michigan State University, 603 Wilson Road, East Lansing, MI 48824
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23
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Fiorentino FP, Marchesi I, Giordano A. On the role of retinoblastoma family proteins in the establishment and maintenance of the epigenetic landscape. J Cell Physiol 2013; 228:276-84. [PMID: 22718354 DOI: 10.1002/jcp.24141] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
RB family members are negative regulators of the cell cycle, involved in numerous biological processes such as cellular senescence, development and differentiation. Disruption of RB family pathways are linked to loss of cell cycle control, cellular immortalization and cancer. RB family, and in particular the most studied member RB/p105, has been considered a tumor suppressor gene by more than three decades, and numerous efforts have been done to understand his molecular activity. However, the epigenetic mechanisms behind Rb-mediated tumor suppression have been uncovered only in recent years. In this review, the role of RB family members in cancer epigenetics will be discussed. We start with an introduction to epigenomes, chromatin modifications and cancer epigenetics. In order to provide a clear picture of the involvement of RB family in the epigenetic field, we describe the RB family role in the epigenetic landscape dynamics based on the heterochromatin variety involved, facultative or constitutive. We want to stress that, despite dissimilar modulations, RB family is involved in both mammalian varieties of heterochromatin establishment and maintenance and that disruption of RB family pathways drives to alterations of both heterochromatin structures, thus to the global epigenetic landscape.
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Affiliation(s)
- Francesco Paolo Fiorentino
- Department of Biology, Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, Pennsylvania 19122, USA.
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24
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Abstract
Tea is one of the most consumed beverages worldwide, and green tea is the least processed from the buds of the Camellia sinensis plant. The most abundant component of green tea is (-)-epigallocatechin-3-gallate (EGCG), which has been the focus of many cell culture, animal and clinical trials, revealing that EGCG possesses antiproliferative, antimutagenic, antioxidant, antibacterial, antiviral and chemopreventive effects. In this review we briefly summarize the mechanism of action(s) of the green tea component EGCG, highlighting recent advances in the epigenetic regulation by EGCG. Additionally, we provide an overview of mouse chemoprevention studies and EGCG chemoprevention clinical trials.
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Affiliation(s)
- Laura Schramm
- Department of Biological Sciences, St. John's University, NY 11439, USA
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25
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Morita S, Takahashi RU, Yamashita R, Toyoda A, Horii T, Kimura M, Fujiyama A, Nakai K, Tajima S, Matoba R, Ochiya T, Hatada I. Genome-wide analysis of DNA methylation and expression of microRNAs in breast cancer cells. Int J Mol Sci 2012; 13:8259-8272. [PMID: 22942701 PMCID: PMC3430232 DOI: 10.3390/ijms13078259] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Revised: 06/19/2012] [Accepted: 06/27/2012] [Indexed: 11/16/2022] Open
Abstract
DNA methylation of promoters is linked to transcriptional silencing of protein-coding genes, and its alteration plays important roles in cancer formation. For example, hypermethylation of tumor suppressor genes has been seen in some cancers. Alteration of methylation in the promoters of microRNAs (miRNAs) has also been linked to transcriptional changes in cancers; however, no systematic studies of methylation and transcription of miRNAs have been reported. In the present study, to clarify the relation between DNA methylation and transcription of miRNAs, next-generation sequencing and microarrays were used to analyze the methylation and expression of miRNAs, protein-coding genes, other non-coding RNAs (ncRNAs), and pseudogenes in the human breast cancer cell lines MCF7 and the adriamycin (ADR) resistant cell line MCF7/ADR. DNA methylation in the proximal promoter of miRNAs is tightly linked to transcriptional silencing, as it is with protein-coding genes. In protein-coding genes, highly expressed genes have CpG-rich proximal promoters whereas weakly expressed genes do not. This is only rarely observed in other gene categories, including miRNAs. The present study highlights the epigenetic similarities and differences between miRNA and protein-coding genes.
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Affiliation(s)
- Sumiyo Morita
- Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Gunma 371-8512, Japan; E-Mails: (S.M.); (T.H.); (M.K.)
| | - Ryou-u Takahashi
- Division of Molecular and Cellular Medicine, National Cancer Center Research Institute, 5-1-1, Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; E-Mails: (R.T.); (T.O.)
| | - Riu Yamashita
- Department of Integrative Genomics, Medical Megabank Organization, Tohoku University, 6-3-09, aza Aoba, Aramaki, Aobaku, Sendai 980-8579, Japan; E-Mail:
| | - Atsushi Toyoda
- Center for Genetic Resource Information, National Institute of Genetics, Shizuoka 411-8540, Japan; E-Mails: (A.T.); (A.F.)
| | - Takuro Horii
- Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Gunma 371-8512, Japan; E-Mails: (S.M.); (T.H.); (M.K.)
| | - Mika Kimura
- Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Gunma 371-8512, Japan; E-Mails: (S.M.); (T.H.); (M.K.)
| | - Asao Fujiyama
- Center for Genetic Resource Information, National Institute of Genetics, Shizuoka 411-8540, Japan; E-Mails: (A.T.); (A.F.)
| | - Kenta Nakai
- Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan; E-Mail:
| | - Shoji Tajima
- Laboratory of Epigenetics, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan; E-Mail:
| | - Ryo Matoba
- DNA Chip Research Inc., 1-1-43 Suehirocho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; E-Mail:
| | - Takahiro Ochiya
- Division of Molecular and Cellular Medicine, National Cancer Center Research Institute, 5-1-1, Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; E-Mails: (R.T.); (T.O.)
| | - Izuho Hatada
- Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Gunma 371-8512, Japan; E-Mails: (S.M.); (T.H.); (M.K.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +81-27-220-8057; Fax: +81-27-220-8110
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