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He Z, Yan X, Zhang J, Hu K, Ou M, Wei C, Yang A, Li J, Huang T, Yang M, Ma L. A new raspberry ketone synthesis gene RinPKS4 identified in Rubus idaeus L. by transcriptome analysis. PLoS One 2024; 19:e0306615. [PMID: 39172993 PMCID: PMC11341048 DOI: 10.1371/journal.pone.0306615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 06/20/2024] [Indexed: 08/24/2024] Open
Abstract
Raspberry ketone accounts for the characteristic aroma of the raspberry fruit. In order to explore the genes involved in raspberry ketone synthesis, the transcriptome in fruit tissues of two red raspberry varieties "Polka" and "Orange legend", were sequenced and 24213 single genes were obtained. As the red raspberry fruit ripening, genes involved in flavonoid and anthocyanin synthesis were up-regulated, while those associated with lignin synthesis were down-regulated. A gene (RinPKS4) highly related to raspberry ketone synthesis was identified by transcriptome analysis, and RinPKS4 gene was over-expressed in raspberry in order to further understand the function of RinPKS4 gene in raspberry ketone synthesis. The results showed that the gene expression level of RinPKS4 in the leaf tissues of a transgenic lines increased by about 4-fold and the content of raspberry ketone increased by 42.64% compared with the wide type. This study lays a theoretical foundation for further study on the synthesis and regulation of raspberry ketone in red raspberry.
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Affiliation(s)
- Zhimin He
- College of Bioscience and Resources Environment, Beijing University of Agriculture, Beijing, China
| | - Xihuan Yan
- College of Bioscience and Resources Environment, Beijing University of Agriculture, Beijing, China
| | - Junxin Zhang
- College of Bioscience and Resources Environment, Beijing University of Agriculture, Beijing, China
| | - Kang Hu
- College of Bioscience and Resources Environment, Beijing University of Agriculture, Beijing, China
| | - Mengzhe Ou
- College of Bioscience and Resources Environment, Beijing University of Agriculture, Beijing, China
| | - Chaojun Wei
- Key Laboratory for Northern Urban Agriculture Ministry of Agriculture and Rural Afairs, Beijing University of Agriculture, Beijing, China
| | - Aizhen Yang
- Key Laboratory for Northern Urban Agriculture Ministry of Agriculture and Rural Afairs, Beijing University of Agriculture, Beijing, China
| | - Jing Li
- College of Bioscience and Resources Environment, Beijing University of Agriculture, Beijing, China
- Key Laboratory for Northern Urban Agriculture Ministry of Agriculture and Rural Afairs, Beijing University of Agriculture, Beijing, China
| | - Tiran Huang
- College of Bioscience and Resources Environment, Beijing University of Agriculture, Beijing, China
- Key Laboratory for Northern Urban Agriculture Ministry of Agriculture and Rural Afairs, Beijing University of Agriculture, Beijing, China
| | - Mingfeng Yang
- College of Bioscience and Resources Environment, Beijing University of Agriculture, Beijing, China
- Key Laboratory for Northern Urban Agriculture Ministry of Agriculture and Rural Afairs, Beijing University of Agriculture, Beijing, China
| | - Lanqing Ma
- College of Bioscience and Resources Environment, Beijing University of Agriculture, Beijing, China
- Key Laboratory for Northern Urban Agriculture Ministry of Agriculture and Rural Afairs, Beijing University of Agriculture, Beijing, China
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2
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Do HTT, Shanak S, Barghash A, Helms V. Differential exon usage of developmental genes is associated with deregulated epigenetic marks. Sci Rep 2023; 13:12256. [PMID: 37507411 PMCID: PMC10382575 DOI: 10.1038/s41598-023-38879-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
Alternative exon usage is known to affect a large portion of genes in mammalian genomes. Importantly, different splice isoforms sometimes possess distinctly different protein functions. Here, we analyzed data from the Human Epigenome Atlas for 11 different human adult tissues and for 8 cultured cells that mimic early developmental stages. We found a significant enrichment of cases where differential usage of exons in various developmental stages of human cells and tissues is associated with differential epigenetic modifications in the flanking regions of individual exons. Many of the genes that were differentially regulated at the exon level and showed deregulated histone marks at the respective exon flanks are functionally associated with development and metabolism.
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Affiliation(s)
| | - Siba Shanak
- Department of Biology and Biotechnology, Arab American University, Jenin, Palestine
| | - Ahmad Barghash
- Department of Computer Science, German Jordanian University, Amman, Jordan
| | - Volkhard Helms
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany.
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3
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Binda O, Kimenyi Ishimwe AB, Galloy M, Jacquet K, Corpet A, Fradet-Turcotte A, Côté J, Lomonte P. The TUDOR domain of SMN is an H3K79 me1 histone mark reader. Life Sci Alliance 2023; 6:e202201752. [PMID: 36882285 PMCID: PMC9993015 DOI: 10.26508/lsa.202201752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 02/28/2023] [Accepted: 03/01/2023] [Indexed: 03/09/2023] Open
Abstract
Spinal muscular atrophy is the leading genetic cause of infant mortality and results from depleted levels of functional survival of motor neuron (SMN) protein by either deletion or mutation of the SMN1 gene. SMN is characterized by a central TUDOR domain, which mediates the association of SMN with arginine methylated (Rme) partners, such as coilin, fibrillarin, and RNA pol II (RNA polymerase II). Herein, we biochemically demonstrate that SMN also associates with histone H3 monomethylated on lysine 79 (H3K79me1), defining SMN as not only the first protein known to associate with the H3K79me1 histone modification but also the first histone mark reader to recognize both methylated arginine and lysine residues. Mutational analyzes provide evidence that SMNTUDOR associates with H3 via an aromatic cage. Importantly, most SMNTUDOR mutants found in spinal muscular atrophy patients fail to associate with H3K79me1.
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Affiliation(s)
- Olivier Binda
- Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U1315, LabEx DEV2CAN, Institut NeuroMyoGène-Pathophysiology and Genetics of Neuron and Muscle (INMG-PGNM), Team Chromatin Dynamics, Nuclear Domains, Virus, Lyon, France
- University of Ottawa, Faculty of Medicine, Department of Cellular and Molecular Medicine, Ontario, Canada
| | - Aimé Boris Kimenyi Ishimwe
- Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U1315, LabEx DEV2CAN, Institut NeuroMyoGène-Pathophysiology and Genetics of Neuron and Muscle (INMG-PGNM), Team Chromatin Dynamics, Nuclear Domains, Virus, Lyon, France
| | - Maxime Galloy
- Université Laval Cancer Research Center, Université Laval, Québec, Canada; Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Québec, Canada; and Oncology Division, Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Québec, Canada
| | - Karine Jacquet
- Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U1315, LabEx DEV2CAN, Institut NeuroMyoGène-Pathophysiology and Genetics of Neuron and Muscle (INMG-PGNM), Team Chromatin Dynamics, Nuclear Domains, Virus, Lyon, France
| | - Armelle Corpet
- Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U1315, LabEx DEV2CAN, Institut NeuroMyoGène-Pathophysiology and Genetics of Neuron and Muscle (INMG-PGNM), Team Chromatin Dynamics, Nuclear Domains, Virus, Lyon, France
| | - Amélie Fradet-Turcotte
- Université Laval Cancer Research Center, Université Laval, Québec, Canada; Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Québec, Canada; and Oncology Division, Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Québec, Canada
| | - Jocelyn Côté
- University of Ottawa, Faculty of Medicine, Department of Cellular and Molecular Medicine, Ontario, Canada
| | - Patrick Lomonte
- Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U1315, LabEx DEV2CAN, Institut NeuroMyoGène-Pathophysiology and Genetics of Neuron and Muscle (INMG-PGNM), Team Chromatin Dynamics, Nuclear Domains, Virus, Lyon, France
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4
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Bodaszewska-Lubas M, Liao Y, Zegar A, Szelest O, Dobrucki J, Bulek K. Dominant-Negative Form of SIGIRR: SIGIRR ΔE8 Promotes Tumor Growth Through Regulation of Metabolic Pathways. J Interferon Cytokine Res 2022; 42:482-492. [PMID: 35900274 PMCID: PMC9527062 DOI: 10.1089/jir.2022.0095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Colorectal carcinoma is the leading cause of cancer-related death. Previously we have shown that tumor suppressor single immunoglobulin interleukin-1-related receptor (SIGIRR) is frequently inactivated in human colorectal cancer by the increased expression of a novel SIGIRR isoform (SIGIRRΔE8). SIGIRRΔE8 showed increased retention in the cytoplasm and loss of complex glycan modification compared to the full-length SIGIRR. Now we found that the arginine residues located in the C-terminus of SIGIRRΔE8 serve as an endoplasmic reticulum retention signal and are required for resident protein ribophorin 1 (RPN1) interaction. In addition, we found that SIGIRRΔE8 exerts a direct impact on cell metabolism through interaction with the adenosine triphosphate synthase in the colorectal cancer cells. SIGIRRΔE8 expression promoted the metabolic shift through upregulation of mammalian target of rapamycin signaling pathway and dysregulation of mitochondrial function to promote survival and proliferation of colon cancer cells in xenograft model.
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Affiliation(s)
- Malgorzata Bodaszewska-Lubas
- Department of Immunology, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Yun Liao
- Department of Inflammation and Immunity, Cleveland Clinic, Lerner Research Institute, Cleveland, Ohio, USA
| | - Aneta Zegar
- Department of Immunology, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Oskar Szelest
- Department of Cell Biophysics, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Jurek Dobrucki
- Department of Cell Biophysics, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Katarzyna Bulek
- Department of Immunology, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Krakow, Poland.,Department of Inflammation and Immunity, Cleveland Clinic, Lerner Research Institute, Cleveland, Ohio, USA
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5
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Ebrahimie E, Rahimirad S, Tahsili M, Mohammadi-Dehcheshmeh M. Alternative RNA splicing in stem cells and cancer stem cells: Importance of transcript-based expression analysis. World J Stem Cells 2021; 13:1394-1416. [PMID: 34786151 PMCID: PMC8567453 DOI: 10.4252/wjsc.v13.i10.1394] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 06/21/2021] [Accepted: 09/14/2021] [Indexed: 02/06/2023] Open
Abstract
Alternative ribonucleic acid (RNA) splicing can lead to the assembly of different protein isoforms with distinctive functions. The outcome of alternative splicing (AS) can result in a complete loss of function or the acquisition of new functions. There is a gap in knowledge of abnormal RNA splice variants promoting cancer stem cells (CSCs), and their prospective contribution in cancer progression. AS directly regulates the self-renewal features of stem cells (SCs) and stem-like cancer cells. Notably, octamer-binding transcription factor 4A spliced variant of octamer-binding transcription factor 4 contributes to maintaining stemness properties in both SCs and CSCs. The epithelial to mesenchymal transition pathway regulates the AS events in CSCs to maintain stemness. The alternative spliced variants of CSCs markers, including cluster of differentiation 44, aldehyde dehydrogenase, and doublecortin-like kinase, α6β1 integrin, have pivotal roles in increasing self-renewal properties and maintaining the pluripotency of CSCs. Various splicing analysis tools are considered in this study. LeafCutter software can be considered as the best tool for differential splicing analysis and identification of the type of splicing events. Additionally, LeafCutter can be used for efficient mapping splicing quantitative trait loci. Altogether, the accumulating evidence re-enforces the fact that gene and protein expression need to be investigated in parallel with alternative splice variants.
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Affiliation(s)
- Esmaeil Ebrahimie
- School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide 5005, South Australia, Australia
- La Trobe Genomics Research Platform, School of Life Sciences, College of Science, Health and Engineering, La Trobe University, Melbourne 3086, Australia
- School of Biosciences, The University of Melbourne, Melbourne 3010, Australia,
| | - Samira Rahimirad
- Department of Medical Genetics, National Institute of Genetic Engineering and Biotechnology, Tehran 1497716316, Iran
- Division of Urology, Department of Surgery, McGill University and the Research Institute of the McGill University Health Centre, Montreal H4A 3J1, Quebec, Canada
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6
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Xu SJ, Lombroso SI, Fischer DK, Carpenter MD, Marchione DM, Hamilton PJ, Lim CJ, Neve RL, Garcia BA, Wimmer ME, Pierce RC, Heller EA. Chromatin-mediated alternative splicing regulates cocaine-reward behavior. Neuron 2021; 109:2943-2966.e8. [PMID: 34480866 PMCID: PMC8454057 DOI: 10.1016/j.neuron.2021.08.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 06/14/2021] [Accepted: 08/10/2021] [Indexed: 10/20/2022]
Abstract
Neuronal alternative splicing is a key gene regulatory mechanism in the brain. However, the spliceosome machinery is insufficient to fully specify splicing complexity. In considering the role of the epigenome in activity-dependent alternative splicing, we and others find the histone modification H3K36me3 to be a putative splicing regulator. In this study, we found that mouse cocaine self-administration caused widespread differential alternative splicing, concomitant with the enrichment of H3K36me3 at differentially spliced junctions. Importantly, only targeted epigenetic editing can distinguish between a direct role of H3K36me3 in splicing and an indirect role via regulation of splice factor expression elsewhere on the genome. We targeted Srsf11, which was both alternatively spliced and H3K36me3 enriched in the brain following cocaine self-administration. Epigenetic editing of H3K36me3 at Srsf11 was sufficient to drive its alternative splicing and enhanced cocaine self-administration, establishing the direct causal relevance of H3K36me3 to alternative splicing of Srsf11 and to reward behavior.
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Affiliation(s)
- Song-Jun Xu
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sonia I Lombroso
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Delaney K Fischer
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Marco D Carpenter
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Dylan M Marchione
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Peter J Hamilton
- Department of Brain and Cognitive Sciences, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Carissa J Lim
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rachel L Neve
- Gene Delivery Technology Core, Massachusetts General Hospital, Cambridge, MA 02139, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mathieu E Wimmer
- Department of Psychology, Temple University, Philadelphia, PA 19121, USA
| | - R Christopher Pierce
- Department of Psychiatry, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
| | - Elizabeth A Heller
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA,19104, USA; Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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7
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Fang X, Poulsen R, Zhao L, Wang J, Rivkees SA, Wendler CC. Knockdown of DNA methyltransferase 1 reduces DNA methylation and alters expression patterns of cardiac genes in embryonic cardiomyocytes. FEBS Open Bio 2021. [PMID: 34235895 PMCID: PMC8329956 DOI: 10.1002/2211-5463.13252] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 06/14/2021] [Accepted: 07/07/2021] [Indexed: 12/12/2022] Open
Abstract
We previously found that DNA methyltransferase 3a (DNMT3a) plays an important role in regulating embryonic cardiomyocyte gene expression, morphology, and function. In this study, we investigated the role of the most abundant DNMT in mammalian cells, DNMT1, in these processes. It is known that DNMT1 is essential for embryonic development, during which it is involved in regulating cardiomyocyte DNA methylation and gene expression. We used siRNA to knock down DNMT1 expression in primary cultures of mouse embryonic cardiomyocytes. Immunofluorescence staining and multielectrode array were, respectively, utilized to evaluate cardiomyocyte growth and electrophysiology. RNA sequencing (RNA‐Seq) and multiplex bisulfite sequencing were, respectively, performed to examine gene expression and promoter methylation. At 72 h post‐transfection, reduction of DNMT1 expression decreased the number and increased the size of embryonic cardiomyocytes. Beat frequency and the amplitude of field action potentials were decreased by DNMT1 siRNA. RNA‐Seq analysis identified 801 up‐regulated genes and 494 down‐regulated genes in the DNMT1 knockdown cells when compared to controls. Pathway analysis of the differentially expressed genes revealed pathways that were associated with cell death and survival, cell morphology, cardiac function, and cardiac disease. Alternative splicing analysis identified 929 differentially expressed exons, including 583 up‐regulated exons and 308 down‐regulated exons. Moreover, decreased methylation levels were found in the promoters of cardiac genes Myh6, Myh7, Myh7b, Tnnc1, Tnni3, Tnnt2, Nppa, Nppb, mef2c, mef2d, Camta2, Cdkn1A, and Cdkn1C. Of these 13 genes, 6 (Myh6, Tnnc1, Tnni3, Tnnt2, Nppa, Nppb) and 1 (Cdkn1C) had increased or decreased gene expression, respectively. Altogether, these data show that DNMT1 is important in embryonic cardiomyocytes by regulating DNA methylation, gene expression, gene splicing, and cell function.
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Affiliation(s)
- Xiefan Fang
- Department of Pediatrics, Child Health Research Institute, College of Medicine, University of Florida, Gainesville, FL, USA.,Charles River Laboratories, Inc., Reno, NV, USA
| | - Ryan Poulsen
- Department of Pediatrics, Child Health Research Institute, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Lu Zhao
- Charles River Laboratories, Inc., Reno, NV, USA
| | | | - Scott A Rivkees
- Department of Pediatrics, Child Health Research Institute, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Christopher C Wendler
- Department of Pediatrics, Child Health Research Institute, College of Medicine, University of Florida, Gainesville, FL, USA
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8
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Xu P, Zhang L, Xiao Y, Li W, Hu Z, Zhang R, Li J, Wu F, Xi Y, Zou Q, Wang Z, Guo R, Ma H, Dong S, Xiao M, Yang Z, Ren X, Wei C, Yu W. UHRF1 regulates alternative splicing by binding to splicing factors and U snRNAs. Hum Mol Genet 2021; 30:2110-2122. [PMID: 34196368 DOI: 10.1093/hmg/ddab178] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 06/08/2021] [Accepted: 06/24/2021] [Indexed: 12/12/2022] Open
Abstract
The well-established functions of UHRF1 converge to DNA biological processes, as exemplified by DNA methylation maintenance and DNA damage repair during cell cycles. However, the potential effect of UHRF1 on RNA metabolism is largely unexplored. Here, we revealed that UHRF1 serves as a novel alternative RNA splicing regulator. The protein interactome of UHRF1 identified various splicing factors. Among them, SF3B3 could interact with UHRF1 directly and participate in UHRF1-regulated alternative splicing events. Furthermore, we interrogated the RNA interactome of UHRF1, and surprisingly, we identified U snRNAs, the canonical spliceosome component, in the UHRF1-associated RNA components. Unexpectedly, we found H3R2 methylation status determines the binding preference of U snRNA, especially U2 snRNA. The involvement of U snRNAs in UHRF1-containing complex and their binding preference to specific chromatin configuration imply a finely orchestrated mechanism at play. Our results provided the resources and pinpointed the molecular basis of UHRF1-mediated alternative RNA splicing, which will help us better our understanding of the physiological and pathological roles of UHRF1 in disease development.
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Affiliation(s)
- Peng Xu
- Shanghai Public Health Clinical Centre and Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China
| | - Lan Zhang
- Shanghai Public Health Clinical Centre and Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China.,State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, Guangdong, 510060, China
| | - Yao Xiao
- Shanghai Public Health Clinical Centre and Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China
| | - Wei Li
- Shanghai Public Health Clinical Centre and Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China
| | - Zhiqiang Hu
- Department of Plant & Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Rukui Zhang
- Shanghai Public Health Clinical Centre and Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China
| | - Jin Li
- Shanghai Public Health Clinical Centre and Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China
| | - Feizhen Wu
- Key Laboratory of Medical Epigenetics and Metabolism, Institute of Clinical Science of Zhongshan Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Yanping Xi
- Shanghai Public Health Clinical Centre and Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China.,Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, 200011, China
| | - Qingping Zou
- Shanghai Public Health Clinical Centre and Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China
| | - Zhentian Wang
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Rui Guo
- Key Laboratory of Medical Epigenetics and Metabolism, Institute of Clinical Science of Zhongshan Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Honghui Ma
- Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Shihua Dong
- Shanghai Public Health Clinical Centre and Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China
| | - Min Xiao
- Shanghai Public Health Clinical Centre and Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China.,Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, 200011, China
| | - Zhicong Yang
- Shanghai Public Health Clinical Centre and Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China
| | - Xiaoguang Ren
- Shanghai Public Health Clinical Centre and Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China
| | - Chaochun Wei
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wenqiang Yu
- Shanghai Public Health Clinical Centre and Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China
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9
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Ehx G, Larouche JD, Durette C, Laverdure JP, Hesnard L, Vincent K, Hardy MP, Thériault C, Rulleau C, Lanoix J, Bonneil E, Feghaly A, Apavaloaei A, Noronha N, Laumont CM, Delisle JS, Vago L, Hébert J, Sauvageau G, Lemieux S, Thibault P, Perreault C. Atypical acute myeloid leukemia-specific transcripts generate shared and immunogenic MHC class-I-associated epitopes. Immunity 2021; 54:737-752.e10. [PMID: 33740418 DOI: 10.1016/j.immuni.2021.03.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 10/24/2020] [Accepted: 02/26/2021] [Indexed: 12/11/2022]
Abstract
Acute myeloid leukemia (AML) has not benefited from innovative immunotherapies, mainly because of the lack of actionable immune targets. Using an original proteogenomic approach, we analyzed the major histocompatibility complex class I (MHC class I)-associated immunopeptidome of 19 primary AML samples and identified 58 tumor-specific antigens (TSAs). These TSAs bore no mutations and derived mainly (86%) from supposedly non-coding genomic regions. Two AML-specific aberrations were instrumental in the biogenesis of TSAs, intron retention, and epigenetic changes. Indeed, 48% of TSAs resulted from intron retention and translation, and their RNA expression correlated with mutations of epigenetic modifiers (e.g., DNMT3A). AML TSA-coding transcripts were highly shared among patients and were expressed in both blasts and leukemic stem cells. In AML patients, the predicted number of TSAs correlated with spontaneous expansion of cognate T cell receptor clonotypes, accumulation of activated cytotoxic T cells, immunoediting, and improved survival. These TSAs represent attractive targets for AML immunotherapy.
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Affiliation(s)
- Grégory Ehx
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada; Department of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Jean-David Larouche
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada; Department of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Chantal Durette
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Jean-Philippe Laverdure
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Leslie Hesnard
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada; Department of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Krystel Vincent
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada; Department of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Marie-Pierre Hardy
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Catherine Thériault
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Caroline Rulleau
- Centre de recherche de l'Hôpital Maisonneuve-Rosemont, Montréal, QC, Canada
| | - Joël Lanoix
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Eric Bonneil
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Albert Feghaly
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Anca Apavaloaei
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada; Department of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Nandita Noronha
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada; Department of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Céline M Laumont
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada; Department of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Jean-Sébastien Delisle
- Department of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada; Centre de recherche de l'Hôpital Maisonneuve-Rosemont, Montréal, QC, Canada; Division of Hematology, Maisonneuve-Rosemont Hospital, Montreal, QC H1T 2M4, Canada
| | - Luca Vago
- Unit of Immunogenetics, Leukemia Genomics and Immunobiology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Josée Hébert
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada; Department of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada; Division of Hematology, Maisonneuve-Rosemont Hospital, Montreal, QC H1T 2M4, Canada
| | - Guy Sauvageau
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada; Department of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada; Division of Hematology, Maisonneuve-Rosemont Hospital, Montreal, QC H1T 2M4, Canada
| | - Sébastien Lemieux
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada; Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada; Department of Chemistry, Université de Montréal, Montreal, QC H3C 3J7, Canada.
| | - Claude Perreault
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada; Department of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada.
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10
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Agirre E, Oldfield AJ, Bellora N, Segelle A, Luco RF. Splicing-associated chromatin signatures: a combinatorial and position-dependent role for histone marks in splicing definition. Nat Commun 2021; 12:682. [PMID: 33514745 PMCID: PMC7846797 DOI: 10.1038/s41467-021-20979-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 01/05/2021] [Indexed: 12/14/2022] Open
Abstract
Alternative splicing relies on the combinatorial recruitment of splicing regulators to specific RNA binding sites. Chromatin has been shown to impact this recruitment. However, a limited number of histone marks have been studied at a global level. In this work, a machine learning approach, applied to extensive epigenomics datasets in human H1 embryonic stem cells and IMR90 foetal fibroblasts, has identified eleven chromatin modifications that differentially mark alternatively spliced exons depending on the level of exon inclusion. These marks act in a combinatorial and position-dependent way, creating characteristic splicing-associated chromatin signatures (SACS). In support of a functional role for SACS in coordinating splicing regulation, changes in the alternative splicing of SACS-marked exons between ten different cell lines correlate with changes in SACS enrichment levels and recruitment of the splicing regulators predicted by RNA motif search analysis. We propose the dynamic nature of chromatin modifications as a mechanism to rapidly fine-tune alternative splicing when necessary. Chromatin is known to regulate splicing by modulating recruitment of splicing factors. Using machine learning approaches, the authors have underlined a chromatin code for alternative splicing regulation that is conserved amongst cell lines.
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Affiliation(s)
- E Agirre
- Institute of Human Genetics, UMR9002 CNRS-University of Montpellier, 34000, Montpellier, France.,Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - A J Oldfield
- Institute of Human Genetics, UMR9002 CNRS-University of Montpellier, 34000, Montpellier, France
| | - N Bellora
- Institute of Nuclear Technologies for Health (INTECNUS), National Scientific and Technical Research Council (CONICET), Bariloche, 8400, Argentina
| | - A Segelle
- Institute of Human Genetics, UMR9002 CNRS-University of Montpellier, 34000, Montpellier, France
| | - R F Luco
- Institute of Human Genetics, UMR9002 CNRS-University of Montpellier, 34000, Montpellier, France.
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11
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Schmitz U, Shah JS, Dhungel BP, Monteuuis G, Luu PL, Petrova V, Metierre C, Nair SS, Bailey CG, Saunders VA, Turhan AG, White DL, Branford S, Clark SJ, Hughes TP, Wong JJL, Rasko JE. Widespread Aberrant Alternative Splicing despite Molecular Remission in Chronic Myeloid Leukaemia Patients. Cancers (Basel) 2020; 12:cancers12123738. [PMID: 33322625 PMCID: PMC7764299 DOI: 10.3390/cancers12123738] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/04/2020] [Accepted: 12/07/2020] [Indexed: 12/11/2022] Open
Abstract
Simple Summary This study provides new insights into the changing transcriptomic and epigenomic landscapes in chronic myeloid leukaemia (CML) patients who are receiving tyrosine kinase inhibitor (TKI) therapy (often life-long). Alternative splicing, vital for cellular homeostasis, is dysregulated in human cancers. Remarkably, we found abnormal splicing patterns despite molecular remission in peripheral blood cells of chronic-phase CML patients. This phenomenon is independent of the TKI drug used and in striking contrast to the normalisation of gene expression and DNA methylation patterns. Abstract Vast transcriptomics and epigenomics changes are characteristic of human cancers, including leukaemia. At remission, we assume that these changes normalise so that omics-profiles resemble those of healthy individuals. However, an in-depth transcriptomic and epigenomic analysis of cancer remission has not been undertaken. A striking exemplar of targeted remission induction occurs in chronic myeloid leukaemia (CML) following tyrosine kinase inhibitor (TKI) therapy. Using RNA sequencing and whole-genome bisulfite sequencing, we profiled samples from chronic-phase CML patients at diagnosis and remission and compared these to healthy donors. Remarkably, our analyses revealed that abnormal splicing distinguishes remission samples from normal controls. This phenomenon is independent of the TKI drug used and in striking contrast to the normalisation of gene expression and DNA methylation patterns. Most remarkable are the high intron retention (IR) levels that even exceed those observed in the diagnosis samples. Increased IR affects cell cycle regulators at diagnosis and splicing regulators at remission. We show that aberrant splicing in CML is associated with reduced expression of specific splicing factors, histone modifications and reduced DNA methylation. Our results provide novel insights into the changing transcriptomic and epigenomic landscapes of CML patients during remission. The conceptually unanticipated observation of widespread aberrant alternative splicing after remission induction warrants further exploration. These results have broad implications for studying CML relapse and treating minimal residual disease.
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Affiliation(s)
- Ulf Schmitz
- Computational BioMedicine Laboratory Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia; (U.S.); (V.P.)
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia; (J.S.S.); (B.P.D.); (G.M.); (C.M.); (C.G.B.)
- Faculty of Medicine & Health, The University of Sydney, Camperdown, NSW 2050, Australia;
| | - Jaynish S. Shah
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia; (J.S.S.); (B.P.D.); (G.M.); (C.M.); (C.G.B.)
- Faculty of Medicine & Health, The University of Sydney, Camperdown, NSW 2050, Australia;
| | - Bijay P. Dhungel
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia; (J.S.S.); (B.P.D.); (G.M.); (C.M.); (C.G.B.)
- Faculty of Medicine & Health, The University of Sydney, Camperdown, NSW 2050, Australia;
| | - Geoffray Monteuuis
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia; (J.S.S.); (B.P.D.); (G.M.); (C.M.); (C.G.B.)
| | - Phuc-Loi Luu
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; (P.-L.L.); (S.J.C.)
| | - Veronika Petrova
- Computational BioMedicine Laboratory Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia; (U.S.); (V.P.)
| | - Cynthia Metierre
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia; (J.S.S.); (B.P.D.); (G.M.); (C.M.); (C.G.B.)
| | - Shalima S. Nair
- Kinghorn Centre for Clinical Genomics Core Facility, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia;
- St Vincent’s Clinical School, Faculty of Medicine, University of New South Wales, Darlinghurst, NSW 2010, Australia
| | - Charles G. Bailey
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia; (J.S.S.); (B.P.D.); (G.M.); (C.M.); (C.G.B.)
- Faculty of Medicine & Health, The University of Sydney, Camperdown, NSW 2050, Australia;
| | - Verity A. Saunders
- Cancer Program, Precision Medicine Theme, South Australian Health & Medical Research Institute, Adelaide, SA 50000, Australia; (V.A.S.); (D.L.W.)
| | - Ali G. Turhan
- APHP, Division of Hematology, Paris Sud University Hospitals and Inserm U935 INGESTEM Pluripotent Stem Cell Infrastructure 78 Rue du Général Leclerc, 94275 Le Kremlin Bicetre, France;
| | - Deborah L. White
- Cancer Program, Precision Medicine Theme, South Australian Health & Medical Research Institute, Adelaide, SA 50000, Australia; (V.A.S.); (D.L.W.)
- School of Medicine, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5000, Australia; (S.B.); (T.P.H.)
- Australasian Leukaemia and Lymphoma Group, Richmond, VIC 3121, Australia
- School of Biological Sciences, Faculty of Sciences, University of Adelaide, Adelaide, SA 5000, Australia
- South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia
| | - Susan Branford
- School of Medicine, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5000, Australia; (S.B.); (T.P.H.)
- School of Biological Sciences, Faculty of Sciences, University of Adelaide, Adelaide, SA 5000, Australia
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, SA Pathology, Adelaide, SA 5000, Australia
- School of Pharmacy and Medical Science, Division of Health Sciences, University of South Australia, Adelaide, SA 5000, Australia
| | - Susan J. Clark
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; (P.-L.L.); (S.J.C.)
- St Vincent’s Clinical School, University of New South Wales, Darlinghurst, NSW 2010, Australia
| | - Timothy P. Hughes
- School of Medicine, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5000, Australia; (S.B.); (T.P.H.)
- Australasian Leukaemia and Lymphoma Group, Richmond, VIC 3121, Australia
- School of Pharmacy and Medical Science, Division of Health Sciences, University of South Australia, Adelaide, SA 5000, Australia
- Department of Haematology, Centre for Cancer Biology, SA Pathology, Adelaide, SA 5001, Australia
| | - Justin J.-L. Wong
- Faculty of Medicine & Health, The University of Sydney, Camperdown, NSW 2050, Australia;
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
| | - John E.J. Rasko
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia; (J.S.S.); (B.P.D.); (G.M.); (C.M.); (C.G.B.)
- Faculty of Medicine & Health, The University of Sydney, Camperdown, NSW 2050, Australia;
- Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia
- Correspondence: ; Tel.: +61-2-9565-6160
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12
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Hu Q, Greene CS, Heller EA. Specific histone modifications associate with alternative exon selection during mammalian development. Nucleic Acids Res 2020; 48:4709-4724. [PMID: 32319526 PMCID: PMC7229819 DOI: 10.1093/nar/gkaa248] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 03/23/2020] [Accepted: 04/02/2020] [Indexed: 12/29/2022] Open
Abstract
Alternative splicing (AS) is frequent during early mouse embryonic development. Specific histone post-translational modifications (hPTMs) have been shown to regulate exon splicing by either directly recruiting splice machinery or indirectly modulating transcriptional elongation. In this study, we hypothesized that hPTMs regulate expression of alternatively spliced genes for specific processes during differentiation. To address this notion, we applied an innovative machine learning approach to relate global hPTM enrichment to AS regulation during mammalian tissue development. We found that specific hPTMs, H3K36me3 and H3K4me1, play a role in skipped exon selection among all the tissues and developmental time points examined. In addition, we used iterative random forest model and found that interactions of multiple hPTMs most strongly predicted splicing when they included H3K36me3 and H3K4me1. Collectively, our data demonstrated a link between hPTMs and alternative splicing which will drive further experimental studies on the functional relevance of these modifications to alternative splicing.
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Affiliation(s)
- Qiwen Hu
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
| | - Casey S Greene
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
| | - Elizabeth A Heller
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
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13
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Bamodu O, Chao TY. Dissecting the functional pleiotropism of lysine demethylase 5B in physiology and pathology. JOURNAL OF CANCER RESEARCH AND PRACTICE 2020. [DOI: 10.4103/jcrp.jcrp_5_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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14
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Shi Y, Su Z, Yang H, Wang W, Jin G, He G, Siddique AN, Zhang L, Zhu A, Xue R, Zhang C. Alternative splicing coupled to nonsense-mediated mRNA decay contributes to the high-altitude adaptation of maca (Lepidium meyenii). Gene 2019; 694:7-18. [PMID: 30716438 DOI: 10.1016/j.gene.2018.12.082] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 12/25/2018] [Accepted: 12/30/2018] [Indexed: 12/31/2022]
Abstract
Alpine plants remain the least studied plant communities in terrestrial ecosystems. However, how they adapt to high-altitude environments is far from clear. Here, we used RNA-seq to investigate a typical alpine plant maca (Lepidium meyenii) to understand its high-altitude adaptation at transcriptional and post-transcriptional level. At transcriptional level, we found that maca root significantly up-regulated plant immunity genes in day-time comparing to night-time, and up-regulated abiotic (cold/osmotic) stress response genes in Nov and Dec comparing to Oct. In addition, 17 positively selected genes were identified, which could be involved in mitochondrion. At post-transcriptional level, we found that maca had species-specific characterized alternative splicing (AS) profile which could be influenced by stress environments. For example, the alternative 3' splice site events (A3SS, 39.62%) were predominate AS events in maca, rather than intron retention (IR, 23.17%). Interestingly, besides serine/arginine-rich (SR) proteins and long non-coding RNAs (lncRNAs), a lot of components in nonsense-mediated mRNA decay (NMD) were identified under differential alternative splicing (DAS), supporting AS coupled to NMD as essential mechanisms for maca's stress responses and high-altitude adaptation. Taken together, we first attempted to unveil maca's high-altitude adaptation mechanisms based on transcriptome and post-transcriptome evidence. Our data provided valuable insights to understand the high-altitude adaptation of alpine plants.
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Affiliation(s)
- Yong Shi
- Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Zechun Su
- Alpine Economic Plant Research Institute, Yunnan Academy of Agricultural Sciences, Lijiang, Yunnan 674100, China
| | - Hong Yang
- Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenzhi Wang
- Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; School of Life Sciences, Southwest Forestry University, Kunming 650224, China
| | - Guihua Jin
- Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guiqing He
- Alpine Economic Plant Research Institute, Yunnan Academy of Agricultural Sciences, Lijiang, Yunnan 674100, China
| | - Abu Nasar Siddique
- Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Department of Biotechnology, Bacha Khan University, Charsadda 24420, Pakistan
| | - Liangsheng Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Andan Zhu
- Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Runguang Xue
- Alpine Economic Plant Research Institute, Yunnan Academy of Agricultural Sciences, Lijiang, Yunnan 674100, China.
| | - Chengjun Zhang
- Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
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15
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Ullah F, Hamilton M, Reddy ASN, Ben-Hur A. Exploring the relationship between intron retention and chromatin accessibility in plants. BMC Genomics 2018; 19:21. [PMID: 29304739 PMCID: PMC5756433 DOI: 10.1186/s12864-017-4393-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 12/15/2017] [Indexed: 11/29/2022] Open
Abstract
Background Intron retention (IR) is the most prevalent form of alternative splicing in plants. IR, like other forms of alternative splicing, has an important role in increasing gene product diversity and regulating transcript functionality. Splicing is known to occur co-transcriptionally and is influenced by the speed of transcription which in turn, is affected by chromatin structure. It follows that chromatin structure may have an important role in the regulation of splicing, and there is preliminary evidence in metazoans to suggest that this is indeed the case; however, nothing is known about the role of chromatin structure in regulating IR in plants. DNase I-seq is a useful experimental tool for genome-wide interrogation of chromatin accessibility, providing information on regions of chromatin with very high likelihood of cleavage by the enzyme DNase I, known as DNase I Hypersensitive Sites (DHSs). While it is well-established that promoter regions are highly accessible and are over-represented with DHSs, not much is known about DHSs in the bodies of genes, and their relationship to splicing in general, and IR in particular. Results In this study we use publicly available DNase I-seq data in arabidopsis and rice to investigate the relationship between IR and chromatin structure. We find that IR events are highly enriched in DHSs in both species. This implies that chromatin is more open in retained introns, which is consistent with a kinetic model of the process whereby higher speeds of transcription in those regions give less time for the spliceosomal machinery to recognize and splice out those introns co-transcriptionally. The more open chromatin in IR can also be the result of regulation mediated by DNA-binding proteins. To test this, we performed an exhaustive search for footprints left by DNA-binding proteins that are associated with IR. We identified several hundred short sequence elements that exhibit footprints in their DNase I-seq coverage, the telltale sign for binding events of a regulatory protein, protecting its binding site from cleavage by DNase I. A highly significant fraction of those sequence elements are conserved between arabidopsis and rice, a strong indication of their functional importance. Conclusions In this study we have established an association between IR and chromatin accessibility, and presented a mechanistic hypothesis that explains the observed association from the perspective of the co-transcriptional nature of splicing. Furthermore, we identified conserved sequence elements for DNA-binding proteins that affect splicing. Electronic supplementary material The online version of this article (10.1186/s12864-017-4393-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fahad Ullah
- Computer Science Department, Colorado State University, 1873 Campus Delivery, Fort Collins, 80523, CO, USA
| | - Michael Hamilton
- Computer Science Department, Colorado State University, 1873 Campus Delivery, Fort Collins, 80523, CO, USA
| | - Anireddy S N Reddy
- Department of Biology, Colorado State University, 1878 Campus Delivery, Fort Collins, 80523, CO, USA
| | - Asa Ben-Hur
- Computer Science Department, Colorado State University, 1873 Campus Delivery, Fort Collins, 80523, CO, USA.
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16
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He R, Kidder BL. H3K4 demethylase KDM5B regulates global dynamics of transcription elongation and alternative splicing in embryonic stem cells. Nucleic Acids Res 2017; 45:6427-6441. [PMID: 28402433 PMCID: PMC5499819 DOI: 10.1093/nar/gkx251] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 04/03/2017] [Indexed: 02/04/2023] Open
Abstract
Epigenetic regulation of chromatin plays a critical role in controlling embryonic stem (ES) cell self-renewal and pluripotency. However, the roles of histone demethylases and activating histone modifications such as trimethylated histone 3 lysine 4 (H3K4me3) in transcriptional events such as RNA polymerase II (RNAPII) elongation and alternative splicing are largely unknown. In this study, we show that KDM5B, which demethylates H3K4me3, plays an integral role in regulating RNAPII occupancy, transcriptional initiation and elongation, and alternative splicing events in ES cells. Depletion of KDM5B leads to altered RNAPII promoter occupancy, and decreased RNAPII initiation and elongation rates at active genes and at genes marked with broad H3K4me3 domains. Moreover, our results demonstrate that spreading of H3K4me3 from promoter to gene body regions, which is mediated by depletion of KDM5B, modulates RNAPII elongation rates and RNA splicing in ES cells. We further show that KDM5B is enriched nearby alternatively spliced exons, and depletion of KDM5B leads to altered levels of H3K4 methylation in alternatively spliced exon regions, which is accompanied by differential expression of these alternatively splice exons. Altogether, our data indicate an epigenetic role for KDM5B in regulating RNAPII elongation and alternative splicing, which may support the diverse mRNA repertoire in ES cells.
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Affiliation(s)
- Runsheng He
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA.,Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Benjamin L Kidder
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA.,Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI 48201, USA
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17
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Hu Q, Kim EJ, Feng J, Grant GR, Heller EA. Histone posttranslational modifications predict specific alternative exon subtypes in mammalian brain. PLoS Comput Biol 2017; 13:e1005602. [PMID: 28609483 PMCID: PMC5487056 DOI: 10.1371/journal.pcbi.1005602] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 06/27/2017] [Accepted: 05/30/2017] [Indexed: 12/14/2022] Open
Abstract
A compelling body of literature, based on next generation chromatin immunoprecipitation and RNA sequencing of reward brain regions indicates that the regulation of the epigenetic landscape likely underlies chronic drug abuse and addiction. It is now critical to develop highly innovative computational strategies to reveal the relevant regulatory transcriptional mechanisms that may underlie neuropsychiatric disease. We have analyzed chromatin regulation of alternative splicing, which is implicated in cocaine exposure in mice. Recent literature has described chromatin-regulated alternative splicing, suggesting a novel function for drug-induced neuroepigenetic remodeling. However, the extent of the genome-wide association between particular histone modifications and alternative splicing remains unexplored. To address this, we have developed novel computational approaches to model the association between alternative splicing and histone posttranslational modifications in the nucleus accumbens (NAc), a brain reward region. Using classical statistical methods and machine learning to combine ChIP-Seq and RNA-Seq data, we found that specific histone modifications are strongly associated with various aspects of differential splicing. H3K36me3 and H3K4me1 have the strongest association with splicing indicating they play a significant role in alternative splicing in brain reward tissue.
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Affiliation(s)
- Qiwen Hu
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Eun Ji Kim
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, United States of America
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Jian Feng
- Department of Biological Science, Florida State University, Tallahassee, FL, United States of America
| | - Gregory R. Grant
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, United States of America
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Elizabeth A. Heller
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, United States of America
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA, United States of America
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
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18
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Hou Y, Huang H, Hu W, Liu H, Sun X. Histone modifications influence skipped exons inclusion. J Bioinform Comput Biol 2017; 15:1750003. [PMID: 28178888 DOI: 10.1142/s0219720017500032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Alternative splicing (AS), by which individual genes can produce multiple mRNA, associates with genomic complexity, disease, and development. Histone modifications show important roles in both transcription initiation and mRNA splicing. Here, we intended to find the link between AS and histone modifications in flanking regions through analyzing publicly available data in two human cell lines, GM12878 and K562 cell lines. According to exon inclusion levels, exons were classified into three types, included skipped exons, excluded skipped exons and expressed constitutive exons. We revealed that the inclusion levels of skipped exons (SEs) were negatively correlated with the enrichment of active histone marks in SEs, indicating a role of histone modifications in AS. We also found that active histone modifications were enriched in the upstream exons of SEs, especially around 5[Formula: see text] splicing sites. We inferred that the histone modifications around the 5[Formula: see text] splicing sites in upstream exon of the SEs could help RNA Polymerase II complex to recruit the effector proteins and facilitate AS. It was indicated that nucleosome occupancy had little influence on the inclusion levels of SEs. At last, we proposed an integrated model that describe how histone modifications affected the pre-mRNA splicing.
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Affiliation(s)
- Yue Hou
- 1 State Key Laboratory of Bioelectronics, School of Biology Science and Medical Engineering, Southeast University, Nanjing, P. R. China
| | - Huan Huang
- 1 State Key Laboratory of Bioelectronics, School of Biology Science and Medical Engineering, Southeast University, Nanjing, P. R. China
| | - Wenqiao Hu
- 1 State Key Laboratory of Bioelectronics, School of Biology Science and Medical Engineering, Southeast University, Nanjing, P. R. China
| | - Hongde Liu
- 1 State Key Laboratory of Bioelectronics, School of Biology Science and Medical Engineering, Southeast University, Nanjing, P. R. China
| | - Xiao Sun
- 1 State Key Laboratory of Bioelectronics, School of Biology Science and Medical Engineering, Southeast University, Nanjing, P. R. China
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Escudero-Hernández C, Martínez-Abad B, Ruipérez V, Garrote JA, Arranz E. New IL-15 receptor-α splicing variants identified in intestinal epithelial Caco-2 cells. Innate Immun 2016; 23:44-53. [PMID: 27794069 DOI: 10.1177/1753425916674263] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
IL-15 is a pleiotropic cytokine related to IL-2 which acts at a broader level than its counterpart. It is presented through its specific high-affinity receptor, IL-15Rα. Both cytokine and receptor are tightly regulated at multiple levels and are widely distributed. Thus, deregulation of their expression leads to an inflammatory immune response. Variants of splicing of IL-15Rα have been described in immune and barrier cells; however, their presence has not been focused on intestinal epithelial cells. In this study, we describe five new alternative variants of splicing of IL-15Rα in Caco-2 cells. Four of them were expressed into proteins inside Caco-2 cells, but these were unable to bind IL-15 or to follow the secretory pathway. However, the expression of mRNA itself might be relevant to diseases such as celiac disease, inflammatory bowel disease or colorectal cancer.
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Affiliation(s)
- Celia Escudero-Hernández
- 1 Mucosal Immunology Laboratory, Instituto de Biología y Genética Molecular (IBGM), University of Valladolid-CSIC, Valladolid, Spain
| | - Beatriz Martínez-Abad
- 1 Mucosal Immunology Laboratory, Instituto de Biología y Genética Molecular (IBGM), University of Valladolid-CSIC, Valladolid, Spain
| | - Violeta Ruipérez
- 1 Mucosal Immunology Laboratory, Instituto de Biología y Genética Molecular (IBGM), University of Valladolid-CSIC, Valladolid, Spain
| | - José A Garrote
- 1 Mucosal Immunology Laboratory, Instituto de Biología y Genética Molecular (IBGM), University of Valladolid-CSIC, Valladolid, Spain.,2 Laboratory of Molecular Genetics, Hospital Universitario Rio Hortega, Valladolid, Spain
| | - Eduardo Arranz
- 1 Mucosal Immunology Laboratory, Instituto de Biología y Genética Molecular (IBGM), University of Valladolid-CSIC, Valladolid, Spain
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20
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Dong X, Wang X, Zhang F, Tian W. Genome-Wide Identification of Regulatory Sequences Undergoing Accelerated Evolution in the Human Genome. Mol Biol Evol 2016; 33:2565-75. [PMID: 27401230 PMCID: PMC5026254 DOI: 10.1093/molbev/msw128] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Accelerated evolution of regulatory sequence can alter the expression pattern of target genes, and cause phenotypic changes. In this study, we used DNase I hypersensitive sites (DHSs) to annotate putative regulatory sequences in the human genome, and conducted a genome-wide analysis of the effects of accelerated evolution on regulatory sequences. Working under the assumption that local ancient repeat elements of DHSs are under neutral evolution, we discovered that ∼0.44% of DHSs are under accelerated evolution (ace-DHSs). We found that ace-DHSs tend to be more active than background DHSs, and are strongly associated with epigenetic marks of active transcription. The target genes of ace-DHSs are significantly enriched in neuron-related functions, and their expression levels are positively selected in the human brain. Thus, these lines of evidences strongly suggest that accelerated evolution on regulatory sequences plays important role in the evolution of human-specific phenotypes.
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Affiliation(s)
- Xinran Dong
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai, P.R. China
| | - Xiao Wang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai, P.R. China
| | - Feng Zhang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai, P.R. China
| | - Weidong Tian
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai, P.R. China Children's Hospital of Fudan University, Shanghai, P.R. China
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Cariaga-Martinez A, Saiz-Ruiz J, Alelú-Paz R. From Linkage Studies to Epigenetics: What We Know and What We Need to Know in the Neurobiology of Schizophrenia. Front Neurosci 2016; 10:202. [PMID: 27242407 PMCID: PMC4862989 DOI: 10.3389/fnins.2016.00202] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Accepted: 04/25/2016] [Indexed: 01/15/2023] Open
Abstract
Schizophrenia is a complex psychiatric disorder characterized by the presence of positive, negative, and cognitive symptoms that lacks a unifying neuropathology. In the present paper, we will review the current understanding of molecular dysregulation in schizophrenia, including genetic and epigenetic studies. In relation to the latter, basic research suggests that normal cognition is regulated by epigenetic mechanisms and its dysfunction occurs upon epigenetic misregulation, providing new insights into missing heritability of complex psychiatric diseases, referring to the discrepancy between epidemiological heritability and the proportion of phenotypic variation explained by DNA sequence difference. In schizophrenia the absence of consistently replicated genetic effects together with evidence for lasting changes in gene expression after environmental exposures suggest a role of epigenetic mechanisms. In this review we will focus on epigenetic modifications as a key mechanism through which environmental factors interact with individual's genetic constitution to affect risk of psychotic conditions throughout life.
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Affiliation(s)
- Ariel Cariaga-Martinez
- Laboratory for Neuroscience of Mental Disorders Elena Pessino, Department of Medicine and Medical Specialties, School of Medicine, Alcalá University Madrid, Spain
| | - Jerónimo Saiz-Ruiz
- Department of Psychiatry, Ramón y Cajal Hospital, IRYCISMadrid, Spain; Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM)Madrid, Spain
| | - Raúl Alelú-Paz
- Laboratory for Neuroscience of Mental Disorders Elena Pessino, Department of Medicine and Medical Specialties, School of Medicine, Alcalá UniversityMadrid, Spain; Department of Psychiatry, Ramón y Cajal Hospital, IRYCISMadrid, Spain
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Long Noncoding RNA-Directed Epigenetic Regulation of Gene Expression Is Associated With Anxiety-like Behavior in Mice. Biol Psychiatry 2015; 78:848-59. [PMID: 25792222 PMCID: PMC4532653 DOI: 10.1016/j.biopsych.2015.02.004] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 02/03/2015] [Accepted: 02/04/2015] [Indexed: 01/29/2023]
Abstract
BACKGROUND RNA-directed regulation of epigenetic processes has recently emerged as an important feature of mammalian differentiation and development. Perturbation of this regulatory system in the brain may contribute to the development of neuropsychiatric disorders. METHODS RNA sequencing was used to identify changes in the experience-dependent expression of long noncoding RNAs (lncRNAs) within the medial prefrontal cortex of adult mice. Transcripts were validated by real-time quantitative polymerase chain reaction and a candidate lncRNA, Gomafu, was selected for further investigation. The functional role of this schizophrenia-related lncRNA was explored in vivo by antisense oligonucleotide-mediated gene knockdown in the medial prefrontal cortex, followed by behavioral training and assessment of fear-related anxiety. Long noncoding RNA-directed epigenetic regulation of gene expression was investigated by chromatin and RNA immunoprecipitation assays. RESULTS RNA sequencing analysis revealed changes in the expression of a significant number of genes related to neural plasticity and stress, as well as the dynamic regulation of lncRNAs. In particular, we detected a significant downregulation of Gomafu lncRNA. Our results revealed that Gomafu plays a role in mediating anxiety-like behavior and suggest that this may occur through an interaction with a key member of the polycomb repressive complex 1, BMI1, which regulates the expression of the schizophrenia-related gene beta crystallin (Crybb1). We also demonstrated a novel role for Crybb1 in mediating fear-induced anxiety-like behavior. CONCLUSIONS Experience-dependent expression of lncRNAs plays an important role in the epigenetic regulation of adaptive behavior, and the perturbation of Gomafu may be related to anxiety and the development of neuropsychiatric disorders.
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Xu Y, Li X, Lin J, Wang Z, Yang Q, Chang Y. Transcriptome sequencing and analysis of major genes involved in calcium signaling pathways in pear plants (Pyrus calleryana Decne.). BMC Genomics 2015; 16:738. [PMID: 26424153 PMCID: PMC4590731 DOI: 10.1186/s12864-015-1887-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 08/28/2015] [Indexed: 11/17/2022] Open
Abstract
Background Pears (Pyrus spp. L.) are an important genus of trees that produce one of the world’s oldest fruit crops. Salinity stress is a common limiting factor for plant productivity that significantly affects the flavor and nutritional quality of pear fruits. Much research has shown that calcium signaling pathways, mediated by Calcineurin B-like proteins (CBLs) and their interacting kinases (CIPKs), are closely associated with responses to stresses, including salt. However, little is known about the molecular mechanisms that govern the relationship between salt stress and calcium signaling pathways in pear plants. The available genomic information for pears has promoted much functional genomic analysis and molecular breeding of the genus. This provided an ample foundation for characterizing the transcriptome of pear under salt stress. Results A high-throughput Illumina RNA-seq technology was used to identify a total of 78,695 unigenes that were successfully annotated by BLASTX analysis, using the publicly available protein database. Additionally, 2,855 novel transcripts, 218,167 SNPs, 23,248 indels and 18,322 alternative splicing events occurred. Assembled unique sequences were annotated and classified with Gene Ontology (GO), Clusters of Orthologous Group (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, which revealed that the main activated genes in pear are predominately involved in functions such as basic physiological processes, metabolic pathways, operation of cellular components, signal transduction mechanisms, and other molecular activities. Through targeted searches of the annotations, the majority of the genes involved in calcium signaling pathways were identified, among which, four genes were validated by molecular cloning, while 11 were validated by RT-qPCR expression profiles under salt stress treatment. Conclusions These results facilitate a better understanding of the molecular genetics and functional genomic mechanisms of salt stress in pear plants. Furthermore, they provide a valuable foundation for additional research on the molecular biology and functional genomics of pear and related species. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1887-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuanyuan Xu
- Jiangsu Academy of Agricultural Sciences; Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Horticulture, Nanjing, 210014, People's Republic of China
| | - Xiaogang Li
- Jiangsu Academy of Agricultural Sciences; Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Horticulture, Nanjing, 210014, People's Republic of China
| | - Jing Lin
- Jiangsu Academy of Agricultural Sciences; Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Horticulture, Nanjing, 210014, People's Republic of China.
| | - Zhonghua Wang
- Jiangsu Academy of Agricultural Sciences; Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Horticulture, Nanjing, 210014, People's Republic of China
| | - Qingsong Yang
- Jiangsu Academy of Agricultural Sciences; Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Horticulture, Nanjing, 210014, People's Republic of China
| | - Youhong Chang
- Jiangsu Academy of Agricultural Sciences; Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Horticulture, Nanjing, 210014, People's Republic of China.
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24
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Zheng Z, Wei X, Hildebrandt A, Schmidt B. A computational method for studying the relation between alternative splicing and DNA methylation. Nucleic Acids Res 2015; 44:e19. [PMID: 26365234 PMCID: PMC4737180 DOI: 10.1093/nar/gkv906] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 08/29/2015] [Indexed: 01/10/2023] Open
Abstract
Alternative splicing is an important mechanism in eukaryotes that expands the transcriptome and proteome significantly. It plays an important role in a number of biological processes. Understanding its regulation is hence an important challenge. Recently, increasing evidence has been collected that supports an involvement of intragenic DNA methylation in the regulation of alternative splicing. The exact mechanisms of regulation, however, are largely unknown, and speculated to be complex: different methylation profiles might exist, each of which could be associated with a different regulation mechanism. We present a computational technique that is able to determine such stable methylation patterns and allows to correlate these patterns with inclusion propensity of exons. Pattern detection is based on dynamic time warping (DTW) of methylation profiles, a sophisticated similarity measure for signals that can be non-trivially transformed. We design a flexible self-organizing map approach to pattern grouping. Exemplary application on available data sets indicates that stable patterns which correlate non-trivially with exon inclusion do indeed exist. To improve the reliability of these predictions, further studies on larger data sets will be required. We have thus taken great care that our software runs efficiently on modern hardware, so that it can support future studies on large-scale data sets.
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Affiliation(s)
- Zejun Zheng
- Bioinformatics Institute, Singapore 138671, Singapore
| | - Xiaona Wei
- Institute of Bioengineering and Nanotechnology, Singapore 138669, Singapore
| | - Andreas Hildebrandt
- Institut für Informatik, Johannes Gutenberg Universität Mainz, 55099 Mainz, Germany
| | - Bertil Schmidt
- Institut für Informatik, Johannes Gutenberg Universität Mainz, 55099 Mainz, Germany
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25
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Wang K, Cao K, Hannenhalli S. Chromatin and Genomic determinants of alternative splicing. ACM-BCB ... ... : THE ... ACM CONFERENCE ON BIOINFORMATICS, COMPUTATIONAL BIOLOGY AND BIOMEDICINE. ACM CONFERENCE ON BIOINFORMATICS, COMPUTATIONAL BIOLOGY AND BIOMEDICINE 2015; 2015:345-354. [PMID: 28825057 DOI: 10.1145/2808719.2808755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Alternative splicing significantly contributes to proteomic diversity and mis-regulation of splicing can cause diseases in human. Although both genomic and chromatin features have been shown to associate with splicing, the mechanisms by which various chromatin marks influence splicing is not clear for the most part. Moreover, it is not known whether the influence of specific genomic features on splicing is potentially modulated by the chromatin context. Here we report a deep neural network (DNN) model for predicting exon inclusion based on comprehensive genomic and chromatin features. Our analysis in three cell lines shows that, while both genomic and chromatin features can predict splicing to varying degrees, genomic features are the primary drivers of splicing, and the predictive power of chromatin features can largely be explained by their correlation with genomic features; chromatin features do not yield substantial independent contribution to splicing predictability. However, our model identified specific interactions between chromatin and genomic features suggesting that the effect of genomic elements may be modulated by chromatin context.
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Affiliation(s)
- Kun Wang
- Center for Bioinformatics and Computational Biology, University of Maryland
| | - Kan Cao
- Cell Biology Molecular Genetics, University of Maryland
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26
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Fang X, Robinson J, Wang-Hu J, Jiang L, Freeman DA, Rivkees SA, Wendler CC. cAMP induces hypertrophy and alters DNA methylation in HL-1 cardiomyocytes. Am J Physiol Cell Physiol 2015. [PMID: 26224577 DOI: 10.1152/ajpcell.00058.2015] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
cAMP is a highly regulated secondary messenger involved in many biological processes. Chronic activation of the cAMP pathway by catecholamines results in cardiac hypertrophy and fibrosis; however, the mechanism by which elevated cAMP leads to cardiomyopathy is not fully understood. To address this issue, we increased intracellular cAMP levels in HL-1 cardiomyocytes, a cell line derived from adult mouse atrium, using either the stable cAMP analog N(6),2'-O-dibutyryladenosine 3',5'-cyclic monophosphate (DBcAMP) or phosphodiesterase (PDE) inhibitors caffeine and theophylline. Elevated cAMP levels increased cell size and altered expression levels of cardiac genes and micro-RNAs associated with hypertrophic cardiomyopathy (HCM), including Myh6, Myh7, Myh7b, Tnni3, Anp, Bnp, Gata4, Mef2c, Mef2d, Nfatc1, miR208a, and miR208b. In addition, DBcAMP altered the expression of DNA methyltransferases (Dnmts) and Tet methylcytosine dioxygenases (Tets), enzymes that regulate genomic DNA methylation levels. Changes in expression of DNA methylation genes induced by elevated cAMP led to increased global DNA methylation in HL-1 cells. In contrast, inhibition of DNMT activity with 5-azacytidine treatment decreased global DNA methylation levels and blocked the increased expression of several HCM genes (Myh7, Gata4, Mef2c, Nfatc1, Myh7b, Tnni3, and Bnp) observed with DBcAMP treatment. These results demonstrate that cAMP induces cardiomyocyte hypertrophy and altered HCM gene expression in vitro and that DNA methylation patterns mediate the upregulation of HCM genes induced by cAMP. These data identify a previously unknown mechanism by which elevated levels of cAMP lead to increased expression of genes associated with cardiomyocyte hypertrophy.
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Affiliation(s)
- Xiefan Fang
- Department of Pediatrics, Child Health Research Institute, College of Medicine, University of Florida, Gainesville, Florida
| | - Jourdon Robinson
- Department of Pediatrics, Child Health Research Institute, College of Medicine, University of Florida, Gainesville, Florida
| | - John Wang-Hu
- Department of Pediatrics, Child Health Research Institute, College of Medicine, University of Florida, Gainesville, Florida
| | - Lingli Jiang
- Department of Pediatrics, Child Health Research Institute, College of Medicine, University of Florida, Gainesville, Florida
| | - Daniel A Freeman
- Department of Pediatrics, Child Health Research Institute, College of Medicine, University of Florida, Gainesville, Florida
| | - Scott A Rivkees
- Department of Pediatrics, Child Health Research Institute, College of Medicine, University of Florida, Gainesville, Florida
| | - Christopher C Wendler
- Department of Pediatrics, Child Health Research Institute, College of Medicine, University of Florida, Gainesville, Florida
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27
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González-Vallinas J, Pagès A, Singh B, Eyras E. A semi-supervised approach uncovers thousands of intragenic enhancers differentially activated in human cells. BMC Genomics 2015; 16:523. [PMID: 26169177 PMCID: PMC4501197 DOI: 10.1186/s12864-015-1704-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 06/15/2015] [Indexed: 02/06/2023] Open
Abstract
Background Transcriptional enhancers are generally known to regulate gene transcription from afar. Their activation involves a series of changes in chromatin marks and recruitment of protein factors. These enhancers may also occur inside genes, but how many may be active in human cells and their effects on the regulation of the host gene remains unclear. Results We describe a novel semi-supervised method based on the relative enrichment of chromatin signals between 2 conditions to predict active enhancers. We applied this method to the tumoral K562 and the normal GM12878 cell lines to predict enhancers that are differentially active in one cell type. These predictions show enhancer-like properties according to positional distribution, correlation with gene expression and production of enhancer RNAs. Using this model, we predict 10,365 and 9777 intragenic active enhancers in K562 and GM12878, respectively, and relate the differential activation of these enhancers to expression and splicing differences of the host genes. Conclusions We propose that the activation or silencing of intragenic transcriptional enhancers modulate the regulation of the host gene by means of a local change of the chromatin and the recruitment of enhancer-related factors that may interact with the RNA directly or through the interaction with RNA binding proteins. Predicted enhancers are available at http://regulatorygenomics.upf.edu/Projects/enhancers.html. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1704-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Amadís Pagès
- Universitat Pompeu Fabra, Dr Aiguader 88, E08003, Barcelona, Spain.
| | - Babita Singh
- Universitat Pompeu Fabra, Dr Aiguader 88, E08003, Barcelona, Spain.
| | - Eduardo Eyras
- Universitat Pompeu Fabra, Dr Aiguader 88, E08003, Barcelona, Spain. .,Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluís Companys 23, E08010, Barcelona, Spain.
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28
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Warns JA, Davie JR, Dhasarathy A. Connecting the dots: chromatin and alternative splicing in EMT. Biochem Cell Biol 2015; 94:12-25. [PMID: 26291837 DOI: 10.1139/bcb-2015-0053] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Nature has devised sophisticated cellular machinery to process mRNA transcripts produced by RNA Polymerase II, removing intronic regions and connecting exons together, to produce mature RNAs. This process, known as splicing, is very closely linked to transcription. Alternative splicing, or the ability to produce different combinations of exons that are spliced together from the same genomic template, is a fundamental means of regulating protein complexity. Similar to transcription, both constitutive and alternative splicing can be regulated by chromatin and its associated factors in response to various signal transduction pathways activated by external stimuli. This regulation can vary between different cell types, and interference with these pathways can lead to changes in splicing, often resulting in aberrant cellular states and disease. The epithelial to mesenchymal transition (EMT), which leads to cancer metastasis, is influenced by alternative splicing events of chromatin remodelers and epigenetic factors such as DNA methylation and non-coding RNAs. In this review, we will discuss the role of epigenetic factors including chromatin, chromatin remodelers, DNA methyltransferases, and microRNAs in the context of alternative splicing, and discuss their potential involvement in alternative splicing during the EMT process.
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Affiliation(s)
- Jessica A Warns
- a Department of Basic Sciences, University of North Dakota School of Medicine and Health Sciences, 501 N. Columbia Road Stop 9061, Grand Forks, ND 58202-9061, USA
| | - James R Davie
- b Children's Hospital Research Institute of Manitoba, John Buhler Research Centre, Winnipeg, Manitoba R3E 3P4, Canada
| | - Archana Dhasarathy
- a Department of Basic Sciences, University of North Dakota School of Medicine and Health Sciences, 501 N. Columbia Road Stop 9061, Grand Forks, ND 58202-9061, USA
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29
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Agirre E, Bellora N, Alló M, Pagès A, Bertucci P, Kornblihtt AR, Eyras E. A chromatin code for alternative splicing involving a putative association between CTCF and HP1α proteins. BMC Biol 2015; 13:31. [PMID: 25934638 PMCID: PMC4446157 DOI: 10.1186/s12915-015-0141-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 04/22/2015] [Indexed: 12/20/2022] Open
Abstract
Background Alternative splicing is primarily controlled by the activity of splicing factors and by the elongation of the RNA polymerase II (RNAPII). Recent experiments have suggested a new complex network of splicing regulation involving chromatin, transcription and multiple protein factors. In particular, the CCCTC-binding factor (CTCF), the Argonaute protein AGO1, and members of the heterochromatin protein 1 (HP1) family have been implicated in the regulation of splicing associated with chromatin and the elongation of RNAPII. These results raise the question of whether these proteins may associate at the chromatin level to modulate alternative splicing. Results Using chromatin immunoprecipitation sequencing (ChIP-Seq) data for CTCF, AGO1, HP1α, H3K27me3, H3K9me2, H3K36me3, RNAPII, total H3 and 5metC and alternative splicing arrays from two cell lines, we have analyzed the combinatorial code of their binding to chromatin in relation to the alternative splicing patterns between two cell lines, MCF7 and MCF10. Using Machine Learning techniques, we identified the changes in chromatin signals that are most significantly associated with splicing regulation between these two cell lines. Moreover, we have built a map of the chromatin signals on the pre-mRNA, that is, a chromatin-based RNA-map, which can explain 606 (68.55%) of the regulated events between MCF7 and MCF10. This chromatin code involves the presence of HP1α, CTCF, AGO1, RNAPII and histone marks around regulated exons and can differentiate patterns of skipping and inclusion. Additionally, we found a significant association of HP1α and CTCF activities around the regulated exons and a putative DNA binding site for HP1α. Conclusions Our results show that a considerable number of alternative splicing events could have a chromatin-dependent regulation involving the association of HP1α and CTCF near regulated exons. Additionally, we find further evidence for the involvement of HP1α and AGO1 in chromatin-related splicing regulation. Electronic supplementary material The online version of this article (doi:10.1186/s12915-015-0141-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Eneritz Agirre
- Universitat Pompeu Fabra, E08003, Barcelona, Spain. .,Present address: Institute of Human Genetics, CNRS UPR 1142, Montpellier, France.
| | - Nicolás Bellora
- Universitat Pompeu Fabra, E08003, Barcelona, Spain. .,Present address: INIBIOMA, CONICET-UNComahue, Bariloche, Río Negro, Argentina.
| | - Mariano Alló
- IFIBYNE-UBA-CONICET, Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, (C1428EHA), Buenos Aires, Argentina. .,Present address: European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany.
| | - Amadís Pagès
- Universitat Pompeu Fabra, E08003, Barcelona, Spain. .,Centre for Genomic Regulation, E08003, Barcelona, Spain.
| | - Paola Bertucci
- IFIBYNE-UBA-CONICET, Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, (C1428EHA), Buenos Aires, Argentina. .,Present address: European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany.
| | - Alberto R Kornblihtt
- IFIBYNE-UBA-CONICET, Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, (C1428EHA), Buenos Aires, Argentina.
| | - Eduardo Eyras
- Universitat Pompeu Fabra, E08003, Barcelona, Spain. .,Catalan Institution of Research and Advanced Studies (ICREA), E08010, Barcelona, Spain.
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30
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Sun X, Zuo F, Ru Y, Guo J, Yan X, Sablok G. SplicingTypesAnno: annotating and quantifying alternative splicing events for RNA-Seq data. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2015; 119:53-62. [PMID: 25720307 DOI: 10.1016/j.cmpb.2015.02.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 01/16/2015] [Accepted: 02/06/2015] [Indexed: 06/04/2023]
Abstract
Alternative splicing plays a key role in the regulation of the central dogma. Four major types of alternative splicing have been classified as intron retention, exon skipping, alternative 5 splice sites or alternative donor sites, and alternative 3 splice sites or alternative acceptor sites. A few algorithms have been developed to detect splice junctions from RNA-Seq reads. However, there are few tools targeting at the major alternative splicing types at the exon/intron level. This type of analysis may reveal subtle, yet important events of alternative splicing, and thus help gain deeper understanding of the mechanism of alternative splicing. This paper describes a user-friendly R package, extracting, annotating and analyzing alternative splicing types for sequence alignment files from RNA-Seq. SplicingTypesAnno can: (1) provide annotation for major alternative splicing at exon/intron level. By comparing the annotation from GTF/GFF file, it identifies the novel alternative splicing sites; (2) offer a convenient two-level analysis: genome-scale annotation for users with high performance computing environment, and gene-scale annotation for users with personal computers; (3) generate a user-friendly web report and additional BED files for IGV visualization. SplicingTypesAnno is a user-friendly R package for extracting, annotating and analyzing alternative splicing types at exon/intron level for sequence alignment files from RNA-Seq. It is publically available at https://sourceforge.net/projects/splicingtypes/files/ or http://genome.sdau.edu.cn/research/software/SplicingTypesAnno.html.
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Affiliation(s)
- Xiaoyong Sun
- Agricultural Big-Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian, Shandong 271018, China.
| | - Fenghua Zuo
- College of Information Engineering, Taishan Medical University, Taian, Shandong 271000, China
| | - Yuanbin Ru
- Department of Biomedical Informatics, Windber Research Institute, Windber, PA 15963, USA
| | - Jiqiang Guo
- Applied Statistics Center, Columbia University, New York, NY 10027, USA
| | - Xiaoyan Yan
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine, No. 42 Wenhua West Road, Jinan, Shandong 250011, China
| | - Gaurav Sablok
- Plant Functional Biology and Climate Change Cluster (C3), University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia
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Liu H, Jin T, Guan J, Zhou S. Histone modifications involved in cassette exon inclusions: a quantitative and interpretable analysis. BMC Genomics 2014; 15:1148. [PMID: 25526687 PMCID: PMC4378014 DOI: 10.1186/1471-2164-15-1148] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 11/20/2014] [Indexed: 11/16/2022] Open
Abstract
Background Chromatin structure and epigenetic modifications have been shown to involve in the co-transcriptional splicing of RNA precursors. In particular, some studies have suggested that some types of histone modifications (HMs) may participate in the alternative splicing and function as exon marks. However, most existing studies pay attention to the qualitative relationship between epigenetic modifications and exon inclusion. The quantitative analysis that reveals to what extent each type of epigenetic modification is responsible for exon inclusion is very helpful for us to understand the splicing process. Results In this paper, we focus on the quantitative analysis of HMs’ influence on the inclusion of cassette exons (CEs) into mature RNAs. With the high-throughput ChIP-seq and RNA-seq data obtained from ENCODE website, we modeled the association of HMs with CE inclusions by logistic regression whose coefficients are meaningful and interpretable for us to reveal the effect of each type of HM. Three type of HMs, H3K36me3, H3K9me3 and H4K20me1, were found to play major role in CE inclusions. HMs’ effect on CE inclusions is conservative across cell types, and does not depend on the expression levels of the genes hosting CEs. HMs located in the flanking regions of CEs were also taken into account in our analysis, and HMs within bounded flanking regions were shown to affect moderately CE inclusions. Moreover, we also found that HMs on CEs whose length is approximately close to nucleosomal-DNA length affect greatly on CE inclusion. Conclusions We suggested that a few types of HMs correlate closely to alternative splicing and perhaps function jointly with splicing machinery to regulate the inclusion level of exons. Our findings are helpful to understand HMs’ effect on exon definition, as well as the mechanism of co-transcriptional splicing. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1148) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | - Shuigeng Zhou
- Shanghai Key Lab of Intelligent Information Processing, and School of Computer Science, Fudan University, 200433 Shanghai, China.
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Podlaha O, De S, Gonen M, Michor F. Histone modifications are associated with transcript isoform diversity in normal and cancer cells. PLoS Comput Biol 2014; 10:e1003611. [PMID: 24901363 PMCID: PMC4046914 DOI: 10.1371/journal.pcbi.1003611] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 03/26/2014] [Indexed: 11/29/2022] Open
Abstract
Mechanisms that generate transcript diversity are of fundamental importance in eukaryotes. Although a large fraction of human protein-coding genes and lincRNAs produce more than one mRNA isoform each, the regulation of this phenomenon is still incompletely understood. Much progress has been made in deciphering the role of sequence-specific features as well as DNA-and RNA-binding proteins in alternative splicing. Recently, however, several experimental studies of individual genes have revealed a direct involvement of epigenetic factors in alternative splicing and transcription initiation. While histone modifications are generally correlated with overall gene expression levels, it remains unclear how histone modification enrichment affects relative isoform abundance. Therefore, we sought to investigate the associations between histone modifications and transcript diversity levels measured by the rates of transcription start-site switching and alternative splicing on a genome-wide scale across protein-coding genes and lincRNAs. We found that the relationship between enrichment levels of epigenetic marks and transcription start-site switching is similar for protein-coding genes and lincRNAs. Furthermore, we found associations between splicing rates and enrichment levels of H2az, H3K4me1, H3K4me2, H3K4me3, H3K9ac, H3K9me3, H3K27ac, H3K27me3, H3K36me3, H3K79me2, and H4K20me, marks traditionally associated with enhancers, transcription initiation, transcriptional repression, and others. These patterns were observed in both normal and cancer cell lines. Additionally, we developed a novel computational method that identified 840 epigenetically regulated candidate genes and predicted transcription start-site switching and alternative exon splicing with up to 92% accuracy based on epigenetic patterning alone. Our results suggest that the epigenetic regulation of transcript isoform diversity may be a relatively common genome-wide phenomenon representing an avenue of deregulation in tumor development. Traditionally, the regulation of gene expression was thought to be largely based on DNA and RNA sequence motifs. However, this dogma has recently been challenged as other factors, such as epigenetic patterning of the genome, have become better understood. Sparse but convincing experimental evidence suggests that the epigenetic background, in the form of histone modifications, acts as an additional layer of regulation determining how transcripts are processed. Here we developed a computational approach to investigate the genome-wide prevalence and the level of association between the enrichment of epigenetic marks and transcript diversity generated via alternative transcription start sites and splicing. We found that the role of epigenetic patterning in alternative transcription start-site switching is likely to be the same for all genes whereas the role of epigenetic patterns in splicing is likely gene-specific. Furthermore, we show that epigenetic data alone can be used to predict the inclusion pattern of an exon. These findings have significant implications for a better understanding of the regulation of transcript diversity in humans as well as the modifications arising during tumor development.
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Affiliation(s)
- Ondrej Podlaha
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, and Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Subhajyoti De
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, United States of America; Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, Colorado, United States of America; Molecular Oncology Program, University of Colorado Cancer Center, Aurora, Colorado, United States of America
| | - Mithat Gonen
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Franziska Michor
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, and Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
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Suzuki MG, Ito H, Aoki F. Effects of RNAi-mediated knockdown of histone methyltransferases on the sex-specific mRNA expression of Imp in the silkworm Bombyx mori. Int J Mol Sci 2014; 15:6772-96. [PMID: 24758924 PMCID: PMC4013661 DOI: 10.3390/ijms15046772] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 03/25/2014] [Accepted: 04/10/2014] [Indexed: 12/11/2022] Open
Abstract
Sexual differentiation in Bombyx mori is controlled by sex-specific splicing of Bmdsx, which results in the omission of exons 3 and 4 in a male-specific manner. In B. mori, insulin-like growth factor II mRNA-binding protein (Imp) is a male-specific factor involved in male-specific splicing of Bmdsx. Male-specific Imp mRNA results from the male-specific inclusion of exon 8. To verify the link between histone methylation and alternative RNA processing in Imp, we examined the effects of RNAi-mediated knockdown of several histone methyltransferases on the sex-specific mRNA expression of Imp. As a result, male-specific expression of Imp mRNA was completely abolished when expression of the H3K79 methyltransferase DOT1L was repressed to <10% of that in control males. Chromatin immunoprecipitation-quantitative PCR analysis revealed a higher distribution of H3K79me2 in normal males than in normal females across Imp. RNA polymerase II (RNAP II) processivity assays indicated that RNAi knockdown of DOT1L in males caused a twofold decrease in RNAP II processivity compared to that in control males, with almost equivalent levels to those observed in normal females. Inhibition of RNAP II-mediated elongation in male cells repressed the male-specific splicing of Imp. Our data suggest the possibility that H3K79me2 accumulation along Imp is associated with the male-specific alternative processing of Imp mRNA that results from increased RNAP II processivity.
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Affiliation(s)
- Masataka G Suzuki
- Division of Biological Sciences, Department of Integrated Biosciences, Graduate School of Frontier Sciences, the University of Tokyo, 302 Bioscience-Bldg, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan.
| | - Haruka Ito
- Division of Biological Sciences, Department of Integrated Biosciences, Graduate School of Frontier Sciences, the University of Tokyo, 302 Bioscience-Bldg, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan.
| | - Fugaku Aoki
- Division of Biological Sciences, Department of Integrated Biosciences, Graduate School of Frontier Sciences, the University of Tokyo, 302 Bioscience-Bldg, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan.
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34
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Guo A, Zheng CX, Yang YY. Differential expression of SLOW WALKER2 homologue in ovules of female sterile mutant and fertile clone of Pinus tabulaeformis. Russ J Dev Biol 2014. [DOI: 10.1134/s1062360414020052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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35
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Schoch H, Abel T. Transcriptional co-repressors and memory storage. Neuropharmacology 2014; 80:53-60. [PMID: 24440532 DOI: 10.1016/j.neuropharm.2014.01.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 01/03/2014] [Accepted: 01/04/2014] [Indexed: 12/26/2022]
Abstract
Epigenetic modifications are a central mechanism for regulating chromatin structure and gene expression in the brain. A wide array of histone- and DNA-modifying enzymes have been identified as critical regulators of neuronal function, memory formation, and as causative agents in neurodevelopmental and neuropsychiatric disorders. Chromatin modifying enzymes are frequently incorporated into large multi-protein co-activator and co-repressor complexes, where the activity of multiple enzymes is both spatially and temporally coordinated. In this review, we discuss negative regulation of gene expression by co-repressor complexes, and the role of co-repressors and their binding partners in neuronal function, memory, and disease.
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Affiliation(s)
- Hannah Schoch
- Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ted Abel
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
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36
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Kanski R, Sneeboer MAM, van Bodegraven EJ, Sluijs JA, Kropff W, Vermunt MW, Creyghton MP, De Filippis L, Vescovi A, Aronica E, van Tijn P, van Strien ME, Hol EM. Histone acetylation in astrocytes suppresses GFAP and stimulates a re-organization of the intermediate filament network. J Cell Sci 2014; 127:4368-80. [DOI: 10.1242/jcs.145912] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Glial Fibrillary Acidic Protein (GFAP) is the main intermediate filament in astrocytes and is regulated by epigenetic mechanisms during development. We demonstrate that histone acetylation controls GFAP expression also in mature astrocytes. Inhibition of histone deacetylases (HDACs) with Trichostatin-A or Sodium-butyrate reduced GFAP expression in primary human astrocytes and astrocytoma cells. Since splicing occurs co-transcriptional, we investigated whether histone acetylation changes the ratio between the canonical isoform GFAPα and the alternative GFAPδ splice-variant. We observed that decreased transcription of GFAP enhanced alternative isoform expression, as HDAC inhibition increased the GFAPδ/α ratio favouring GFAPδ. Expression of GFAPδ was dependent on the presence and binding of the splicing factors of the SR protein family. Inhibition of HDAC activity also resulted in aggregation of the GFAP network, reminiscent to our earlier findings of a GFAPδ-induced network collapse. Together, our data demonstrate that HDAC inhibition results in changes in transcription, splicing, and organization of GFAP. These data imply that a tight regulation of histone acetylation in astrocytes is essential, since dysregulation of gene expression causes aggregation of GFAP, a hallmark of human diseases like Alexander's disease.
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37
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Cameron RC, Duncan EJ, Dearden PK. Biased gene expression in early honeybee larval development. BMC Genomics 2013; 14:903. [PMID: 24350621 PMCID: PMC3878232 DOI: 10.1186/1471-2164-14-903] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 12/12/2013] [Indexed: 12/25/2022] Open
Abstract
Background Female larvae of the honeybee (Apis mellifera) develop into either queens or workers depending on nutrition. This nutritional stimulus triggers different developmental trajectories, resulting in adults that differ from each other in physiology, behaviour and life span. Results To understand how these trajectories are established we have generated a comprehensive atlas of gene expression throughout larval development. We found substantial differences in gene expression between worker and queen-destined larvae at 6 hours after hatching. Some of these early changes in gene expression are maintained throughout larval development, indicating that caste-specific developmental trajectories are established much earlier than previously thought. Within our gene expression data we identified processes that potentially underlie caste differentiation. Queen-destined larvae have higher expression of genes involved in transcription, translation and protein folding early in development with a later switch to genes involved in energy generation. Using RNA interference, we were able to demonstrate that one of these genes, hexamerin 70b, has a role in caste differentiation. Both queen and worker developmental trajectories are associated with the expression of genes that have alternative splice variants, although only a single variant of a gene tends to be differentially expressed in a given caste. Conclusions Our data, based on the biases in gene expression early in development together with published data, supports the idea that caste development in the honeybee consists of two phases; an initial biased phase of development, where larvae can still switch to the other caste by differential feeding, followed by commitment to a particular developmental trajectory.
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Affiliation(s)
| | | | - Peter K Dearden
- Laboratory for Evolution and Development, Gravida, the National Centre for Growth and Development and Genetics Otago, Department of Biochemistry, University of Otago, Dunedin, Aotearoa-New Zealand.
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38
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Lu Y, Zhou Y, Tian W. Combining Hi-C data with phylogenetic correlation to predict the target genes of distal regulatory elements in human genome. Nucleic Acids Res 2013; 41:10391-402. [PMID: 24003029 PMCID: PMC3905853 DOI: 10.1093/nar/gkt785] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Defining the target genes of distal regulatory elements (DREs), such as enhancer, repressors and insulators, is a challenging task. The recently developed Hi-C technology is designed to capture chromosome conformation structure by high-throughput sequencing, and can be potentially used to determine the target genes of DREs. However, Hi-C data are noisy, making it difficult to directly use Hi-C data to identify DRE-target gene relationships. In this study, we show that DREs-gene pairs that are confirmed by Hi-C data are strongly phylogenetic correlated, and have thus developed a method that combines Hi-C read counts with phylogenetic correlation to predict long-range DRE-target gene relationships. Analysis of predicted DRE-target gene pairs shows that genes regulated by large number of DREs tend to have essential functions, and genes regulated by the same DREs tend to be functionally related and co-expressed. In addition, we show with a couple of examples that the predicted target genes of DREs can help explain the causal roles of disease-associated single-nucleotide polymorphisms located in the DREs. As such, these predictions will be of importance not only for our understanding of the function of DREs but also for elucidating the causal roles of disease-associated noncoding single-nucleotide polymorphisms.
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Affiliation(s)
- Yulan Lu
- State Key Laboratory of Genetic Engineering, Department of Biostatistics and Computational Biology, School of Life Science, Fudan University, Shanghai 200433, China
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39
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Liao W, Jordaan G, Srivastava MK, Dubinett S, Sharma S, Sharma S. Effect of epigenetic histone modifications on E-cadherin splicing and expression in lung cancer. Am J Cancer Res 2013; 3:374-389. [PMID: 23977447 PMCID: PMC3744017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Accepted: 07/29/2013] [Indexed: 06/02/2023] Open
Abstract
We have identified an alternatively spliced, non-functional aberrant E-cadherin transcript that lacks exon 11 and is over expressed in malignant cells as compared to the normal non-malignant cells. This increase in the aberrant transcript is a mechanism of loss of E-cadherin gene expression as it is rapidly degraded by the nonsense mediated decay pathway. To study the mechanism of this gene missplicing we analyzed the role of histone epigenetic modifications in lung cancer cell lines. The treatment of low E-cadherin lung cancer cell lines with histone deacetylase inhibitor (HDACi, MS-275) resulted in the preferential expression of the correctly spliced transcripts in the low E-cadherin expressing cell lines only. Chromatin immunoprecipitation (ChIP) assays revealed that the histone hypoacetylation levels correlate with aberrant exon 11 splicing as there is more aberrant splicing in cell lines with E-cadherin promoter hypoacetylation. Inactivation of histone deacetylases (HDAC) 1, 2 and 3 resulted in an increase in E-cadherin expression and an increase in the ratio of the correctly spliced E-cadherin transcript. As transcription of the gene is closely linked to splicing, we considered the possibility that change in E-cadherin transcription correlates with splicing. The Zeb1 epithelial-mesenchymal transformation (EMT) inducer silences E-cadherin expression and could also alter the splicing of this exon. Inhibition of the E-cadherin promoter transcription with Zeb1 expression increases aberrant splicing and the reverse is observed when Zeb1 is knocked down. The role of HDAC inhibitors was also studied in vivo in a immunodeficient mouse xenograft model. Exposure of mice to HDACi resulted in growth inhibition, increase in E-cadherin expression, alteration of aberrant splicing and the reversal of EMT in mouse tumors. The findings support the modulation of E-cadherin exon 11 inclusion or exclusion by histone epigenetic modifications as they change the overall chromatin structure. The results provide an interesting link between epigenetic alterations in cancer cells and gene splicing in addition to their effect on gene silencing.
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Affiliation(s)
- Wei Liao
- UCLA West Los Angeles VA Medical Center, Division of Hematology OncologyLos Angeles, California
| | - Gwen Jordaan
- UCLA West Los Angeles VA Medical Center, Division of Hematology OncologyLos Angeles, California
| | - Minu K Srivastava
- UCLA West Los Angeles VA Medical Center, Division of Hematology OncologyLos Angeles, California
- Molecular Medicine Laboratory, Veterans Affairs Greater Los Angeles Healthcare SystemLos Angeles, California
| | - Steven Dubinett
- UCLA West Los Angeles VA Medical Center, Division of Hematology OncologyLos Angeles, California
- Molecular Medicine Laboratory, Veterans Affairs Greater Los Angeles Healthcare SystemLos Angeles, California
- Division of Pulmonary and Critical Care Medicine, UCLALos Angeles, California
| | - Sherven Sharma
- UCLA West Los Angeles VA Medical Center, Division of Hematology OncologyLos Angeles, California
- Molecular Medicine Laboratory, Veterans Affairs Greater Los Angeles Healthcare SystemLos Angeles, California
- Division of Pulmonary and Critical Care Medicine, UCLALos Angeles, California
| | - Sanjai Sharma
- UCLA West Los Angeles VA Medical Center, Division of Hematology OncologyLos Angeles, California
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40
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Slieker RC, Bos SD, Goeman JJ, Bovée JVMG, Talens RP, van der Breggen R, Suchiman HED, Lameijer EW, Putter H, van den Akker EB, Zhang Y, Jukema JW, Slagboom PE, Meulenbelt I, Heijmans BT. Identification and systematic annotation of tissue-specific differentially methylated regions using the Illumina 450k array. Epigenetics Chromatin 2013; 6:26. [PMID: 23919675 PMCID: PMC3750594 DOI: 10.1186/1756-8935-6-26] [Citation(s) in RCA: 178] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 06/28/2013] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND DNA methylation has been recognized as a key mechanism in cell differentiation. Various studies have compared tissues to characterize epigenetically regulated genomic regions, but due to differences in study design and focus there still is no consensus as to the annotation of genomic regions predominantly involved in tissue-specific methylation. We used a new algorithm to identify and annotate tissue-specific differentially methylated regions (tDMRs) from Illumina 450k chip data for four peripheral tissues (blood, saliva, buccal swabs and hair follicles) and six internal tissues (liver, muscle, pancreas, subcutaneous fat, omentum and spleen with matched blood samples). RESULTS The majority of tDMRs, in both relative and absolute terms, occurred in CpG-poor regions. Further analysis revealed that these regions were associated with alternative transcription events (alternative first exons, mutually exclusive exons and cassette exons). Only a minority of tDMRs mapped to gene-body CpG islands (13%) or CpG islands shores (25%) suggesting a less prominent role for these regions than indicated previously. Implementation of ENCODE annotations showed enrichment of tDMRs in DNase hypersensitive sites and transcription factor binding sites. Despite the predominance of tissue differences, inter-individual differences in DNA methylation in internal tissues were correlated with those for blood for a subset of CpG sites in a locus- and tissue-specific manner. CONCLUSIONS We conclude that tDMRs preferentially occur in CpG-poor regions and are associated with alternative transcription. Furthermore, our data suggest the utility of creating an atlas cataloguing variably methylated regions in internal tissues that correlate to DNA methylation measured in easy accessible peripheral tissues.
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Affiliation(s)
- Roderick C Slieker
- Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Steffan D Bos
- Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
- Netherlands Consortium for Healthy Aging, PO Box 9600, Leiden 2300, RC, The Netherlands
| | - Jelle J Goeman
- Medical Statistics, Leiden University Medical Center, Leiden, The Netherlands
| | - Judith VMG Bovée
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Rudolf P Talens
- Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ruud van der Breggen
- Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - H Eka D Suchiman
- Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Eric-Wubbo Lameijer
- Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Hein Putter
- Medical Statistics, Leiden University Medical Center, Leiden, The Netherlands
| | - Erik B van den Akker
- Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
- The Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
| | - Yanju Zhang
- Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - J Wouter Jukema
- Department of Cardiology, Leiden University Medical Center, Leiden, The Netherlands
| | - P Eline Slagboom
- Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
- Netherlands Consortium for Healthy Aging, PO Box 9600, Leiden 2300, RC, The Netherlands
| | - Ingrid Meulenbelt
- Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
- Netherlands Consortium for Healthy Aging, PO Box 9600, Leiden 2300, RC, The Netherlands
| | - Bastiaan T Heijmans
- Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
- Netherlands Consortium for Healthy Aging, PO Box 9600, Leiden 2300, RC, The Netherlands
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Wan J, Oliver VF, Zhu H, Zack DJ, Qian J, Merbs SL. Integrative analysis of tissue-specific methylation and alternative splicing identifies conserved transcription factor binding motifs. Nucleic Acids Res 2013; 41:8503-14. [PMID: 23887936 PMCID: PMC3794605 DOI: 10.1093/nar/gkt652] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The exact role of intragenic DNA methylation in regulating tissue-specific gene regulation is unclear. Recently, the DNA-binding protein CTCF has been shown to participate in the regulation of alternative splicing in a DNA methylation-dependent manner. To globally evaluate the relationship between DNA methylation and tissue-specific alternative splicing, we performed genome-wide DNA methylation profiling of mouse retina and brain. In protein-coding genes, tissue-specific differentially methylated regions (T-DMRs) were preferentially located in exons and introns. Gene ontology and evolutionary conservation analysis suggest that these T-DMRs are likely to be biologically relevant. More than 14% of alternatively spliced genes were associated with a T-DMR. T-DMR-associated genes were enriched for developmental genes, suggesting that a specific set of alternatively spliced genes may be regulated through DNA methylation. Novel DNA sequences motifs overrepresented in T-DMRs were identified as being associated with positive and/or negative regulation of alternative splicing in a position-dependent context. The majority of these evolutionarily conserved motifs contain a CpG dinucleotide. Some transcription factors, which recognize these motifs, are known to be involved in splicing. Our results suggest that DNA methylation-dependent alternative splicing is widespread and lay the foundation for further mechanistic studies of the role of DNA methylation in tissue-specific splicing regulation.
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Affiliation(s)
- Jun Wan
- Department of Ophthalmology, Wilmer Institute, Johns Hopkins University School of Medicine, 600 North Wolfe Street, 21287 Baltimore, MD, USA, Department of Pharmacology and Molecular Science, Johns Hopkins University School of Medicine, 600 North Wolfe Street, 21287 Baltimore, MD, USA, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, 600 North Wolfe Street, 21287 Baltimore, MD, USA, Department of Neuroscience, Johns Hopkins University School of Medicine, 600 North Wolfe Street, 21287 Baltimore, MD, USA, Institute of Genetic Medicine, Johns Hopkins University School of Medicine, 600 North Wolfe Street, 21287 Baltimore, MD, USA and Institut de la Vision, 17 rue Moreau, 75012 Paris, France
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CpG islands under selective pressure are enriched with H3K4me3, H3K27ac and H3K36me3 histone modifications. BMC Evol Biol 2013; 13:145. [PMID: 23837650 PMCID: PMC3711888 DOI: 10.1186/1471-2148-13-145] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 07/04/2013] [Indexed: 11/30/2022] Open
Abstract
Background Histone modification is an epigenetic mechanism that influences gene regulation in eukaryotes. In particular, histone modifications in CpG islands (CGIs) are associated with different chromatin states and with transcription activity. Changes in gene expression play a crucial role in adaptation and evolution. Results In this paper, we have studied, using a computational biology approach, the relationship between histone modifications in CGIs and selective pressure in Homo sapiens. We considered three histone modifications: histone H3 lysine 4 trimethylation (H3K4me3), histone H3 lysine 27 acetylation (H3K27ac) and histone H3 lysine 36 trimethylation (H3K36me3), and we used the publicly available genomic-scale histone modification data of thirteen human cell lines. To define regions under selective pressure, we used three distinct signatures that mark selective events from different evolutionary periods. We found that CGIs under selective pressure showed significant enrichments for histone modifications. Conclusion Our result suggests that, CGIs that have undergone selective events are characterized by epigenetic signatures, in particular, histone modifications that are distinct from CGIs with no evidence of selection.
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43
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Ye YH, Woolfit M, Huttley GA, Rancès E, Caragata EP, Popovici J, O'Neill SL, McGraw EA. Infection with a Virulent Strain of Wolbachia Disrupts Genome Wide-Patterns of Cytosine Methylation in the Mosquito Aedes aegypti. PLoS One 2013; 8:e66482. [PMID: 23840485 PMCID: PMC3686743 DOI: 10.1371/journal.pone.0066482] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Accepted: 05/07/2013] [Indexed: 11/24/2022] Open
Abstract
Background Cytosine methylation is one of several reversible epigenetic modifications of DNA that allow a greater flexibility in the relationship between genotype and phenotype. Methylation in the simplest models dampens gene expression by modifying regions of DNA critical for transcription factor binding. The capacity to methylate DNA is variable in the insects due to diverse histories of gene loss and duplication of DNA methylases. Mosquitoes like Drosophila melanogaster possess only a single methylase, DNMT2. Description Here we characterise the methylome of the mosquito Aedes aegypti and examine its relationship to transcription and test the effects of infection with a virulent strain of the endosymbiont Wolbachia on the stability of methylation patterns. Conclusion We see that methylation in the A. aegypti genome is associated with reduced transcription and is most common in the promoters of genes relating to regulation of transcription and metabolism. Similar gene classes are also methylated in aphids and honeybees, suggesting either conservation or convergence of methylation patterns. In addition to this evidence of evolutionary stability, we also show that infection with the virulent wMelPop Wolbachia strain induces additional methylation and demethylation events in the genome. While most of these changes seem random with respect to gene function and have no detected effect on transcription, there does appear to be enrichment of genes associated with membrane function. Given that Wolbachia lives within a membrane-bound vacuole of host origin and retains a large number of genes for transporting host amino acids, inorganic ions and ATP despite a severely reduced genome, these changes might represent an evolved strategy for manipulating the host environments for its own gain. Testing for a direct link between these methylation changes and expression, however, will require study across a broader range of developmental stages and tissues with methods that detect splice variants.
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Affiliation(s)
- Yixin H. Ye
- School of Biological Sciences, Monash University, Melbourne, Australia
| | - Megan Woolfit
- School of Biological Sciences, Monash University, Melbourne, Australia
| | - Gavin A. Huttley
- The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Edwige Rancès
- School of Biological Sciences, Monash University, Melbourne, Australia
| | - Eric P. Caragata
- School of Biological Sciences, Monash University, Melbourne, Australia
| | - Jean Popovici
- School of Biological Sciences, Monash University, Melbourne, Australia
| | - Scott L. O'Neill
- School of Biological Sciences, Monash University, Melbourne, Australia
| | - Elizabeth A. McGraw
- School of Biological Sciences, Monash University, Melbourne, Australia
- * E-mail:
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Quinlivan EP, Crider KS, Zhu JH, Maneval DR, Hao L, Li Z, Rasmussen SA, Berry RJ, Bailey LB. Hypomethylation of serum blood clot DNA, but not plasma EDTA-blood cell pellet DNA, from vitamin B12-deficient subjects. PLoS One 2013; 8:e65241. [PMID: 23785415 PMCID: PMC3681792 DOI: 10.1371/journal.pone.0065241] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Accepted: 04/22/2013] [Indexed: 12/20/2022] Open
Abstract
Vitamin B12, a co-factor in methyl-group transfer, is important in maintaining DNA (deoxycytidine) methylation. Using two independent assays we examined the effect of vitamin B12-deficiency (plasma vitamin B12<148 pmol/L) on DNA methylation in women of childbearing age. Coagulated blood clot DNA from vitamin B12-deficient women had significantly (p<0.001) lower percentage deoxycytidine methylation (3.23±0.66%; n = 248) and greater [3 H]methyl-acceptance (42,859±9,699 cpm; n = 17) than DNA from B12-replete women (4.44±0.18%; n = 128 and 26,049±2,814 cpm; n = 11) [correlation between assays: r = -0.8538; p<0.001; n = 28]. In contrast, uncoagulated EDTA-blood cell pellet DNA from vitamin B12-deficient and B12-replete women exhibited similar percentage methylation (4.45±0.15%; n = 77 vs. 4.47±0.15%; n = 47) and [3 H]methyl-acceptance (27,378±4,094 cpm; n = 17 vs. 26,610±2,292 cpm; n = 11). Therefore, in simultaneously collected paired blood samples, vitamin B12-deficiency was associated with decreased DNA methylation only in coagulated samples. These findings highlight the importance of sample collection methods in epigenetic studies, and the potential impact biological processes can have on DNA methylation during collection.
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Affiliation(s)
- Eoin P Quinlivan
- Biomedical Mass Spectrometry Laboratory, Clinical and Translational Science Institute, University of Florida, Gainesville, Florida, United States of America.
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Abstract
Epigenetic genome marking and chromatin regulation are central to establishing tissue-specific gene expression programs, and hence to several biological processes. Until recently, the only known epigenetic mark on DNA in mammals was 5-methylcytosine, established and propagated by DNA methyltransferases and generally associated with gene repression. All of a sudden, a host of new actors—novel cytosine modifications and the ten eleven translocation (TET) enzymes—has appeared on the scene, sparking great interest. The challenge is now to uncover the roles they play and how they relate to DNA demethylation. Knowledge is accumulating at a frantic pace, linking these new players to essential biological processes (e.g. cell pluripotency and development) and also to cancerogenesis. Here, we review the recent progress in this exciting field, highlighting the TET enzymes as epigenetic DNA modifiers, their physiological roles, and their functions in health and disease. We also discuss the need to find relevant TET interactants and the newly discovered TET–O-linked N-acetylglucosamine transferase (OGT) pathway.
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Shin JH, Li RW, Gao Y, Bickhart DM, Liu GE, Li W, Wu S, Li CJ. Butyrate Induced IGF2 Activation Correlated with Distinct Chromatin Signatures Due to Histone Modification. GENE REGULATION AND SYSTEMS BIOLOGY 2013; 7:57-70. [PMID: 23645985 PMCID: PMC3623616 DOI: 10.4137/grsb.s11243] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Histone modification has emerged as a very important mechanism regulating the transcriptional status of the genome. Insulin-like growth factor 2 (IGF2) is a peptide hormone controlling various cellular processes, including proliferation and apoptosis. H19 gene is closely linked to IGF2 gene, and IGF2 and H19 are reciprocally regulated imprinted genes. The epigenetic signature of H19 promoter (hypermethylation) on the paternal allele plays a vital role in allowing the expression of the paternal allele of IGF2.46 Our previous studies demonstrate that butyrate regulates the expression of IGF2 as well as genes encoding IGF Binding proteins. To obtain further understanding of histone modification and its regulatory potentials in controlling IGF2/H19 gene expression, we investigated the histone modification status of some key histones associated with the expression of IGF2/H19 genes in bovine cells using RNA-seq in combination with Chip-seq technology. A high-resolution map of the major chromatin modification at the IGF2/H19 locus induced by butyrate was constructed to illustrate the fundamental association of the chromatin modification landscape that may play a role in the activation of the IGF2 gene. High-definition epigenomic landscape mapping revealed that IGF2 and H19 have distinct chromatin modification patterns at their coding and promoter regions, such as TSSs and TTSs. Moreover, the correlation between the differentially methylated regions (DMRs) of IGF2/H19 locus and histone modification (acetylation and methylation) indicated that epigenetic signatures/markers of DNA methylation, histone methylation and histone acetylation were differentially distributed on the expressed IGF2 and silenced H19 genes. Our evidence also suggests that butyrate-induced regional changes of histone acetylation statusin the upstream regulation domain of H19 may be related to the reduced expression of H19 and strong activation of IGF2. Our results provided insights into the mechanism of butyrate-induced loss of imprinting (LOI) of IGF2 and regulation of gene expression by histone modification.
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Affiliation(s)
- Joo Heon Shin
- Lieber Institute for Brain Development, Johns Hopkins University, Baltimore, Maryland, United States of America
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A New Exon Derived from a Mammalian Apparent LTR Retrotransposon of the SUPT16H Gene. Int J Genomics 2013; 2013:387594. [PMID: 23671841 PMCID: PMC3647538 DOI: 10.1155/2013/387594] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Accepted: 02/12/2013] [Indexed: 11/28/2022] Open
Abstract
The SUPT16H gene known as FACTP140 is required for the transcription of other genes. For transcription, genes need to be complexed with accessory factors, including transcription factors and RNA polymerase II. One such factor, FACT, interacts with histones H2A/H2B for nucleosome disassembly and transcription elongation. The SUPT16H gene has a transcript and many expressed sequence tags (ESTs). We were especially interested in an MaLR-derived transcript (EST, BX333035) that included a new exon introduced by a transposable element, a mammalian apparent LTR retrotransposon (MaLR). The MaLR was detected ranging from humans to galagos, indicating the MaLR in the SUPT16H gene is integrated into the primate ancestor genome. A new exon was created by alternative donor site provided by the MaLR. The original transcript and the MaLR-derived transcript were expressed in various human, rhesus monkey, and other primate tissues. Additionally, we identified a new alternative transcript that included the MaLR, but there was no significant difference in the expression of the original transcript and the MaLR-derived transcript. Interestingly, the new alternative transcript and the MaLR-derived transcript had the MaLR sequence in the new exon, but they had different structures by adopting different 3′ splice sites. From this study, we verified transposable elements that contributed to transcriptome diversity.
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Jordaan G, Liao W, Sharma S. E-cadherin gene re-expression in chronic lymphocytic leukemia cells by HDAC inhibitors. BMC Cancer 2013; 13:88. [PMID: 23432814 PMCID: PMC3586366 DOI: 10.1186/1471-2407-13-88] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 02/20/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The tumor suppressor gene E-cadherin gene is frequently silenced in chronic lymphocytic leukemia (CLL) cells and results in wnt-pathway activation. We analyzed the role of histone epigenetic modifications in E-cadherin gene silencing. METHODS CLL specimens were treated with histone deacetylase inhibitor (HDACi) MS-275 and analyzed for E-cadherin expression with western blot and RT-PCR analysis. The downstream effects of HDACi treated leukemic cells were studied by analyzing the effect on wnt-pathway signaling. HDACi induced alterations in E-cadherin splicing were investigated by transcript specific real time PCR analysis. RESULTS Treatment of CLL specimens with histone deacetylase inhibitors (HDACi) treatment resulted in an increase of the E-cadherin RNA transcript (5 to 119 fold increase, n=10) in eight out of ten CLL specimens indicating that this gene is down regulated by histone hypoacetylation in a majority of CLL specimens. The E-cadherin re-expression in CLL specimens was noted by western blot analysis as well. Besides epigenetic silencing another mechanism of E-cadherin inactivation is aberrant exon 11 splicing resulting in an alternatively spliced transcript that lacks exon 11 and is degraded by the non-sense mediated decay (NMD) pathway. Our chromatin immunoprecipitation experiments show that HDACi increased the acetylation of histones H3 and H4 in the E-cadherin promoter region. This also affected the E-cadherin exon 11 splicing pattern as HDACi treated CLL specimens preferentially expressed the correctly spliced transcript and not the exon 11 skipped aberrant transcript. The re-expressed E- cadherin binds to β-catenin with inhibition of the active wnt-beta-catenin pathway in these cells. This resulted in a down regulation of two wnt target genes, LEF and cyclinD1 and the wnt pathway reporter. CONCLUSION The E-cadherin gene is epigenetically modified and hypoacetylated in CLL leukemic cells. Treatment of CLL specimens with HDACi MS-275 activates transcription from this silent gene with expression of more correctly spliced E-cadherin transcripts as compared to the aberrant exon11 skipped transcripts that in turn inhibits the wnt signaling pathway. The data highlights the role of epigenetic modifications in altering gene splicing patterns.
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Affiliation(s)
- Gwen Jordaan
- Division of Hematology-Oncology, Greater Los Angeles VA Healthcare Center, UCLA School of Medicine, 11301 Wilshire Blvd, LA, CA 90073, USA
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Ehrlich M, Lacey M. DNA methylation and differentiation: silencing, upregulation and modulation of gene expression. Epigenomics 2013; 5:553-68. [PMID: 24059801 PMCID: PMC3864898 DOI: 10.2217/epi.13.43] [Citation(s) in RCA: 145] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Differentiation-related DNA methylation is receiving increasing attention, partly owing to new, whole-genome analyses. These revealed that cell type-specific differential methylation in gene bodies is more frequent than in promoters. We review new insights into the functionality of DNA methylation during differentiation, with emphasis on the methylomes of myoblasts, myotubes and skeletal muscle versus non-muscle samples. Biostatistical analyses of data from reduced representation bisulfite sequencing are discussed. Lastly, a model is presented for how promoter and intragenic DNA hypermethylation affect gene expression, including increasing the efficiency of polycomb silencing at some promoters, downmodulating other promoters rather than silencing them, counteracting enhancers with heterologous specificity, altering chromatin conformation by inhibiting the binding of CTCF, modulating mRNA transcript levels by inhibiting overlapping promoters of noncoding RNA genes or by regulating the use of alternative mRNA promoters, modulating transcription termination, regulating alternative splicing and acting as barriers to the spread of activating chromatin.
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Affiliation(s)
- Melanie Ehrlich
- Hayward Human Genetics Program, Tulane Cancer Center, and Center for Bioinformatics & Genomics, Tulane Health Sciences Center, New Orleans, LA 70112, USA.
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Guibert S, Weber M. Functions of DNA Methylation and Hydroxymethylation in Mammalian Development. Curr Top Dev Biol 2013; 104:47-83. [DOI: 10.1016/b978-0-12-416027-9.00002-4] [Citation(s) in RCA: 125] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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