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Habib AM, Cox JJ, Okorokov AL. Out of the dark: the emerging roles of lncRNAs in pain. Trends Genet 2024:S0168-9525(24)00096-9. [PMID: 38926010 DOI: 10.1016/j.tig.2024.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 06/28/2024]
Abstract
The dark genome, the nonprotein-coding part of the genome, is replete with long noncoding RNAs (lncRNAs). These functionally versatile transcripts, with specific temporal and spatial expression patterns, are critical gene regulators that play essential roles in health and disease. In recent years, FAAH-OUT was identified as the first lncRNA associated with an inherited human pain insensitivity disorder. Several other lncRNAs have also been studied for their contribution to chronic pain and genome-wide association studies are frequently identifying single nucleotide polymorphisms that map to lncRNAs. For a long time overlooked, lncRNAs are coming out of the dark and into the light as major players in human pain pathways and as potential targets for new RNA-based analgesic medicines.
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Affiliation(s)
- Abdella M Habib
- College of Medicine, QU Health, Qatar University, PO Box 2713, Doha, Qatar
| | - James J Cox
- Wolfson Institute for Biomedical Research, Division of Medicine, University College London, London, WC1E 6BT, UK.
| | - Andrei L Okorokov
- Wolfson Institute for Biomedical Research, Division of Medicine, University College London, London, WC1E 6BT, UK.
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2
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Ferrer J, Dimitrova N. Transcription regulation by long non-coding RNAs: mechanisms and disease relevance. Nat Rev Mol Cell Biol 2024; 25:396-415. [PMID: 38242953 PMCID: PMC11045326 DOI: 10.1038/s41580-023-00694-9] [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] [Accepted: 12/11/2023] [Indexed: 01/21/2024]
Abstract
Long non-coding RNAs (lncRNAs) outnumber protein-coding transcripts, but their functions remain largely unknown. In this Review, we discuss the emerging roles of lncRNAs in the control of gene transcription. Some of the best characterized lncRNAs have essential transcription cis-regulatory functions that cannot be easily accomplished by DNA-interacting transcription factors, such as XIST, which controls X-chromosome inactivation, or imprinted lncRNAs that direct allele-specific repression. A growing number of lncRNA transcription units, including CHASERR, PVT1 and HASTER (also known as HNF1A-AS1) act as transcription-stabilizing elements that fine-tune the activity of dosage-sensitive genes that encode transcription factors. Genetic experiments have shown that defects in such transcription stabilizers often cause severe phenotypes. Other lncRNAs, such as lincRNA-p21 (also known as Trp53cor1) and Maenli (Gm29348) contribute to local activation of gene transcription, whereas distinct lncRNAs influence gene transcription in trans. We discuss findings of lncRNAs that elicit a function through either activation of their transcription, transcript elongation and processing or the lncRNA molecule itself. We also discuss emerging evidence of lncRNA involvement in human diseases, and their potential as therapeutic targets.
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Affiliation(s)
- Jorge Ferrer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Madrid, Spain.
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK.
| | - Nadya Dimitrova
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.
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3
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Jayakumar S, Patel M, Boulet F, Aziz H, Brooke GN, Tummala H, Pradeepa MM. PSIP1/LEDGF reduces R-loops at transcription sites to maintain genome integrity. Nat Commun 2024; 15:361. [PMID: 38191578 PMCID: PMC10774266 DOI: 10.1038/s41467-023-44544-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 12/18/2023] [Indexed: 01/10/2024] Open
Abstract
R-loops that accumulate at transcription sites pose a persistent threat to genome integrity. PSIP1 is a chromatin protein associated with transcriptional elongation complex, possesses histone chaperone activity, and is implicated in recruiting RNA processing and DNA repair factors to transcription sites. Here, we show that PSIP1 interacts with R-loops and other proteins involved in R-loop homeostasis, including PARP1. Genome-wide mapping of PSIP1, R-loops and γ-H2AX in PSIP1-depleted human and mouse cell lines revealed an accumulation of R-loops and DNA damage at gene promoters in the absence of PSIP1. R-loop accumulation causes local transcriptional arrest and transcription-replication conflict, leading to DNA damage. PSIP1 depletion increases 53BP1 foci and reduces RAD51 foci, suggesting altered DNA repair choice. Furthermore, PSIP1 depletion increases the sensitivity of cancer cells to PARP1 inhibitors and DNA-damaging agents that induce R-loop-induced DNA damage. These findings provide insights into the mechanism through which PSIP1 maintains genome integrity at the site of transcription.
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Affiliation(s)
- Sundarraj Jayakumar
- Blizard Institute; Faculty of Medicine and Dentistry, Queen Mary University of London, London, UK
- Bhabha Atomic Research Centre, Mumbai, India
| | - Manthan Patel
- Blizard Institute; Faculty of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Fanny Boulet
- Blizard Institute; Faculty of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Hadicha Aziz
- Blizard Institute; Faculty of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Greg N Brooke
- School of Life Sciences, University of Essex, Colchester, UK
| | - Hemanth Tummala
- Blizard Institute; Faculty of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Madapura M Pradeepa
- Blizard Institute; Faculty of Medicine and Dentistry, Queen Mary University of London, London, UK.
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4
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Sundarraj J, Taylor GC, von Kriegsheim A, Pradeepa MM. H3K36me3 and PSIP1/LEDGF associate with several DNA repair proteins, suggesting their role in efficient DNA repair at actively transcribing loci. Wellcome Open Res 2021; 2:83. [PMID: 34541330 PMCID: PMC8422350 DOI: 10.12688/wellcomeopenres.11589.4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2021] [Indexed: 12/15/2022] Open
Abstract
Background: Trimethylation at histone H3 at lysine 36 (H3K36me3) is associated with expressed gene bodies and recruit proteins implicated in transcription, splicing and DNA repair. PC4 and SF2 interacting protein (PSIP1/LEDGF) is a transcriptional coactivator, possesses an H3K36me3 reader PWWP domain. Alternatively spliced isoforms of PSIP1 binds to H3K36me3 and suggested to function as adaptor proteins to recruit transcriptional modulators, splicing factors and proteins that promote homology-directed repair (HDR), to H3K36me3 chromatin. Methods: We performed chromatin immunoprecipitation of H3K36me3 followed by quantitative mass spectrometry (qMS) to identify proteins associated with H3K36 trimethylated chromatin in mouse embryonic stem cells (mESCs). We also performed stable isotope labelling with amino acids in cell culture (SILAC) followed by qMS for a longer isoform of PSIP1 (PSIP/p75) and MOF/KAT8 in mESCs and mouse embryonic fibroblasts ( MEFs). Furthermore, immunoprecipitation followed by western blotting was performed to validate the qMS data. DNA damage in PSIP1 knockout MEFs was assayed by a comet assay. Results: Proteomic analysis shows the association of proteins involved in transcriptional elongation, RNA processing and DNA repair with H3K36me3 chromatin. Furthermore, we show DNA repair proteins like PARP1, gamma H2A.X, XRCC1, DNA ligase 3, SPT16, Topoisomerases and BAZ1B are predominant interacting partners of PSIP /p75. We further validated the association of PSIP/p75 with PARP1, hnRNPU and gamma H2A.X and also demonstrated accumulation of damaged DNA in PSIP1 knockout MEFs. Conclusions: In contrast to the previously demonstrated role of H3K36me3 and PSIP/p75 in promoting homology-directed repair (HDR), our data support a wider role of H3K36me3 and PSIP1 in maintaining the genome integrity by recruiting proteins involved in DNA damage response pathways to the actively transcribed loci.
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Affiliation(s)
- Jayakumar Sundarraj
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, E1 2AT, UK
- Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Mumbai, 40085, India
| | - Gillian C.A. Taylor
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Alex von Kriegsheim
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Madapura M Pradeepa
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, E1 2AT, UK
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
- School of Biological Sciences, University of Essex, Colchester, CO4 3SQ, UK
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5
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Sundarraj J, Taylor GC, von Kriegsheim A, Pradeepa MM. H3K36me3 and PSIP1/LEDGF associate with several DNA repair proteins, suggesting their role in efficient DNA repair at actively transcribing loci. Wellcome Open Res 2021; 2:83. [PMID: 34541330 PMCID: PMC8422350 DOI: 10.12688/wellcomeopenres.11589.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/05/2021] [Indexed: 11/20/2022] Open
Abstract
Background: Trimethylation at histone H3 at lysine 36 (H3K36me3) is associated with expressed gene bodies and recruit proteins implicated in transcription, splicing and DNA repair. PC4 and SF2 interacting protein (PSIP1/LEDGF) is a transcriptional coactivator, possesses an H3K36me3 reader PWWP domain. Alternatively spliced isoforms of PSIP1 binds to H3K36me3 and suggested to function as adaptor proteins to recruit transcriptional modulators, splicing factors and proteins that promote homology-directed repair (HDR), to H3K36me3 chromatin. Methods: We performed chromatin immunoprecipitation of H3K36me3 followed by quantitative mass spectrometry (qMS) to identify proteins associated with H3K36 trimethylated chromatin in mouse embryonic stem cells (mESCs). We also performed stable isotope labelling with amino acids in cell culture (SILAC) followed by qMS for a longer isoform of PSIP1 (PSIP/p75) and MOF/KAT8 in mESCs and mouse embryonic fibroblasts ( MEFs). Furthermore, immunoprecipitation followed by western blotting was performed to validate the qMS data. DNA damage in PSIP1 knockout MEFs was assayed by a comet assay. Results: Proteomic analysis shows the association of proteins involved in transcriptional elongation, RNA processing and DNA repair with H3K36me3 chromatin. Furthermore, we show DNA repair proteins like PARP1, gamma H2A.X, XRCC1, DNA ligase 3, SPT16, Topoisomerases and BAZ1B are predominant interacting partners of PSIP /p75. We further validated the association of PSIP/p75 with PARP1, hnRNPU and gamma H2A.X and also demonstrated accumulation of damaged DNA in PSIP1 knockout MEFs. Conclusions: In contrast to the previously demonstrated role of H3K36me3 and PSIP/p75 in promoting homology-directed repair (HDR), our data support a wider role of H3K36me3 and PSIP1 in maintaining the genome integrity by recruiting proteins involved in DNA damage response pathways to the actively transcribed loci.
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Affiliation(s)
- Jayakumar Sundarraj
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, E1 2AT, UK
- Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Mumbai, 40085, India
| | - Gillian C.A. Taylor
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Alex von Kriegsheim
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Madapura M Pradeepa
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, E1 2AT, UK
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
- School of Biological Sciences, University of Essex, Colchester, CO4 3SQ, UK
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Novikova EL, Kulakova MA. There and Back Again: Hox Clusters Use Both DNA Strands. J Dev Biol 2021; 9:28. [PMID: 34287306 PMCID: PMC8293171 DOI: 10.3390/jdb9030028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/06/2021] [Accepted: 07/13/2021] [Indexed: 12/25/2022] Open
Abstract
Bilaterian animals operate the clusters of Hox genes through a rich repertoire of diverse mechanisms. In this review, we will summarize and analyze the accumulated data concerning long non-coding RNAs (lncRNAs) that are transcribed from sense (coding) DNA strands of Hox clusters. It was shown that antisense regulatory RNAs control the work of Hox genes in cis and trans, participate in the establishment and maintenance of the epigenetic code of Hox loci, and can even serve as a source of regulatory peptides that switch cellular energetic metabolism. Moreover, these molecules can be considered as a force that consolidates the cluster into a single whole. We will discuss the examples of antisense transcription of Hox genes in well-studied systems (cell cultures, morphogenesis of vertebrates) and bear upon some interesting examples of antisense Hox RNAs in non-model Protostomia.
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Affiliation(s)
- Elena L. Novikova
- Department of Embryology, St. Petersburg State University, Universitetskaya nab. 7–9, 199034 Saint Petersburg, Russia;
- Laboratory of Evolutionary Morphology, Zoological Institute RAS, Universitetskaya nab. 1, 199034 Saint Petersburg, Russia
| | - Milana A. Kulakova
- Department of Embryology, St. Petersburg State University, Universitetskaya nab. 7–9, 199034 Saint Petersburg, Russia;
- Laboratory of Evolutionary Morphology, Zoological Institute RAS, Universitetskaya nab. 1, 199034 Saint Petersburg, Russia
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Fan X, Lou J, Zheng X, Wang Y, Wang J, Luo M, Hu M. Interference with lncRNA NEAT1 promotes the proliferation, migration, and invasion of trophoblasts by upregulating miR-411-5p and inhibiting PTEN expression. Immunopharmacol Immunotoxicol 2021; 43:334-342. [PMID: 33876722 DOI: 10.1080/08923973.2021.1910834] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Background: Preeclampsia (PE) is an idiopathic hypertensive disorder of pregnancy, which is related to abnormal placental villi development. Our previous study has found that lncRNA NEAT1 promotes apoptosis of trophoblasts, but the role of NEAT1 in proliferation, migration, and invasion is still unclear. This study explores the role of NEAT1 in proliferation, migration, and invasion of trophoblasts.Methods: NEAT1 and miR-411-5p levels were detected by quantitative real-time PCR. Colony formation assay detected cell proliferation and transwell assay detected cell migration and invasion. Dual-luciferase reporter assay detected the binding between NEAT1 and miR-411-5p as well as the binding between miR-411-5p and PTEN. RNA pull-down assay detected the combination between NEAT1 and miR-411-5p.Result: NEAT1 was increased and miR-411-5p was reduced in PE patients and human trophoblasts (HTR8/SVneo cells) that were induced with H2O2. Interference with NEAT1 promoted cell proliferation, migration, and invasion, and the miR-411-5p inhibitor reversed the effect of siRNA-NEAT1. The expression of PTEN was promoted in PE patients and HTR8/SVneo cells that were induced with H2O2, while the miR-411-5p mimic inhibited PTEN expression, and the plasmid-mediated PTEN overexpression reversed the effect of the miR-411-5p mimic. Besides, under H2O2 induction, the miR-411-5p mimic promoted cell proliferation, migration, and invasion, and the plasmid-mediated PTEN overexpression reversed the effect of the miR-411-5p mimic.Conclusion: Interference with lncRNA NEAT1 promoted the proliferation, migration, and invasion of trophoblasts and alleviated the development of PE, which was partly mediated by upregulating miR-411-5p and inhibiting PTEN expression.
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Affiliation(s)
- Xufei Fan
- Department of Obstetrics and Gynecology, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Jianyi Lou
- Department of Obstetrics and Gynecology, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Xiujuan Zheng
- Department of Obstetrics and Gynecology, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Ying Wang
- Department of Obstetrics and Gynecology, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Jiayue Wang
- Department of Obstetrics and Gynecology, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Mengmeng Luo
- Department of Obstetrics and Gynecology, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Min Hu
- Department of Obstetrics and Gynecology, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
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8
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He X, Gao K, Lu S, Wu R. LncRNA HOTTIP leads to osteoarthritis progression via regulating miR-663a/ Fyn-related kinase axis. BMC Musculoskelet Disord 2021; 22:67. [PMID: 33435956 PMCID: PMC7802157 DOI: 10.1186/s12891-020-03861-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 12/04/2020] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Long non-coding RNA (lncRNA) has been implicated in the progression of osteoarthritis (OA). This study was aimed to explore the role and molecular mechanism of lncRNA HOXA terminal transcriptional RNA (HOTTIP) in the development of OA. METHODS The expression of HOTTIP, miR-663a and Fyn-related kinase (FRK) in the OA articular cartilage and OA chondrocyte model induced by IL-1β was determined by qRT-PCR. CCK-8, colony formation and flow cytometry were used to determine the cell proliferation and apoptosis of OA chondrocytes. The specific molecular mechanism of HOTTIP in OA chondrocytes was determined by dual luciferase reporter assay, qRT-PCR, western blotting and RNA pull-down. RESULTS The expression of HOTTIP and FRK were up-regulated, while miR-663a was down-regulated in OA cartilage tissues. Knockdown of HOTTIP decreased the proliferation and induced the apoptosis of OA cartilage model cells, while overexpression of HOTTIP increased the proliferation and reduced the apoptosis of OA cartilage model cells. Moreover, HOTTIP could bind to miR-663a as competitive endogenous RNA. Inhibition of miR-663a expression could alleviate the effect of HOTTIP knockdown on the proliferation and apoptosis of OA cartilage model cells. Furthermore, FRK was found to be a direct target of miR-663a, which could markedly down-regulate the expression of FRK in OA chondrocytes, while HOTTIP could remarkably up-regulate the expression of FRK. In addition, miR-663a inhibition increased the proliferation and reduced the apoptosis of OA cells, while FRK knockdown reversed the effect of miR-663a inhibition on the proliferation and apoptosis of OA cells. Meanwhile, overexpression of miR-663a decreased the proliferation and induced the apoptosis of OA cells, while overexpression of FRK reversed the effect of miR-663a overexpression on the proliferation and apoptosis of OA cells. CONCLUSION HOTTIP was involved in the proliferation and apoptosis of OA chondrocytes via miR-663a/ FRK axis, and HOTTIP/miR-663a/FRK might be a potential target for the treatment of OA.
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Affiliation(s)
- Xianwei He
- Department of Orthopaedics, Fudan University Jinshan Hospital, No.1508 Longhang Road, Jinshan District, Shanghai City, 201508, China
| | - Kun Gao
- Ze Tian Xing Zhi Di Cosmetology Clinic, Shanghai, 200000, China
| | - Shuaihua Lu
- Ze Tian Xing Zhi Di Cosmetology Clinic, Shanghai, 200000, China
| | - Rongbo Wu
- Department of Orthopaedics, Fudan University Jinshan Hospital, No.1508 Longhang Road, Jinshan District, Shanghai City, 201508, China.
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Elcheva IA, Spiegelman VS. The Role of cis- and trans-Acting RNA Regulatory Elements in Leukemia. Cancers (Basel) 2020; 12:E3854. [PMID: 33419342 PMCID: PMC7766907 DOI: 10.3390/cancers12123854] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/07/2020] [Accepted: 12/08/2020] [Indexed: 02/06/2023] Open
Abstract
RNA molecules are a source of phenotypic diversity and an operating system that connects multiple genetic and metabolic processes in the cell. A dysregulated RNA network is a common feature of cancer. Aberrant expression of long non-coding RNA (lncRNA), micro RNA (miRNA), and circular RNA (circRNA) in tumors compared to their normal counterparts, as well as the recurrent mutations in functional regulatory cis-acting RNA motifs have emerged as biomarkers of disease development and progression, opening avenues for the design of novel therapeutic approaches. This review looks at the progress, challenges and future prospects of targeting cis-acting and trans-acting RNA elements for leukemia diagnosis and treatment.
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Affiliation(s)
- Irina A. Elcheva
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Pennsylvania State University College of Medicine, P.O. Box 850, MC H085, 500 University Drive, Hershey, PA 17033-0850, USA
| | - Vladimir S. Spiegelman
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Pennsylvania State University College of Medicine, P.O. Box 850, MC H085, 500 University Drive, Hershey, PA 17033-0850, USA
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Hu H, Jia Q, Xi J, Zhou B, Li Z. Integrated analysis of lncRNA, miRNA and mRNA reveals novel insights into the fertility regulation of large white sows. BMC Genomics 2020; 21:636. [PMID: 32928107 PMCID: PMC7490888 DOI: 10.1186/s12864-020-07055-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 09/06/2020] [Indexed: 01/20/2023] Open
Abstract
Background Improving sow fertility is extremely important as it can lead to increased reproductive efficiency and thus profitability for swine producers. There are considerable differences in fertility rates among individual animals, but the underlying molecular mechanisms remain unclear. In this study, by using different types of RNA libraries, we investigated the complete transcriptome of ovarian tissue during the luteal (L) and follicular (F) phases of the estrous cycle in Large White pigs with high (H) and low (L) fecundity, and performed a comprehensive analysis of long noncoding RNAs (lncRNAs), mRNAs and micro RNAs (miRNAs) from 16 samples by combining RNA sequencing (RNA-seq) with bioinformatics. Results In total, 24,447 lncRNAs, 27,370 mRNAs, and 216 known miRNAs were identified in ovarian tissues. The genomic features of lncRNAs, such as length distribution and number of exons, were further analyzed. We selected a threshold of P < 0.05 and |log2 (fold change)| ≥ 1 to obtain the differentially expressed lncRNAs, miRNAs and mRNAs by pairwise comparison (LH vs. LL, FH vs. FL). Bioinformatics analysis of these differentially expressed RNAs revealed multiple significantly enriched pathways (P < 0.05) that were closely involved in the reproductive process, such as ovarian steroidogenesis, lysosome, steroid biosynthesis, and the estrogen and GnRH signaling pathways. Moreover, bioinformatics screening of differentially expressed miRNAs that share common miRNA response elements (MREs) with lncRNAs and their downstream mRNA targets were performed. Finally, we constructed lncRNA–miRNA–mRNA regulation networks. The key genes in these networks were verified by Reverse Transcription Real-time Quantitative PCR (RT-qRCR), which were consistent with the results from RNA-Seq data. Conclusions These results provide further insights into the fertility of pigs andcan contribute to further experimental investigation of the functions of these genes.
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Affiliation(s)
- Huiyan Hu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Hebei Agricultural University, Lekai South Street No. 2596, Baoding, 071000, Hebei, China
| | - Qing Jia
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Hebei Agricultural University, Lekai South Street No. 2596, Baoding, 071000, Hebei, China. .,Engineering Research Center for Agriculture in Hebei Mountainous Areas, Baoding, 071000, Hebei, China.
| | - Jianzhong Xi
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Hebei Agricultural University, Lekai South Street No. 2596, Baoding, 071000, Hebei, China
| | - Bo Zhou
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Hebei Agricultural University, Lekai South Street No. 2596, Baoding, 071000, Hebei, China
| | - Zhiqiang Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Hebei Agricultural University, Lekai South Street No. 2596, Baoding, 071000, Hebei, China
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11
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Shi T, Guo D, Xu H, Su G, Chen J, Zhao Z, Shi J, Wedemeyer M, Attenello F, Zhang L, Lu W. HOTAIRM1, an enhancer lncRNA, promotes glioma proliferation by regulating long-range chromatin interactions within HOXA cluster genes. Mol Biol Rep 2020; 47:2723-2733. [PMID: 32180085 DOI: 10.1007/s11033-020-05371-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 03/04/2020] [Indexed: 01/31/2023]
Abstract
The long noncoding RNA HOTAIRM1 reportedly plays important roles in acute myeloid leukemia, gastric cancer and colorectal cancer. Here, we analyzed potential function of HOTAIRM1 in glioma and asked whether it participates in long-range chromatin interactions. We monitored expression of HOTAIRM1 in glioma tissues and correlated levels with patient survival using the TCGA dataset. HOTAIRM1 was highly expressed in glioma tissue, with high levels associated with shortened patient survival time. We then suppressed HOTAIRM1 activity in the human glioblastoma U251 line using CRISPR-cas9 to knock in a truncating polyA fragment. Reporter analysis of these and control cells confirmed that the HOTAIRM1 locus serves as an active enhancer. We then performed Capture-C analysis to identify target genes of that locus and applied RNA antisense purification to assess chromatin interactions between the HOTAIRM1 locus and HOXA cluster genes. HOTAIRM1 knockdown in glioma cells decreased proliferation and reduced expression of HOXA cluster genes. HOTAIRM1 regulates long-range interactions between the HOTAIRM1 locus and HOXA genes. Our work suggests a new mechanism by which HOTAIRM1 regulates glioma progression by regulating high-order chromatin structure and could suggest novel therapeutic targets to treat an intractable cancer.
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Affiliation(s)
- Tengfei Shi
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Dianhao Guo
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Heming Xu
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Guangsong Su
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Jun Chen
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Zhongfang Zhao
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Jiandang Shi
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Michelle Wedemeyer
- Department of Neurological Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Frank Attenello
- Department of Neurological Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Lei Zhang
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China.
| | - Wange Lu
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China.
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Su G, Guo D, Chen J, Liu M, Zheng J, Wang W, Zhao X, Yin Q, Zhang L, Zhao Z, Shi J, Lu W. A distal enhancer maintaining Hoxa1 expression orchestrates retinoic acid-induced early ESCs differentiation. Nucleic Acids Res 2020; 47:6737-6752. [PMID: 31147716 PMCID: PMC6649716 DOI: 10.1093/nar/gkz482] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/15/2019] [Accepted: 05/21/2019] [Indexed: 11/17/2022] Open
Abstract
Retinoic acid (RA) induces rapid differentiation of embryonic stem cells (ESCs), partly by activating expression of the transcription factor Hoxa1, which regulates downstream target genes that promote ESCs differentiation. However, mechanisms of RA-induced Hoxa1 expression and ESCs early differentiation remain largely unknown. Here, we identify a distal enhancer interacting with the Hoxa1 locus through a long-range chromatin loop. Enhancer deletion significantly inhibited expression of RA-induced Hoxa1 and endoderm master control genes such as Gata4 and Gata6. Transcriptome analysis revealed that RA-induced early ESCs differentiation was blocked in Hoxa1 enhancer knockout cells, suggesting a requirement for the enhancer. Restoration of Hoxa1 expression partly rescued expression levels of ∼40% of genes whose expression changed following enhancer deletion, and ∼18% of promoters of those rescued genes were directly bound by Hoxa1. Our data show that a distal enhancer maintains Hoxa1 expression through long-range chromatin loop and that Hoxa1 directly regulates downstream target genes expression and then orchestrates RA-induced early differentiation of ESCs. This discovery reveals mechanisms of a novel enhancer regulating RA-induced Hoxa genes expression and early ESCs differentiation.
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Affiliation(s)
- Guangsong Su
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin, China
| | - Dianhao Guo
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin, China
| | - Jun Chen
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin, China
| | - Man Liu
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin, China
| | - Jian Zheng
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin, China
| | - Wenbin Wang
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin, China
| | - Xueyuan Zhao
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin, China
| | - Qingqing Yin
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin, China
| | - Lei Zhang
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin, China
| | - Zhongfang Zhao
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin, China
| | - Jiandang Shi
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin, China
| | - Wange Lu
- Department of Stem Cell Biology and Regenerative Medicine, Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
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13
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lncRNAs: function and mechanism in cartilage development, degeneration, and regeneration. Stem Cell Res Ther 2019; 10:344. [PMID: 31753016 PMCID: PMC6873685 DOI: 10.1186/s13287-019-1458-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 09/17/2019] [Accepted: 10/16/2019] [Indexed: 02/06/2023] Open
Abstract
With the increasing incidence of cartilage-related diseases such as osteoarthritis (OA) and intervertebral disc degeneration (IDD), heavier financial and social burdens need to be faced. Unfortunately, there is no satisfactory clinical method to target the pathophysiology of cartilage-related diseases. Many gene expressions, signaling pathways, and biomechanical dysregulations were involved in cartilage development, degeneration, and regeneration. However, the underlying mechanism was not clearly understood. Recently, lots of long non-coding RNAs (lncRNAs) were identified in the biological processes, including cartilage development, degeneration, and regeneration. It is clear that lncRNAs were important in regulating gene expression and maintaining chondrocyte phenotypes and homeostasis. In this review, we summarize the recent researches studying lncRNAs’ expression and function in cartilage development, degeneration, and regeneration and illustrate the potential mechanism of how they act in the pathologic process. With continued efforts, regulating lncRNA expression in the cartilage regeneration may be a promising biological treatment approach.
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14
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da Silva RA, Fuhler GM, Janmaat VT, da C Fernandes CJ, da Silva Feltran G, Oliveira FA, Matos AA, Oliveira RC, Ferreira MR, Zambuzzi WF, Peppelenbosch MP. HOXA cluster gene expression during osteoblast differentiation involves epigenetic control. Bone 2019; 125:74-86. [PMID: 31054377 DOI: 10.1016/j.bone.2019.04.026] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 04/25/2019] [Accepted: 04/30/2019] [Indexed: 01/17/2023]
Abstract
The HOXA gene cluster is generally recognized as a pivotal mediator of positional identity in the skeletal system, expression of different orthologues conferring alternative locational phenotype of the vertebrate bone. Strikingly, however, the molecular mechanisms that regulate orthologue-specific expression of different HOXA cluster members in gestating osteoblasts remain largely obscure, but in analogy to the processes observed in acute lymphatic leukemia it is assumed that alternative methylation of HOXA promoter regions drives position specific expression patterns. In an effort to understand HOXA cluster gene expression in osteogenesis we characterize both expression and the epigenetic landscape of the HOXA gene cluster during in vitro osteoblast formation from mesenchymal precursors. We observe that osteoblast formation per se provokes strong upregulation of HOXA gene cluster expression, in particular of midcluster genes, and paradoxal downregulation of HOXA7 and HOXA10. These differences in expression appear related to promoter methylation. LnRNAs HOTAIR and HOTTIP, known to modulate HOXA expression, are also regulated by their promoter methylation processing, but do not correlate with HOXA cluster expression profile. We thus conclude that HOXA expression is profoundly regulated during osteoblast differentiation through canonical methylation-dependent mechanisms but not through the flanking lnRNAs.
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Affiliation(s)
- Rodrigo A da Silva
- Laboratory of Bioassays and Cellular Dynamics, Department of Chemistry and Biochemistry, Institute of Biosciences, São Paulo State University - UNESP, Botucatu, São Paulo 18618-970, Brazil; Department of Gastroenterology and Hepatology, Erasmus MC, University Medical Center Rotterdam, the Netherlands
| | - Gwenny M Fuhler
- Department of Gastroenterology and Hepatology, Erasmus MC, University Medical Center Rotterdam, the Netherlands
| | - Vincent T Janmaat
- Department of Gastroenterology and Hepatology, Erasmus MC, University Medical Center Rotterdam, the Netherlands
| | - Célio Júnior da C Fernandes
- Laboratory of Bioassays and Cellular Dynamics, Department of Chemistry and Biochemistry, Institute of Biosciences, São Paulo State University - UNESP, Botucatu, São Paulo 18618-970, Brazil
| | - Geórgia da Silva Feltran
- Laboratory of Bioassays and Cellular Dynamics, Department of Chemistry and Biochemistry, Institute of Biosciences, São Paulo State University - UNESP, Botucatu, São Paulo 18618-970, Brazil
| | - Flávia Amadeu Oliveira
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Al. Octávio Pinheiro Brisolla, 9-75, 17012-901 Bauru, São Paulo, Brazil
| | - Adriana Arruda Matos
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Al. Octávio Pinheiro Brisolla, 9-75, 17012-901 Bauru, São Paulo, Brazil
| | - Rodrigo Cardoso Oliveira
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Al. Octávio Pinheiro Brisolla, 9-75, 17012-901 Bauru, São Paulo, Brazil
| | - Marcel Rodrigues Ferreira
- Laboratory of Bioassays and Cellular Dynamics, Department of Chemistry and Biochemistry, Institute of Biosciences, São Paulo State University - UNESP, Botucatu, São Paulo 18618-970, Brazil
| | - Willian F Zambuzzi
- Laboratory of Bioassays and Cellular Dynamics, Department of Chemistry and Biochemistry, Institute of Biosciences, São Paulo State University - UNESP, Botucatu, São Paulo 18618-970, Brazil.
| | - Maikel P Peppelenbosch
- Department of Gastroenterology and Hepatology, Erasmus MC, University Medical Center Rotterdam, the Netherlands.
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15
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Yang QS, Li B, Xu G, Yang SQ, Wang P, Tang HH, Liu YY. Long noncoding RNA LINC00483/microRNA-144 regulates radiosensitivity and epithelial-mesenchymal transition in lung adenocarcinoma by interacting with HOXA10. J Cell Physiol 2019; 234:11805-11821. [PMID: 30714135 DOI: 10.1002/jcp.27886] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 11/08/2018] [Indexed: 01/03/2023]
Abstract
Lung adenocarcinoma (LAD) is the leading cause of cancer death worldwide. Long noncoding RNAs (lncRNAs) have been shown to play an important regulatory role in cancer biology, including that of LAD. The aim of this experiment was to explore the interaction of LINC00483, microRNA-144 (miR-144), and homeobox A10 (HOXA10), and their effects on radio sensitivity and epithelial-mesenchymal transition (EMT) of LAD. Initially, microarray analysis was used to screen out miRNAs and lncRNAs, as well as the differentially expressed genes related to LAD. Following the screening process, the targeting relationship of LINC00483, miR-144, and that of miR-144 and HOXA10 was determined. Following that, the expression of LINC00483, miR-144, messenger RNA (mRNA), as well as protein expression of HOXA10, MMP-2, MMP-9, E-cadherin, vimentin, and N-cadherin that followed in cells was determined. Also, the effect of LINC00483 on cell migration and invasion ability, and cell tumorigenic ability was detected. LINC00483 and HOXA10 were found to be upregulated whereas miR-144 was downregulated in LAD. Silencing of LINC00483 could competitively bind to miR-144, thereby upregulating HOXA10. LINC00483 or HOXA10 silencing led to decreased HOXA10, MMP-2, MMP-9, vimentin, and N-cadherin but elevated miR-144 and E-cadherin. Moreover, after being transfected with silenced LINC00483, the cell proliferation, migration, and invasion were inhibited with enhanced radiosensitivity. Consequently, the data of the study indicates that interference of LINC00483 weakens its competitive binding ability to miR-144, thus reducing HOXA10 expression, and enhancing radiosensitivity in LAD.
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Affiliation(s)
- Qing-Shan Yang
- Department of Radiation Oncology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, P. R. China
| | - Bin Li
- Department of Radiation Oncology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, P. R. China
| | - Ge Xu
- Department of Radiation Oncology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, P. R. China
| | - Si-Qi Yang
- Department of Radiation Oncology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, P. R. China
| | - Peng Wang
- Department of Radiation Oncology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, P. R. China
| | - Huai-Hui Tang
- Department of Radiation Oncology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, P. R. China
| | - Yuan-Yuan Liu
- Department of Internal Neurology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, P. R. China
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16
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Long non-coding RNA HOTTIP affects renal cell carcinoma progression by regulating autophagy via the PI3K/Akt/Atg13 signaling pathway. J Cancer Res Clin Oncol 2018; 145:573-588. [DOI: 10.1007/s00432-018-2808-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 11/30/2018] [Indexed: 12/12/2022]
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17
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Abstract
Noncoding RNAs (ncRNAs) transcribed from active enhancers are known as enhancer RNAs (eRNAs). eRNAs have generally been shown to contribute to transcriptional activation of target genes in cis. In this issue, Tsai et al. (2018) demonstrate that an eRNA expressed from a distal enhancer of Myogenic differentiation1 (MyoD) (DRReRNA) does not regulate its neighboring MyoD; instead, it promotes myogenic differentiation by activating Myogenin, which is located on a different chromosome.
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Affiliation(s)
- Myles G Garstang
- Blizard Institute, Barts and The London School of Medicine and Dentistry, QMUL, London E1 2AT, UK; School of Biological Sciences, University of Essex, Colchester CO4 3SQ, UK
| | - Madapura M M Pradeepa
- Blizard Institute, Barts and The London School of Medicine and Dentistry, QMUL, London E1 2AT, UK; School of Biological Sciences, University of Essex, Colchester CO4 3SQ, UK.
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18
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Camacho CV, Choudhari R, Gadad SS. Long noncoding RNAs and cancer, an overview. Steroids 2018; 133:93-95. [PMID: 29317255 DOI: 10.1016/j.steroids.2017.12.012] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 12/18/2017] [Accepted: 12/20/2017] [Indexed: 12/14/2022]
Abstract
Long noncoding RNAs (lncRNAs) are implicated in several biological processes, including but not limited to cardiovascular physiology, reproduction, differentiation, metabolism, DNA repair, and inflammation. Under normal physiological conditions, expression of lncRNAs is tissue-specific and tightly regulated. In contrast, prevalent cancer types exhibit aberrant expression of lncRNAs. In this context, lncRNAs can drive cancer cell characteristics by controlling gene expression programs related to tumor suppressive and oncogenic functions. Hence, they can be excellent biomarkers and targets for therapeutic intervention in cancers. Understanding the molecular mechanisms by which lncRNAs drive cancer progression will improve our understanding of the etiology of cancer and suggest new ways to treat this disease. This review will provide a perspective on the role of lncRNAs in cancer initiation and progression.
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Affiliation(s)
- Cristel V Camacho
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, United States
| | - Ramesh Choudhari
- Center of Emphasis in Cancer, Paul L. Foster School of Medicine, Department of Biomedical Sciences, Texas Tech University Health Sciences Center, El Paso, TX 79905, United States
| | - Shrikanth S Gadad
- Center of Emphasis in Cancer, Paul L. Foster School of Medicine, Department of Biomedical Sciences, Texas Tech University Health Sciences Center, El Paso, TX 79905, United States; Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, United States.
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19
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Pavlaki I, Alammari F, Sun B, Clark N, Sirey T, Lee S, Woodcock DJ, Ponting CP, Szele FG, Vance KW. The long non-coding RNA Paupar promotes KAP1-dependent chromatin changes and regulates olfactory bulb neurogenesis. EMBO J 2018; 37:embj.201798219. [PMID: 29661885 PMCID: PMC5978383 DOI: 10.15252/embj.201798219] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 03/05/2018] [Accepted: 03/08/2018] [Indexed: 01/08/2023] Open
Abstract
Many long non‐coding RNAs (lncRNAs) are expressed during central nervous system (CNS) development, yet their in vivo roles and mechanisms of action remain poorly understood. Paupar, a CNS‐expressed lncRNA, controls neuroblastoma cell growth by binding and modulating the activity of transcriptional regulatory elements in a genome‐wide manner. We show here that the Paupar lncRNA directly binds KAP1, an essential epigenetic regulatory protein, and thereby regulates the expression of shared target genes important for proliferation and neuronal differentiation. Paupar promotes KAP1 chromatin occupancy and H3K9me3 deposition at a subset of distal targets, through the formation of a ribonucleoprotein complex containing Paupar, KAP1 and the PAX6 transcription factor. Paupar‐KAP1 genome‐wide co‐occupancy reveals a fourfold enrichment of overlap between Paupar and KAP1 bound sequences, the majority of which also appear to associate with PAX6. Furthermore, both Paupar and Kap1 loss‐of‐function in vivo disrupt olfactory bulb neurogenesis. These observations provide important conceptual insights into the trans‐acting modes of lncRNA‐mediated epigenetic regulation and the mechanisms of KAP1 genomic recruitment, and identify Paupar and Kap1 as regulators of neurogenesis in vivo.
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Affiliation(s)
- Ioanna Pavlaki
- Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Farah Alammari
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Bin Sun
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Neil Clark
- MRC Human Genetics Unit, The Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Tamara Sirey
- MRC Human Genetics Unit, The Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Sheena Lee
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Dan J Woodcock
- Warwick Systems Biology Centre, University of Warwick, Coventry, UK
| | - Chris P Ponting
- MRC Human Genetics Unit, The Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Francis G Szele
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Keith W Vance
- Department of Biology and Biochemistry, University of Bath, Bath, UK
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20
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Singh DK, Gholamalamdari O, Jadaliha M, Ling Li X, Lin YC, Zhang Y, Guang S, Hashemikhabir S, Tiwari S, Zhu YJ, Khan A, Thomas A, Chakraborty A, Macias V, Balla AK, Bhargava R, Janga SC, Ma J, Prasanth SG, Lal A, Prasanth KV. PSIP1/p75 promotes tumorigenicity in breast cancer cells by promoting the transcription of cell cycle genes. Carcinogenesis 2017. [PMID: 28633434 DOI: 10.1093/carcin/bgx062] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Breast cancer (BC) is a highly heterogeneous disease, both at the pathological and molecular level, and several chromatin-associated proteins play crucial roles in BC initiation and progression. Here, we demonstrate the role of PSIP1 (PC4 and SF2 interacting protein)/p75 (LEDGF) in BC progression. PSIP1/p75, previously identified as a chromatin-adaptor protein, is found to be upregulated in basal-like/triple negative breast cancer (TNBC) patient samples and cell lines. Immunohistochemistry in tissue arrays showed elevated levels of PSIP1 in metastatic invasive ductal carcinoma. Survival data analyses revealed that the levels of PSIP1 showed a negative association with TNBC patient survival. Depletion of PSIP1/p75 significantly reduced the tumorigenicity and metastatic properties of TNBC cell lines while its over-expression promoted tumorigenicity. Further, gene expression studies revealed that PSIP1 regulates the expression of genes controlling cell-cycle progression, cell migration and invasion. Finally, by interacting with RNA polymerase II, PSIP1/p75 facilitates the association of RNA pol II to the promoter of cell cycle genes and thereby regulates their transcription. Our findings demonstrate an important role of PSIP1/p75 in TNBC tumorigenicity by promoting the expression of genes that control the cell cycle and tumor metastasis.
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Affiliation(s)
- Deepak K Singh
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, IL 61801,USA, Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Omid Gholamalamdari
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, IL 61801,USA, Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Mahdieh Jadaliha
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, IL 61801,USA, Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Xiao Ling Li
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, IL 61801,USA, Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Yo-Chuen Lin
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, IL 61801,USA, Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Yang Zhang
- Department of Bioengineering, Beckman Institute of Advanced Science and Technology, UIUC, Urbana, IL 61801, USA
| | - Shuomeng Guang
- Department of Bioengineering, Beckman Institute of Advanced Science and Technology, UIUC, Urbana, IL 61801, USA
| | - Seyedsasan Hashemikhabir
- Department of Biohealth Informatics, School of Informatics and Computing, Indiana University Purdue University Indianapolis, Indianapolis, IN 46202,USA
| | - Saumya Tiwari
- Department of Bioengineering, Beckman Institute of Advanced Science and Technology, UIUC, Urbana, IL 61801, USA
| | - Yuelin J Zhu
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, IL 61801,USA, Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Abid Khan
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, IL 61801,USA, Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | | | - Arindam Chakraborty
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, IL 61801,USA, Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Virgilia Macias
- Department of Pathology, College of Medicine, University of Illinois at Chicago,Chicago, IL 60612, USA
| | - Andre K Balla
- Department of Pathology, College of Medicine, University of Illinois at Chicago,Chicago, IL 60612, USA
| | - Rohit Bhargava
- Department of Bioengineering, Beckman Institute of Advanced Science and Technology, UIUC, Urbana, IL 61801, USA.,Departments of Electrical and Computer Engineering, Mechanical Science and Engineering, Chemical and Biomolecular Engineering and Chemistry, UIUC, Urbana, IL, USA
| | - Sarath Chandra Janga
- Department of Biohealth Informatics, School of Informatics and Computing, Indiana University Purdue University Indianapolis, Indianapolis, IN 46202,USA
| | - Jian Ma
- Department of Bioengineering, Beckman Institute of Advanced Science and Technology, UIUC, Urbana, IL 61801, USA.,School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Supriya G Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, IL 61801,USA, Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Ashish Lal
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, IL 61801,USA, Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Kannanganattu V Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, IL 61801,USA, Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
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21
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Sundarraj J, Taylor GC, von Kriegsheim A, Pradeepa MM. ---Proteomic analysis of H3K36me3 and PSIP1/p75 (LEDGF) complexes reveal their wider role in DNA repair. Wellcome Open Res 2017; 2:83. [PMID: 34541330 PMCID: PMC8422350 DOI: 10.12688/wellcomeopenres.11589.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2021] [Indexed: 11/20/2022] Open
Abstract
Background: Trimethylation at histone H3 at lysine 36 (H3K36me3) is associated with expressed gene bodies and recruit proteins implicated in transcription, splicing and DNA repair. PC4 and SF2 interacting protein ( PSIP1/LEDGF) is a transcriptional coactivator, possesses a H3K36me3 reader PWWP domain. Alternatively spliced isoforms of PSIP1 binds to H3K36me3 and suggested to function as adaptor proteins to recruit transcriptional modulators, splicing factors and proteins that promote homology directed repair (HDR), to H3K36me3 chromatin. Methods: We performed chromatin immunoprecipitation of H3K36me3 followed by quantitative mass spectrometry to identify proteins associated with H3K36 trimethylated chromatin in mouse embryonic stem cells (mESCs). Furthermore, we performed stable isotope labelling with amino acids in cell culture (SILAC) for a longer isoform of PSIP1 (p75) and MOF/KAT8 in mESCs and mouse embryonic fibroblasts (MEFS). Results: Proteomic analysis of H3K36me3 chromatin show association of proteins involved in transcriptional elongation, RNA processing and DNA repair with H3K36me3 chromatin. Furthermore, we show DNA repair proteins like PARP1, gamma H2A.X, XRCC1, DNA ligase 3, SPT16, Topoisomerases and BAZ1B are predominant interacting partners of PSIP1/p75. We validated the association of PSIP1/p75 with gamma H2A.X, an early marker of DNA damage and also demonstrated accumulation of damaged DNA in PSIP1 knockout MEFs. Conclusions: In contrast to the previously demonstrated role of H3K36me3 and PSIP1/p75 in promoting HDR in mammals, our data supports the wider role of H3K36me3 and PSIP1 in maintaining the genome integrity by recruiting several DNA repair proteins to transcribed gene bodies.
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Affiliation(s)
- Jayakumar Sundarraj
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, E1 2AT, UK
- Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Mumbai, 40085, India
| | - Gillian C.A. Taylor
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Alex von Kriegsheim
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Madapura M Pradeepa
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, E1 2AT, UK
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
- School of Biological Sciences, University of Essex, Colchester, CO4 3SQ, UK
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22
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Sundarraj J, Taylor GC, von Kriegsheim A, Pradeepa MM. ---Proteomic analysis of H3K36me3 and PSIP1/p75 (LEDGF) complexes reveal their wider role in DNA repair. Wellcome Open Res 2017; 2:83. [PMID: 34541330 PMCID: PMC8422350 DOI: 10.12688/wellcomeopenres.11589.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2021] [Indexed: 11/20/2022] Open
Abstract
Background: Trimethylation at histone H3 at lysine 36 (H3K36me3) is associated with expressed gene bodies and recruit proteins implicated in transcription, splicing and DNA repair. PC4 and SF2 interacting protein ( PSIP1/LEDGF) is a transcriptional coactivator, possesses a H3K36me3 reader PWWP domain. Alternatively spliced isoforms of PSIP1 binds to H3K36me3 and suggested to function as adaptor proteins to recruit transcriptional modulators, splicing factors and proteins that promote homology directed repair (HDR), to H3K36me3 chromatin. Methods: We performed chromatin immunoprecipitation of H3K36me3 followed by quantitative mass spectrometry to identify proteins associated with H3K36 trimethylated chromatin in mouse embryonic stem cells (mESCs). Furthermore, we performed stable isotope labelling with amino acids in cell culture (SILAC) for a longer isoform of PSIP1 (p75) and MOF/KAT8 in mESCs and mouse embryonic fibroblasts (MEFS). Results: Proteomic analysis of H3K36me3 chromatin show association of proteins involved in transcriptional elongation, RNA processing and DNA repair with H3K36me3 chromatin. Furthermore, we show DNA repair proteins like PARP1, gamma H2A.X, XRCC1, DNA ligase 3, SPT16, Topoisomerases and BAZ1B are predominant interacting partners of PSIP1/p75. We validated the association of PSIP1/p75 with gamma H2A.X, an early marker of DNA damage and also demonstrated accumulation of damaged DNA in PSIP1 knockout MEFs. Conclusions: In contrast to the previously demonstrated role of H3K36me3 and PSIP1/p75 in promoting HDR in mammals, our data supports the wider role of H3K36me3 and PSIP1 in maintaining the genome integrity by recruiting several DNA repair proteins to transcribed gene bodies.
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Affiliation(s)
- Jayakumar Sundarraj
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, E1 2AT, UK
- Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Mumbai, 40085, India
| | - Gillian C.A. Taylor
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Alex von Kriegsheim
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Madapura M Pradeepa
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, E1 2AT, UK
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
- School of Biological Sciences, University of Essex, Colchester, CO4 3SQ, UK
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23
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Wang KC, Chang HY. Transcription coactivator and lncRNA duet evoke Hox genes. PLoS Genet 2017; 13:e1006797. [PMID: 28662057 PMCID: PMC5490938 DOI: 10.1371/journal.pgen.1006797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Kevin C. Wang
- Program in Epithelial Biology and Department of Dermatology, Stanford University School of Medicine, Stanford, California, United States of America
- Veterans Affairs Healthcare System, Palo Alto, California, United States of America
- * E-mail: (KCW); (HYC)
| | - Howard Y. Chang
- Program in Epithelial Biology and Department of Dermatology, Stanford University School of Medicine, Stanford, California, United States of America
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail: (KCW); (HYC)
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Tao H, Zhang JG, Qin RH, Dai C, Shi P, Yang JJ, Deng ZY, Shi KH. LncRNA GAS5 controls cardiac fibroblast activation and fibrosis by targeting miR-21 via PTEN/MMP-2 signaling pathway. Toxicology 2017; 386:11-18. [PMID: 28526319 DOI: 10.1016/j.tox.2017.05.007] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 05/15/2017] [Accepted: 05/15/2017] [Indexed: 12/16/2022]
Abstract
Long noncoding RNAs (LncRNAs) are aberrantly expressed in many diseases including cardiac fibrosis. LncRNA growth arrest-specific 5 (GAS5) is reported as a significant mediator in the control of cell proliferation and growth; however, the role and function in cardiac fibrosis remain unknown. In this study, we confirmed that GAS5 was lowly expressed in cardiac fibrosis tissues as well as activated cardiac fibroblast. Overexpression of GAS5 inhibited the proliferation of cardiac fibroblast. Moreover, microRNA-21 (miR-21) has been reported to be overexpressed in cardiac fibrosis tissues as well as activated cardiac fibroblast, which is responsible for the progression of cardiac fibrosis. We found that up-regulated GAS5 decreased the expression of miR-21 significantly. Furthermore, GAS5 that upregulated or downregulated the expression of PTEN through miR-21 in cardiac fibroblasts. Taken together, GAS5 plays a suppressive role in cardiac fibrosis via negative regulation of miR-21. These results indicated that GAS5 may be a novel therapeutic target for further research of cardiac fibrosis.
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Affiliation(s)
- Hui Tao
- Department of Cardiothoracic Surgery, The Second Hospital of Anhui Medical University, Hefei, 230601, China
| | - Jia-Gui Zhang
- Department of Cardiothoracic Surgery, The Second Hospital of Anhui Medical University, Hefei, 230601, China
| | - Run-He Qin
- Department of Cardiothoracic Surgery, The Second Hospital of Anhui Medical University, Hefei, 230601, China
| | - Chen Dai
- Department of Cardiothoracic Surgery, The Second Hospital of Anhui Medical University, Hefei, 230601, China
| | - Peng Shi
- Department of Cardiothoracic Surgery, The Second Hospital of Anhui Medical University, Hefei, 230601, China
| | - Jing-Jing Yang
- Department of Pharmacology, The Second Hospital of Anhui Medical University, Hefei, 230601, China, China
| | - Zi-Yu Deng
- Department of Scientific, The Second Hospital of Anhui Medical University, Hefei, 230601, China.
| | - Kai-Hu Shi
- Department of Cardiothoracic Surgery, The Second Hospital of Anhui Medical University, Hefei, 230601, China.
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25
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Abstract
Enhancers control development and cellular function by spatiotemporal regulation of gene expression. Co-occurrence of acetylation of histone H3 at lysine 27 (H3K27ac) and mono methylation of histone H3 at lysine 4 (H3K4me1) has been widely used for identification of active enhancers. However, increasing evidence suggests that using this combination of marks alone for enhancer identification gives an incomplete picture of the active enhancer repertoire. We have shown that the H3 globular domain acetylations, H3K64ac and H3K122ac, and an H4 tail acetylation, H4K16ac, are enriched at active enhancers together with H3K27ac, and also at a large number of enhancers without detectable H3K27ac. We propose that acetylations at these lysine residues of histones H3 and H4 might function by directly affecting chromatin structure, nucleosome-nucleosome interactions, nucleosome stability, and transcription factor accessibility.
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