101
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Schuettengruber B, Bourbon HM, Di Croce L, Cavalli G. Genome Regulation by Polycomb and Trithorax: 70 Years and Counting. Cell 2017; 171:34-57. [DOI: 10.1016/j.cell.2017.08.002] [Citation(s) in RCA: 611] [Impact Index Per Article: 87.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 07/17/2017] [Accepted: 08/01/2017] [Indexed: 01/05/2023]
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102
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Wu DC, Wang SSW, Liu CJ, Wuputra K, Kato K, Lee YL, Lin YC, Tsai MH, Ku CC, Lin WH, Wang SW, Kishikawa S, Noguchi M, Wu CC, Chen YT, Chai CY, Lin CLS, Kuo KK, Yang YH, Miyoshi H, Nakamura Y, Saito S, Nagata K, Lin CS, Yokoyama KK. Reprogramming Antagonizes the Oncogenicity of HOXA13-Long Noncoding RNA HOTTIP Axis in Gastric Cancer Cells. Stem Cells 2017; 35:2115-2128. [PMID: 28782268 DOI: 10.1002/stem.2674] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 06/26/2017] [Accepted: 07/15/2017] [Indexed: 12/26/2022]
Abstract
Reprogramming of cancer cells into induced pluripotent stem cells (iPSCs) is a compelling idea for inhibiting oncogenesis, especially through modulation of homeobox proteins in this reprogramming process. We examined the role of various long noncoding RNAs (lncRNAs)-homeobox protein HOXA13 axis on the switching of the oncogenic function of bone morphogenetic protein 7 (BMP7), which is significantly lost in the gastric cancer cell derived iPS-like cells (iPSLCs). BMP7 promoter activation occurred through the corecruitment of HOXA13, mixed-lineage leukemia 1 lysine N-methyltransferase, WD repeat-containing protein 5, and lncRNA HoxA transcript at the distal tip (HOTTIP) to commit the epigenetic changes to the trimethylation of lysine 4 on histone H3 in cancer cells. By contrast, HOXA13 inhibited BMP7 expression in iPSLCs via the corecruitment of HOXA13, enhancer of zeste homolog 2, Jumonji and AT rich interactive domain 2, and lncRNA HoxA transcript antisense RNA (HOTAIR) to various cis-element of the BMP7 promoter. Knockdown experiments demonstrated that HOTTIP contributed positively, but HOTAIR regulated negatively to HOXA13-mediated BMP7 expression in cancer cells and iPSLCs, respectively. These findings indicate that the recruitment of HOXA13-HOTTIP and HOXA13-HOTAIR to different sites in the BMP7 promoter is crucial for the oncogenic fate of human gastric cells. Reprogramming with octamer-binding protein 4 and Jun dimerization protein 2 can inhibit tumorigenesis by switching off BMP7. Stem Cells 2017;35:2115-2128.
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Affiliation(s)
- Deng-Chyang Wu
- Division of Gastroenterology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan.,Center for Stem Cell Research, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Internal Medicine, Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung, Taiwan
| | - Sophie S W Wang
- Division of Gastroenterology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan.,Center for Stem Cell Research, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chung-Jung Liu
- Division of Gastroenterology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan.,Center for Stem Cell Research, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Kenly Wuputra
- Graduate Institute of Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Kohsuke Kato
- Department of Infection Biology, Graduate School of Comprehensive Human Sciences, the University of Tsukuba, Tsukuba, Japan
| | | | - Ying-Chu Lin
- School of Dentistry, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ming-Ho Tsai
- Graduate Institute of Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chia-Chen Ku
- Graduate Institute of Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Wen-Hsin Lin
- Graduate Institute of Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Shin-Wei Wang
- Division of Gastroenterology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan.,Center for Stem Cell Research, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Shotaro Kishikawa
- Gene Engineering Division, RIKEN BioResource Center, Tsukuba, Ibaraki, Japan
| | - Michiya Noguchi
- Cell Engineering Division, RIKEN BioResource Center, Tsukuba, Ibaraki, Japan
| | - Chu-Chieh Wu
- Department of Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Pathology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yi-Ting Chen
- Department of Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Pathology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chee-Yin Chai
- Department of Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Pathology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chen-Lung Steve Lin
- Department of Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan.,Graduate Institute of Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Kung-Kai Kuo
- Center for Stem Cell Research, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ya-Han Yang
- Center for Stem Cell Research, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan.,Graduate Institute of Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Hiroyuki Miyoshi
- Department of Physiology, Keio University School of Medicine, Shinanomachi, Tokyo, Japan
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Center, Tsukuba, Ibaraki, Japan
| | - Shigeo Saito
- School of Science and Engineering, Teikyo University, Utsunomia, Tochigi, Japan.,Saito Laboratory of Cell Technology, Yaita, Tochigi, Japan
| | - Kyosuke Nagata
- Department of Infection Biology, Graduate School of Comprehensive Human Sciences, the University of Tsukuba, Tsukuba, Japan
| | - Chang-Shen Lin
- Graduate Institute of Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Kazunari K Yokoyama
- Center for Stem Cell Research, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan.,Graduate Institute of Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Infection Biology, Graduate School of Comprehensive Human Sciences, the University of Tsukuba, Tsukuba, Japan.,Department of Molecular Preventive Medicine, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
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103
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lncRNAs and MYC: An Intricate Relationship. Int J Mol Sci 2017; 18:ijms18071497. [PMID: 28704924 PMCID: PMC5535987 DOI: 10.3390/ijms18071497] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 07/05/2017] [Accepted: 07/11/2017] [Indexed: 01/27/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are emerging as important regulators of gene expression networks, acting either at the transcriptional level, by influencing histone modifications, or at the post-transcriptional level, by controlling mRNA stability and translation. Among the gene expression networks known to influence the process of oncogenic transformation, the one controlled by the proto-oncogene MYC is one of the most frequently deregulated in cancer. In B-cell lymphomas, the MYC gene is subject to chromosomal rearrangements that result in MYC overexpression. In many other cancers, the region surrounding MYC is subject to gene amplification. MYC expression is also controlled at the level of protein and mRNA stability. Neoplastic lesions affecting MYC expression are responsible for a drastic change in the number and the type of genes that are transcriptionally controlled by MYC, depending on differential promoter affinities. Transcriptome profiling of tumor samples has shown that several lncRNAs can be found differentially regulated by MYC in different cancer types and many of them can influence cancer cell viability and proliferation. At the same time, lncRNAs have been shown to be able to control the expression of MYC itself, both at transcriptional and post-transcriptional levels. Given that targeting the MYC-dependent transcriptional program has the potential to reach broad anticancer activity, molecular dissection of the complex regulatory mechanisms governing MYC expression will be crucial in the future for the identification of novel therapeutic strategies.
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104
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Liu W, Ding C. Roles of LncRNAs in Viral Infections. Front Cell Infect Microbiol 2017; 7:205. [PMID: 28603696 PMCID: PMC5445353 DOI: 10.3389/fcimb.2017.00205] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 05/08/2017] [Indexed: 12/12/2022] Open
Abstract
Many proteins and signaling pathways participate in anti-viral host responses. Long non-coding RNAs (lncRNAs), a subset of non-coding RNAs greater than 200 nucleotides in length, have been recently described as critical regulators in viral infections. Accumulating research indicates that lncRNAs are important in the development and progression of infectious diseases. LncRNAs are not only involved in anti-viral responses, but in many different virus-host interactions, some of which may be beneficial to the virus. Here we review the current knowledge regarding host and viral lncRNAs and their roles in viral infections. In addition, the potential of using lncRNAs as diagnostic biomarkers is discussed.
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Affiliation(s)
- Weiwei Liu
- Avian infectious Department, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural ScienceShanghai, China
| | - Chan Ding
- Avian infectious Department, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural ScienceShanghai, China
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105
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Ee LS, McCannell KN, Tang Y, Fernandes N, Hardy WR, Green MR, Chu F, Fazzio TG. An Embryonic Stem Cell-Specific NuRD Complex Functions through Interaction with WDR5. Stem Cell Reports 2017; 8:1488-1496. [PMID: 28528697 PMCID: PMC5470077 DOI: 10.1016/j.stemcr.2017.04.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 04/18/2017] [Accepted: 04/20/2017] [Indexed: 11/18/2022] Open
Abstract
The Nucleosome Remodeling and Deacetylase (NuRD) complex is a chromatin regulatory complex that functions as a transcriptional co-repressor in metazoans. The NuRD subunit MBD3 is essential for targeting and assembly of a functional NuRD complex as well as embryonic stem cell (ESC) pluripotency. Three MBD3 isoforms (MBD3A, MBD3B, and MBD3C) are expressed in mouse. Here, we find that the MBD3C isoform contains a unique 50-amino-acid N-terminal region that is necessary for MBD3C to specifically interact with the histone H3 binding protein WDR5. Domain analyses of WDR5 reveal that the H3 binding pocket is required for interaction with MBD3C. We find that while Mbd3c knockout ESCs differentiate normally, MBD3C is redundant with the MBD3A and MBD3B isoforms in regulation of gene expression, with the unique MBD3C N terminus required for this redundancy. Together, our data characterize a unique NuRD complex variant that functions specifically in ESCs. Mbd3c binds Wdr5 through its unique N-terminal domain Wdr5 interaction is critical for Mbd3c function Mbd3c/NuRD can substitute for canonical NuRD complex in ESC gene regulation
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Affiliation(s)
- Ly-Sha Ee
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Kurtis N McCannell
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Yang Tang
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Nancy Fernandes
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - W Rod Hardy
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Michael R Green
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA; Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Feixia Chu
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Thomas G Fazzio
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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106
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Gu P, Chen X, Xie R, Han J, Xie W, Wang B, Dong W, Chen C, Yang M, Jiang J, Chen Z, Huang J, Lin T. lncRNA HOXD-AS1 Regulates Proliferation and Chemo-Resistance of Castration-Resistant Prostate Cancer via Recruiting WDR5. Mol Ther 2017; 25:1959-1973. [PMID: 28487115 DOI: 10.1016/j.ymthe.2017.04.016] [Citation(s) in RCA: 145] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 04/07/2017] [Accepted: 04/12/2017] [Indexed: 02/01/2023] Open
Abstract
Castration-resistant prostate cancer (CRPC) that occurs after the failure of androgen deprivation therapy is the leading cause of deaths in prostate cancer patients. Thus, there is an obvious and urgent need to fully understand the mechanism of CRPC and discover novel therapeutic targets. Long noncoding RNAs (lncRNAs) are crucial regulators in many human cancers, yet their potential roles and molecular mechanisms in CRPC are poorly understood. In this study, we discovered that an lncRNA HOXD-AS1 is highly expressed in CRPC cells and correlated closely with Gleason score, T stage, lymph nodes metastasis, and progression-free survival. Knockdown of HOXD-AS1 inhibited the proliferation and chemo-resistance of CRPC cells in vitro and in vivo. Furthermore, we identified several cell cycle, chemo-resistance, and castration-resistance-related genes, including PLK1, AURKA, CDC25C, FOXM1, and UBE2C, that were activated transcriptionally by HOXD-AS1. Further investigation revealed that HOXD-AS1 recruited WDR5 to directly regulate the expression of target genes by mediating histone H3 lysine 4 tri-methylation (H3K4me3). In conclusion, our findings indicate that HOXD-AS1 promotes proliferation, castration resistance, and chemo-resistance in prostate cancer by recruiting WDR5. This sheds a new insight into the regulation of CRPC by lncRNA and provides a potential approach for the treatment of CRPC.
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Affiliation(s)
- Peng Gu
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Xu Chen
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Ruihui Xie
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Jinli Han
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Weibin Xie
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Bo Wang
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Wen Dong
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Changhao Chen
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Meihua Yang
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Junyi Jiang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China; Department of Clinical Laboratory, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Ziyue Chen
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China; Department of Pediatric Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Jian Huang
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.
| | - Tianxin Lin
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China.
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107
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Fanucchi S, Mhlanga MM. Enhancer-Derived lncRNAs Regulate Genome Architecture: Fact or Fiction? Trends Genet 2017; 33:375-377. [PMID: 28359583 DOI: 10.1016/j.tig.2017.03.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 03/09/2017] [Indexed: 01/22/2023]
Abstract
How does the non-coding portion of the genome contribute to the regulation of genome architecture? A recent paper by Tan et al. focuses on the relationship between cis-acting complex-trait-associated lincRNAs and the formation of chromosomal contacts in topologically associating domains (TADs).
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Affiliation(s)
- Stephanie Fanucchi
- Division of Chemical, Systems, and Synthetic Biology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa; Gene Expression and Biophysics Group, Biomedical Translational Research Initiative (BTRI), Council for Scientific and Industrial Research (CSIR) Biosciences, Pretoria, South Africa.
| | - Musa M Mhlanga
- Division of Chemical, Systems, and Synthetic Biology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa; Gene Expression and Biophysics Group, Biomedical Translational Research Initiative (BTRI), Council for Scientific and Industrial Research (CSIR) Biosciences, Pretoria, South Africa.
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108
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109
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Skalska L, Beltran-Nebot M, Ule J, Jenner RG. Regulatory feedback from nascent RNA to chromatin and transcription. Nat Rev Mol Cell Biol 2017; 18:331-337. [PMID: 28270684 DOI: 10.1038/nrm.2017.12] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Transcription and chromatin function are regulated by proteins that bind to DNA, nucleosomes or RNA polymerase II, with specific non-coding RNAs (ncRNAs) functioning to modulate their recruitment or activity. Unlike ncRNAs, nascent pre-mRNA was considered to be primarily a passive player in these processes. In this Opinion article, we describe recently identified interactions between nascent pre-mRNAs and regulatory proteins, highlight commonalities between the functions of nascent pre-mRNA and nascent ncRNA, and propose that both types of RNA have an active role in transcription and chromatin regulation.
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Affiliation(s)
- Lenka Skalska
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
| | - Manuel Beltran-Nebot
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
| | - Jernej Ule
- Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK; and The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Richard G Jenner
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
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110
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Bose DA, Donahue G, Reinberg D, Shiekhattar R, Bonasio R, Berger SL. RNA Binding to CBP Stimulates Histone Acetylation and Transcription. Cell 2017; 168:135-149.e22. [PMID: 28086087 DOI: 10.1016/j.cell.2016.12.020] [Citation(s) in RCA: 245] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 10/10/2016] [Accepted: 12/14/2016] [Indexed: 12/29/2022]
Abstract
CBP/p300 are transcription co-activators whose binding is a signature of enhancers, cis-regulatory elements that control patterns of gene expression in multicellular organisms. Active enhancers produce bi-directional enhancer RNAs (eRNAs) and display CBP/p300-dependent histone acetylation. Here, we demonstrate that CBP binds directly to RNAs in vivo and in vitro. RNAs bound to CBP in vivo include a large number of eRNAs. Using steady-state histone acetyltransferase (HAT) assays, we show that an RNA binding region in the HAT domain of CBP-a regulatory motif unique to CBP/p300-allows RNA to stimulate CBP's HAT activity. At enhancers where CBP interacts with eRNAs, stimulation manifests in RNA-dependent changes in the histone acetylation mediated by CBP, such as H3K27ac, and by corresponding changes in gene expression. By interacting directly with CBP, eRNAs contribute to the unique chromatin structure at active enhancers, which, in turn, is required for regulation of target genes.
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Affiliation(s)
- Daniel A Bose
- Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Greg Donahue
- Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Danny Reinberg
- Department of Molecular Pharmacology and Biochemistry, New York University School of Medicine, New York, NY 10016, USA
| | - Ramin Shiekhattar
- Sylvester Comprehensive Cancer Center, Department of Human Genetics, University of Miami Miller School of Medicine, Biomedical Research Building, Room 719, 1501 NW 10th Avenue, Miami, FL 33136, USA
| | - Roberto Bonasio
- Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shelley L Berger
- Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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111
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Long Noncoding RNA: Genome Organization and Mechanism of Action. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1008:47-74. [PMID: 28815536 DOI: 10.1007/978-981-10-5203-3_2] [Citation(s) in RCA: 195] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
For the last four decades, we have known that noncoding RNAs maintain critical housekeeping functions such as transcription, RNA processing, and translation. However, in the late 1990s and early 2000s, the advent of high-throughput sequencing technologies and computational tools to analyze these large sequencing datasets facilitated the discovery of thousands of small and long noncoding RNAs (lncRNAs) and their functional role in diverse biological functions. For example, lncRNAs have been shown to regulate dosage compensation, genomic imprinting, pluripotency, cell differentiation and development, immune response, etc. Here we review how lncRNAs bring about such copious functions by employing diverse mechanisms such as translational inhibition, mRNA degradation, RNA decoys, facilitating recruitment of chromatin modifiers, regulation of protein activity, regulating the availability of miRNAs by sponging mechanism, etc. In addition, we provide a detailed account of different mechanisms as well as general principles by which lncRNAs organize functionally different nuclear sub-compartments and their impact on nuclear architecture.
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112
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Huynh NPT, Anderson BA, Guilak F, McAlinden A. Emerging roles for long noncoding RNAs in skeletal biology and disease. Connect Tissue Res 2017; 58:116-141. [PMID: 27254479 PMCID: PMC5301950 DOI: 10.1080/03008207.2016.1194406] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Normal skeletal development requires tight coordination of transcriptional networks, signaling pathways, and biomechanical cues, and many of these pathways are dysregulated in pathological conditions affecting cartilage and bone. Recently, a significant role has been identified for long noncoding RNAs (lncRNAs) in developing and maintaining cellular phenotypes, and improvements in sequencing technologies have led to the identification of thousands of lncRNAs across diverse cell types, including the cells within cartilage and bone. It is clear that lncRNAs play critical roles in regulating gene expression. For example, they can function as epigenetic regulators in the nucleus via chromatin modulation to control gene transcription, or in the cytoplasm, where they can function as scaffolds for protein-binding partners or modulate the activity of other coding and noncoding RNAs. In this review, we discuss the growing list of lncRNAs involved in normal development and/or homeostasis of the skeletal system, the potential mechanisms by which these lncRNAs might function, and recent improvements in the methodologies available to study lncRNA functions in vitro and in vivo. Finally, we address the likely utility of lncRNAs as biomarkers and therapeutic targets for diseases of the skeletal system, including osteoarthritis, osteoporosis, and in cancers of the skeletal system.
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Affiliation(s)
- Nguyen P. T. Huynh
- Department of Orthopaedic Surgery, Washington University School of Medicine, St Louis, MO, USA,Shriners Hospitals for Children – St. Louis, St. Louis, MO, USA,Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
| | - Britta A. Anderson
- Department of Orthopaedic Surgery, Washington University School of Medicine, St Louis, MO, USA
| | - Farshid Guilak
- Department of Orthopaedic Surgery, Washington University School of Medicine, St Louis, MO, USA,Shriners Hospitals for Children – St. Louis, St. Louis, MO, USA,Department of Cell Biology, Duke University Medical Center, Durham, NC, USA,Department of Biomedical Engineering, Washington University School of Medicine, St. Louis, MO, USA,Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Audrey McAlinden
- Department of Orthopaedic Surgery, Washington University School of Medicine, St Louis, MO, USA,Department of Cell Biology & Physiology, Washington University School of Medicine, St. Louis, MO, USA,Department of Biomedical Engineering, Washington University School of Medicine, St. Louis, MO, USA
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113
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Davis TL, Rebay I. Master regulators in development: Views from the Drosophila retinal determination and mammalian pluripotency gene networks. Dev Biol 2016; 421:93-107. [PMID: 27979656 DOI: 10.1016/j.ydbio.2016.12.005] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 12/03/2016] [Accepted: 12/03/2016] [Indexed: 02/07/2023]
Abstract
Among the mechanisms that steer cells to their correct fate during development, master regulatory networks are unique in their sufficiency to trigger a developmental program outside of its normal context. In this review we discuss the key features that underlie master regulatory potency during normal and ectopic development, focusing on two examples, the retinal determination gene network (RDGN) that directs eye development in the fruit fly and the pluripotency gene network (PGN) that maintains cell fate competency in the early mammalian embryo. In addition to the hierarchical transcriptional activation, extensive positive transcriptional feedback, and cooperative protein-protein interactions that enable master regulators to override competing cellular programs, recent evidence suggests that network topology must also be dynamic, with extensive rewiring of the interactions and feedback loops required to navigate the correct sequence of developmental transitions to reach a final fate. By synthesizing the in vivo evidence provided by the RDGN with the extensive mechanistic insight gleaned from the PGN, we highlight the unique regulatory capabilities that continual reorganization into new hierarchies confers on master control networks. We suggest that deeper understanding of such dynamics should be a priority, as accurate spatiotemporal remodeling of network topology will undoubtedly be essential for successful stem cell based therapeutic efforts.
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Affiliation(s)
- Trevor L Davis
- Committee on Development, Regeneration, and Stem Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - Ilaria Rebay
- Committee on Development, Regeneration, and Stem Cell Biology, University of Chicago, Chicago, IL 60637, USA; Ben May Department for Cancer Research, University of Chicago, Chicago, IL 60637, USA.
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114
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Long non-coding RNA GAS5 controls human embryonic stem cell self-renewal by maintaining NODAL signalling. Nat Commun 2016; 7:13287. [PMID: 27811843 PMCID: PMC5097163 DOI: 10.1038/ncomms13287] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 09/16/2016] [Indexed: 12/18/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are known players in the regulatory circuitry of the self-renewal in human embryonic stem cells (hESCs). However, most hESC-specific lncRNAs remain uncharacterized. Here we demonstrate that growth-arrest-specific transcript 5 (GAS5), a known tumour suppressor and growth arrest-related lncRNA, is highly expressed and directly regulated by pluripotency factors OCT4 and SOX2 in hESCs. Phenotypic analysis shows that GAS5 knockdown significantly impairs hESC self-renewal, but its overexpression significantly promotes hESC self-renewal. Using RNA sequencing and functional analysis, we demonstrate that GAS5 maintains NODAL signalling by protecting NODAL expression from miRNA-mediated degradation. Therefore, we propose that the above pluripotency factors, GAS5 and NODAL form a feed-forward signalling loop that maintains hESC self-renewal. As this regulatory function of GAS5 is stem cell specific, our findings also indicate that the functions of lncRNAs may vary in different cell types due to competing endogenous mechanisms.
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115
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Transcription of the non-coding RNA upperhand controls Hand2 expression and heart development. Nature 2016; 539:433-436. [PMID: 27783597 DOI: 10.1038/nature20128] [Citation(s) in RCA: 249] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 09/29/2016] [Indexed: 12/28/2022]
Abstract
HAND2 is an ancestral regulator of heart development and one of four transcription factors that control the reprogramming of fibroblasts into cardiomyocytes. Deletion of Hand2 in mice results in right ventricle hypoplasia and embryonic lethality. Hand2 expression is tightly regulated by upstream enhancers that reside within a super-enhancer delineated by histone H3 acetyl Lys27 (H3K27ac) modifications. Here we show that transcription of a Hand2-associated long non-coding RNA, which we named upperhand (Uph), is required to maintain the super-enhancer signature and elongation of RNA polymerase II through the Hand2 enhancer locus. Blockade of Uph transcription, but not knockdown of the mature transcript, abolished Hand2 expression, causing right ventricular hypoplasia and embryonic lethality in mice. Given the substantial number of uncharacterized promoter-associated long non-coding RNAs encoded by the mammalian genome, the Uph-Hand2 regulatory partnership offers a mechanism by which divergent non-coding transcription can establish a permissive chromatin environment.
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116
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Long non-coding RNAs: spatial amplifiers that control nuclear structure and gene expression. Nat Rev Mol Cell Biol 2016; 17:756-770. [DOI: 10.1038/nrm.2016.126] [Citation(s) in RCA: 420] [Impact Index Per Article: 52.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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117
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Liu H, Lyu J, Liu H, Gao Y, Guo J, He H, Han Z, Zhang Y, Wu Q. Computational identification of putative lincRNAs in mouse embryonic stem cell. Sci Rep 2016; 6:34892. [PMID: 27713513 PMCID: PMC5054606 DOI: 10.1038/srep34892] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 09/21/2016] [Indexed: 01/19/2023] Open
Abstract
As the regulatory factors, lncRNAs play critical roles in embryonic stem cells. And lincRNAs are most widely studied lncRNAs, however, there might still might exist a large member of uncovered lncRNAs. In this study, we constructed the de novo assembly of transcriptome to detect 6,701 putative long intergenic non-coding transcripts (lincRNAs) expressed in mouse embryonic stem cells (ESCs), which might be incomplete with the lack coverage of 5' ends assessed by CAGE peaks. Comparing the TSS proximal regions between the known lincRNAs and their closet protein coding transcripts, our results revealed that the lincRNA TSS proximal regions are associated with the characteristic genomic and epigenetic features. Subsequently, 1,293 lincRNAs were corrected at their 5' ends using the putative lincRNA TSS regions predicted by the TSS proximal region prediction model based on genomic and epigenetic features. Finally, 43 putative lincRNAs were annotated by Gene Ontology terms. In conclusion, this work provides a novel catalog of mouse ESCs-expressed lincRNAs with the relatively complete transcript length, which might be useful for the investigation of transcriptional and post-transcriptional regulation of lincRNA in mouse ESCs and even mammalian development.
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Affiliation(s)
- Hui Liu
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150001, China
| | - Jie Lyu
- Dan L. Duncan Cancer Center, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Hongbo Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Yang Gao
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150001, China
| | - Jing Guo
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150001, China
| | - Hongjuan He
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150001, China
| | - Zhengbin Han
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150001, China
| | - Yan Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Qiong Wu
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150001, China
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Bouckenheimer J, Assou S, Riquier S, Hou C, Philippe N, Sansac C, Lavabre-Bertrand T, Commes T, Lemaître JM, Boureux A, De Vos J. Long non-coding RNAs in human early embryonic development and their potential in ART. Hum Reprod Update 2016; 23:19-40. [PMID: 27655590 DOI: 10.1093/humupd/dmw035] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Revised: 07/20/2016] [Accepted: 08/23/2016] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Human long non-coding RNAs (lncRNAs) are an emerging category of transcripts with increasingly documented functional roles during development. LncRNAs and roles during human early embryo development have recently begun to be unravelled. OBJECTIVE AND RATIONALE This review summarizes the most recent knowledge on lncRNAs and focuses on their expression patterns and role during early human embryo development and in pluripotent stem cells (PSCs). Public mRNA sequencing (mRNA-seq) data were used to illustrate these expression signatures. SEARCH METHODS The PubMed and EMBASE databases were first interrogated using specific terms, such as 'lncRNAs', to get an extensive overview on lncRNAs up to February 2016, and then using 'human lncRNAs' and 'embryo', 'development', or 'PSCs' to focus on lncRNAs involved in human embryo development or in PSC.Recently published RNA-seq data from human oocytes and pre-implantation embryos (including single-cell data), PSC and a panel of normal and malignant adult tissues were used to describe the specific expression patterns of some lncRNAs in early human embryos. OUTCOMES The existence and the crucial role of lncRNAs in many important biological phenomena in each branch of the life tree are now well documented. The number of identified lncRNAs is rapidly increasing and has already outnumbered that of protein-coding genes. Unlike small non-coding RNAs, a variety of mechanisms of action have been proposed for lncRNAs. The functional role of lncRNAs has been demonstrated in many biological and developmental processes, including cell pluripotency induction, X-inactivation or gene imprinting. Analysis of RNA-seq data highlights that lncRNA abundance changes significantly during human early embryonic development. This suggests that lncRNAs could represent candidate biomarkers for developing non-invasive tests for oocyte or embryo quality. Finally, some of these lncRNAs are also expressed in human cancer tissues, suggesting that reactivation of an embryonic lncRNA program may contribute to human malignancies. WIDER IMPLICATIONS LncRNAs are emerging potential key players in gene expression regulation. Analysis of RNA-seq data from human pre-implantation embryos identified lncRNA signatures that are specific to this critical step. We anticipate that further studies will show that these new transcripts are major regulators of embryo development. These findings might also be used to develop new tests/treatments for improving the pregnancy success rate in IVF procedures or for regenerative medicine applications involving PSC.
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Affiliation(s)
- Julien Bouckenheimer
- Institute for Regenerative Medicine and Biotherapy, CHU Montpellier, Saint-Eloi Hospital, Montpellier F 34000, France.,INSERM, U1183, Montpellier F 34000, France.,Université de Montpellier, Montpellier F 34000, France
| | - Said Assou
- Institute for Regenerative Medicine and Biotherapy, CHU Montpellier, Saint-Eloi Hospital, Montpellier F 34000, France.,INSERM, U1183, Montpellier F 34000, France.,Université de Montpellier, Montpellier F 34000, France
| | - Sébastien Riquier
- Institute for Regenerative Medicine and Biotherapy, CHU Montpellier, Saint-Eloi Hospital, Montpellier F 34000, France.,INSERM, U1183, Montpellier F 34000, France.,Université de Montpellier, Montpellier F 34000, France
| | - Cyrielle Hou
- Institute for Regenerative Medicine and Biotherapy, CHU Montpellier, Saint-Eloi Hospital, Montpellier F 34000, France.,INSERM, U1183, Montpellier F 34000, France.,Université de Montpellier, Montpellier F 34000, France
| | - Nicolas Philippe
- Institute for Regenerative Medicine and Biotherapy, CHU Montpellier, Saint-Eloi Hospital, Montpellier F 34000, France.,INSERM, U1183, Montpellier F 34000, France.,Université de Montpellier, Montpellier F 34000, France.,Coretec, Montpellier, France
| | - Caroline Sansac
- Institute for Regenerative Medicine and Biotherapy, CHU Montpellier, Saint-Eloi Hospital, Montpellier F 34000, France.,INSERM, U1183, Montpellier F 34000, France.,Université de Montpellier, Montpellier F 34000, France
| | | | - Thérèse Commes
- Institute for Regenerative Medicine and Biotherapy, CHU Montpellier, Saint-Eloi Hospital, Montpellier F 34000, France.,INSERM, U1183, Montpellier F 34000, France.,Université de Montpellier, Montpellier F 34000, France.,Institut de Biologie Computationnelle, Montpellier F 34000, France
| | - Jean-Marc Lemaître
- Institute for Regenerative Medicine and Biotherapy, CHU Montpellier, Saint-Eloi Hospital, Montpellier F 34000, France .,INSERM, U1183, Montpellier F 34000, France.,Stem Cell Core Facility SAFE-iPSC, INGESTEM, Saint-Eloi Hospital, Montpellier F 34000, France
| | - Anthony Boureux
- Institute for Regenerative Medicine and Biotherapy, CHU Montpellier, Saint-Eloi Hospital, Montpellier F 34000, France.,INSERM, U1183, Montpellier F 34000, France.,Université de Montpellier, Montpellier F 34000, France
| | - John De Vos
- Institute for Regenerative Medicine and Biotherapy, CHU Montpellier, Saint-Eloi Hospital, Montpellier F 34000, France .,INSERM, U1183, Montpellier F 34000, France.,Université de Montpellier, Montpellier F 34000, France.,Institut de Biologie Computationnelle, Montpellier F 34000, France.,Stem Cell Core Facility SAFE-iPSC, INGESTEM, Saint-Eloi Hospital, Montpellier F 34000, France.,Department of Cell and Tissue Engineering, CHU Montpellier, Saint-Eloi Hospital, Montpellier F 34000, France
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P2RX7-V3 is a novel oncogene that promotes tumorigenesis in uveal melanoma. Tumour Biol 2016; 37:13533-13543. [PMID: 27468714 DOI: 10.1007/s13277-016-5141-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 07/11/2016] [Indexed: 12/17/2022] Open
Abstract
Uveal melanoma (UM) has a high mortality rate for primary intraocular tumors. Approximately half of UM patients present with untreatable and fatal metastases. Long non-coding RNAs (lncRNAs) have emerged as potent regulatory RNAs that play key roles in various cellular processes and tumorigenesis. However, to date, their roles in UM are not well-known. Here, we identified a transcriptional variant transcribed from the P2RX7 gene locus, named P2RX7-V3 (P2RX7 variant 3), which was expressed at a high level in UM cells. P2RX7-V3 silencing revealed that this variant acts as a necessary UM oncoRNA. Knockdown of P2RX7-V3 expression significantly suppressed tumor growth in vitro and in vivo. A genome-wide cDNA array revealed that a variety of genes were dysregulated following P2RX7-V3 silencing. These observations identified P2RX7-V3 that plays a crucial role in UM tumorigenesis and may serve as a useful biomarker in the diagnosis and prognosis treatment of UM in the future.
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120
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Meryet-Figuière M, Lambert B, Gauduchon P, Vigneron N, Brotin E, Poulain L, Denoyelle C. An overview of long non-coding RNAs in ovarian cancers. Oncotarget 2016; 7:44719-44734. [PMID: 26992233 PMCID: PMC5190131 DOI: 10.18632/oncotarget.8089] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 02/23/2016] [Indexed: 12/14/2022] Open
Abstract
As with miRNAs a decade ago, the scientific community recently understood that lncRNAs represent a new layer of complexity in the regulation of gene expression. Although only a subset of lncRNAs has been functionally characterized, it is clear that they are deeply involved in the most critical physiological and pathological biological processes. This review shows that in ovarian carcinoma, data already available testify to the importance of lncRNAs and that the demonstration of an ever-growing role of lncRNAs in the biology of this malignancy can be expected from future studies. We also underline the importance of their relationship with associated protein partners and miRNAs. Together, the available information suggests that the emerging field of lncRNAs will pave the way for a better understanding of ovarian cancer biology and might lead to the development of innovative therapeutic approaches. Moreover, lncRNAs expression signatures either alone or in combination with other types of markers (miRNAs, mRNAs, proteins) could prove useful to predict outcome or treatment follow-up in order to improve the therapeutic care of ovarian carcinoma patients.
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Affiliation(s)
- Matthieu Meryet-Figuière
- Inserm U1199, Biology and Innovative Therapeutics for Locally Aggressive Cancer (BioTICLA) Unit, Caen, France
- Normandie University, Caen, France
- UNICAEN, Caen, France
- Comprehensive Cancer Center CLCC François Baclesse, Unicancer, Caen, France
| | - Bernard Lambert
- Inserm U1199, Biology and Innovative Therapeutics for Locally Aggressive Cancer (BioTICLA) Unit, Caen, France
- Normandie University, Caen, France
- UNICAEN, Caen, France
- Comprehensive Cancer Center CLCC François Baclesse, Unicancer, Caen, France
- CNRS, Paris, France
| | - Pascal Gauduchon
- Inserm U1199, Biology and Innovative Therapeutics for Locally Aggressive Cancer (BioTICLA) Unit, Caen, France
- Normandie University, Caen, France
- UNICAEN, Caen, France
- Comprehensive Cancer Center CLCC François Baclesse, Unicancer, Caen, France
| | - Nicolas Vigneron
- Inserm U1199, Biology and Innovative Therapeutics for Locally Aggressive Cancer (BioTICLA) Unit, Caen, France
- Normandie University, Caen, France
- UNICAEN, Caen, France
- Comprehensive Cancer Center CLCC François Baclesse, Unicancer, Caen, France
| | - Emilie Brotin
- Inserm U1199, Biology and Innovative Therapeutics for Locally Aggressive Cancer (BioTICLA) Unit, Caen, France
- Normandie University, Caen, France
- UNICAEN, Caen, France
- Comprehensive Cancer Center CLCC François Baclesse, Unicancer, Caen, France
| | - Laurent Poulain
- Inserm U1199, Biology and Innovative Therapeutics for Locally Aggressive Cancer (BioTICLA) Unit, Caen, France
- Normandie University, Caen, France
- UNICAEN, Caen, France
- Comprehensive Cancer Center CLCC François Baclesse, Unicancer, Caen, France
| | - Christophe Denoyelle
- Inserm U1199, Biology and Innovative Therapeutics for Locally Aggressive Cancer (BioTICLA) Unit, Caen, France
- Normandie University, Caen, France
- UNICAEN, Caen, France
- Comprehensive Cancer Center CLCC François Baclesse, Unicancer, Caen, France
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121
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Schmitz SU, Grote P, Herrmann BG. Mechanisms of long noncoding RNA function in development and disease. Cell Mol Life Sci 2016; 73:2491-509. [PMID: 27007508 PMCID: PMC4894931 DOI: 10.1007/s00018-016-2174-5] [Citation(s) in RCA: 769] [Impact Index Per Article: 96.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 02/23/2016] [Accepted: 03/01/2016] [Indexed: 11/25/2022]
Abstract
Since decades it has been known that non-protein-coding RNAs have important cellular functions. Deep sequencing recently facilitated the discovery of thousands of novel transcripts, now classified as long noncoding RNAs (lncRNAs), in many vertebrate and invertebrate species. LncRNAs are involved in a wide range of cellular mechanisms, from almost all aspects of gene expression to protein translation and stability. Recent findings implicate lncRNAs as key players of cellular differentiation, cell lineage choice, organogenesis and tissue homeostasis. Moreover, lncRNAs are involved in pathological conditions such as cancer and cardiovascular disease, and therefore provide novel biomarkers and pharmaceutical targets. Here we discuss examples illustrating the versatility of lncRNAs in gene control, development and differentiation, as well as in human disease.
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Affiliation(s)
- Sandra U Schmitz
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195, Berlin, Germany.
| | - Phillip Grote
- Institute of Cardiovascular Regeneration, Center for Molecular Medicine, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany
| | - Bernhard G Herrmann
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195, Berlin, Germany.
- Institute for Medical Genetics, Campus Benjamin Franklin, Charite-University Medicine Berlin, Hindenburgdamm 30, 12203, Berlin, Germany.
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122
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Li J, Jin W, Qin Y, Zhao W, Chang C, Xu C. Expression Profile and Function Analysis of LncRNAs during Priming Phase of Rat Liver Regeneration. PLoS One 2016; 11:e0156128. [PMID: 27326854 PMCID: PMC4915705 DOI: 10.1371/journal.pone.0156128] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 06/06/2016] [Indexed: 01/18/2023] Open
Abstract
Emerging evidences have revealed that long non-coding RNAs (lncRNAs) functioned in a wide range of physiological and pathophysiological processes including rat liver regeneration, and could regulate gene expression in the transcriptional and post-transcriptional levels. However, the underlying mechanism for lncRNAs participation in liver regeneration is largely unknown. To define the mechanisms how the lncRNAs regulate LR, we performed bio-chip technology, high-throughput sequencing and RT-PCR to detect the expression of lncRNAs at 0, 2 and 6 h during LR after 2/3 hepatectomy (PH). The results indicated that 28 lncRNAs were involved in LR. Bioinformatics analysis predicated 465 co-expression target genes including 10 regulatory genes were related to these 28 lncRNAs. Ingenuity Pathway Analysis (IPA) was employed to analyze the signaling pathways and physiological activities that regulated by these genes, and the results suggested that these genes were potentially related to ILK, SAPK/JNK and ERK/MAPK signaling pathways, and possibly regulate many important physiological activities in LR in terms of cell proliferation, cell differentiation, cell survival, apoptosis and necrosis.
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Affiliation(s)
- Jun Li
- College of Life Science, Henan Normal University, Xinxiang 453007, Henan Province, China
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation and Henan Bioengineering Key Laboratory, Henan. Normal University, Xinxiang 453007, Henan Province, China
- Henan engineering laboratory for bioengineering and drug development, Henan Normal University, Xinxiang 453007, Henan Province, China
| | - Wei Jin
- College of Life Science, Henan Normal University, Xinxiang 453007, Henan Province, China
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation and Henan Bioengineering Key Laboratory, Henan. Normal University, Xinxiang 453007, Henan Province, China
- Henan engineering laboratory for bioengineering and drug development, Henan Normal University, Xinxiang 453007, Henan Province, China
| | - Yanli Qin
- College of Life Science, Henan Normal University, Xinxiang 453007, Henan Province, China
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation and Henan Bioengineering Key Laboratory, Henan. Normal University, Xinxiang 453007, Henan Province, China
- Henan engineering laboratory for bioengineering and drug development, Henan Normal University, Xinxiang 453007, Henan Province, China
| | - Weiming Zhao
- College of Life Science, Henan Normal University, Xinxiang 453007, Henan Province, China
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation and Henan Bioengineering Key Laboratory, Henan. Normal University, Xinxiang 453007, Henan Province, China
- Henan engineering laboratory for bioengineering and drug development, Henan Normal University, Xinxiang 453007, Henan Province, China
| | - Cuifang Chang
- College of Life Science, Henan Normal University, Xinxiang 453007, Henan Province, China
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation and Henan Bioengineering Key Laboratory, Henan. Normal University, Xinxiang 453007, Henan Province, China
- Henan engineering laboratory for bioengineering and drug development, Henan Normal University, Xinxiang 453007, Henan Province, China
- * E-mail: (CFC); (CSX)
| | - Cunshuan Xu
- College of Life Science, Henan Normal University, Xinxiang 453007, Henan Province, China
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation and Henan Bioengineering Key Laboratory, Henan. Normal University, Xinxiang 453007, Henan Province, China
- Henan engineering laboratory for bioengineering and drug development, Henan Normal University, Xinxiang 453007, Henan Province, China
- * E-mail: (CFC); (CSX)
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Aaronson Y, Livyatan I, Gokhman D, Meshorer E. Systematic identification of gene family regulators in mouse and human embryonic stem cells. Nucleic Acids Res 2016; 44:4080-9. [PMID: 27084933 PMCID: PMC4872113 DOI: 10.1093/nar/gkw259] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 04/01/2016] [Indexed: 01/22/2023] Open
Abstract
Pluripotent self-renewing embryonic stem cells (ESCs) have been the focus of a growing number of high-throughput experiments, revealing the genome-wide locations of hundreds of transcription factors and histone modifications. While most of these datasets were used in a specific context, all datasets combined offer a comprehensive view of chromatin characteristics and regulatory elements that govern cell states. Here, using hundreds of datasets in ESCs, we generated colocalization maps of chromatin proteins and modifications, and built a discovery pipeline for regulatory proteins of gene families. By comparing genome-wide binding data with over-expression and knockdown analysis of hundreds of genes, we discovered that the pluripotency-related factor NR5A2 separates mitochondrial from cytosolic ribosomal genes, regulating their expression. We further show that genes with a common chromatin profile are enriched for distinct Gene Ontology (GO) categories. Our approach can be generalized to reveal common regulators of any gene group; discover novel gene families, and identify common genomic elements based on shared chromatin features.
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Affiliation(s)
- Yair Aaronson
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Jerusalem 91904, Israel
| | - Ilana Livyatan
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Jerusalem 91904, Israel
| | - David Gokhman
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Jerusalem 91904, Israel
| | - Eran Meshorer
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Jerusalem 91904, Israel The Edmond and Lily Center for Brain Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 91904, Israel
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Wang C, Li G, Wu Y, Xi J, Kang J. LincRNA1230 inhibits the differentiation of mouse ES cells towards neural progenitors. SCIENCE CHINA-LIFE SCIENCES 2016; 59:443-54. [PMID: 26920680 DOI: 10.1007/s11427-016-5008-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 11/13/2015] [Indexed: 01/07/2023]
Abstract
In vitro, mouse embryonic stem (ES) cells can differentiate into many somatic cell types, including neurons and glial cells. When cultured in serum-free medium, ES cells convert spontaneously and efficiently to a neural fate. Previous studies have shown that the neural conversion of mouse ES cells includes both the participation of neural-specific transcription factors and the regulation of epigenetic modifications. However, the intracellular mechanism underlying this intrinsic transition still remains to be further elucidated. Herein, we describe a long intergenic non-coding RNA, LincRNA1230, which participates in the regulation of the neural lineage specification of mouse ES cells. The ectopic forced expression of LincRNA1230 dramatically inhibited mouse ES cells from adopting a neural cell fate, while LincRNA1230 knockdown promoted the conversion of mouse ES cells towards neural progenitors. Mechanistic studies have shown that LincRNA1230 inhibits the activation of early neural genes, such as Pax6 and Sox1, through the modulation of bivalent modifications (tri-methylation of histone3 lysine4 and histone3 lysine27) at the promoters of these genes. The interaction of LincRNA1230 with Wdr5 blocked the localization of Wdr5 at the promoters of early neural genes, thereby inhibiting the enrichment of H3K4me3 modifications at these loci. Collectively, these findings revealed a crucial role for LincRNA1230 in the regulation of the neural differentiation of mouse ES cells.
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Affiliation(s)
- Chenxin Wang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Health Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Science and Technology, Tongji University, Shanghai, 200092, China
| | - Guoping Li
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Health Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Science and Technology, Tongji University, Shanghai, 200092, China
| | - Yukang Wu
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Health Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Science and Technology, Tongji University, Shanghai, 200092, China
| | - Jiajie Xi
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Health Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Science and Technology, Tongji University, Shanghai, 200092, China
| | - Jiuhong Kang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Health Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Science and Technology, Tongji University, Shanghai, 200092, China.
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125
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G Hendrickson D, Kelley DR, Tenen D, Bernstein B, Rinn JL. Widespread RNA binding by chromatin-associated proteins. Genome Biol 2016; 17:28. [PMID: 26883116 PMCID: PMC4756407 DOI: 10.1186/s13059-016-0878-3] [Citation(s) in RCA: 172] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 01/12/2016] [Indexed: 01/01/2023] Open
Abstract
Background Recent evidence suggests that RNA interaction can regulate the activity and localization of chromatin-associated proteins. However, it is unknown if these observations are specialized instances for a few key RNAs and chromatin factors in specific contexts, or a general mechanism underlying the establishment of chromatin state and regulation of gene expression. Results Here, we perform formaldehyde RNA immunoprecipitation (fRIP-Seq) to survey the RNA associated with a panel of 24 chromatin regulators and traditional RNA binding proteins. For each protein that reproducibly bound measurable quantities of bulk RNA (90 % of the panel), we detect enrichment for hundreds to thousands of both noncoding and mRNA transcripts. Conclusion For each protein, we find that the enriched sets of RNAs share distinct biochemical, functional, and chromatin properties. Thus, these data provide evidence for widespread specific and relevant RNA association across diverse classes of chromatin-modifying complexes. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-0878-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- David G Hendrickson
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA. .,Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.
| | - David R Kelley
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA. .,Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.
| | - Danielle Tenen
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA. .,Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.
| | | | - John L Rinn
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA. .,Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA. .,Beth Israel Deaconess Medical Center, Boston, MA, 02215, USA.
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126
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Long noncoding RNAs: a potent source of regulation in immunity and disease. Immunol Cell Biol 2016; 93:277-83. [PMID: 25776990 DOI: 10.1038/icb.2015.2] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 12/06/2014] [Indexed: 12/14/2022]
Abstract
The discovery of functional long noncoding RNAs (lncRNAs) coupled with the ever-increasing accessibility of genomic and transcriptomic technology has led to an explosion of functional and mechanistic investigation and discovery into what was once dismissed as junk DNA. Over the past decade, a significant number of lncRNAs have been found to be involved in a diverse array of processes: from epigenetic modulation, both repressive and activating; to protein scaffolding; to miRNA sequestration; to competitive inhibition; and more. The broad character of these mechanisms means that lncRNAs have the potential for regulation across all biological processes-not least of which are immunity and disease. A number of lncRNAs operating within these two contexts have already been identified and characterized, but untold more remain yet to be discovered. This review aims to provide an overview of the current state of research on lncRNAs involved in immune modulation and disease, with an emphasis on their mechanism and discovery.
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127
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Ouyang J, Hu J, Chen JL. lncRNAs regulate the innate immune response to viral infection. WILEY INTERDISCIPLINARY REVIEWS-RNA 2015; 7:129-43. [PMID: 26667656 PMCID: PMC7169827 DOI: 10.1002/wrna.1321] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Revised: 10/14/2015] [Accepted: 11/04/2015] [Indexed: 01/01/2023]
Abstract
Long noncoding RNAs (lncRNAs) are extensively expressed in mammalian cells and play a crucial role as RNA regulators in various cellular processes. Increasing data reveal that they function in innate antiviral immunity through complex mechanisms. Thousands of lncRNAs are regulated by RNA virus or DNA virus infection. The significant differential expression of lncRNAs is induced by virus or host antiviral signaling mediated by interferons (IFNs) and tumor necrosis factor‐α. In turn, these lncRNAs modulate the host immune response including the pathogen recognition receptor (PRR)‐related signaling, the translocation and activation of transcription factors, the production of IFNs and cytokines, the IFN‐activated JAK‐STAT signaling and the transcription of antiviral IFN‐stimulated genes (ISGs). Using gain‐ or loss‐of‐function analysis, the effect of lncRNAs on viral replication has been investigated to elucidate the essential role of lncRNA in the host–virus interaction. lncRNAs have shown specifically elevated or decreased levels in patients with viral diseases, suggesting the possibility of clinical application as biomarkers. Here we review the current advances of viral infection‐associated host lncRNAs, their functional significance in different aspects of antiviral immune response, the specific mechanisms and unsolved issues. We also summarize the regulation of lncRNAs by viruses, PRR agonists and cytokines. In addition, virus‐encoded lncRNAs and their functional involvement in host–virus interaction are addressed. WIREs RNA 2016, 7:129–143. doi: 10.1002/wrna.1321 This article is categorized under:
RNA Interactions with Proteins and Other Molecules > Protein–RNA Interactions: Functional Implications RNA in Disease and Development > RNA in Disease
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Affiliation(s)
- Jing Ouyang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jiayue Hu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Ji-Long Chen
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
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128
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Carlson HL, Quinn JJ, Yang YW, Thornburg CK, Chang HY, Stadler HS. LncRNA-HIT Functions as an Epigenetic Regulator of Chondrogenesis through Its Recruitment of p100/CBP Complexes. PLoS Genet 2015; 11:e1005680. [PMID: 26633036 PMCID: PMC4669167 DOI: 10.1371/journal.pgen.1005680] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 10/27/2015] [Indexed: 01/23/2023] Open
Abstract
Gene expression profiling in E 11 mouse embryos identified high expression of the long noncoding RNA (lncRNA), LNCRNA-HIT in the undifferentiated limb mesenchyme, gut, and developing genital tubercle. In the limb mesenchyme, LncRNA-HIT was found to be retained in the nucleus, forming a complex with p100 and CBP. Analysis of the genome-wide distribution of LncRNA-HIT-p100/CBP complexes by ChIRP-seq revealed LncRNA-HIT associated peaks at multiple loci in the murine genome. Ontological analysis of the genes contacted by LncRNA-HIT-p100/CBP complexes indicate a primary role for these loci in chondrogenic differentiation. Functional analysis using siRNA-mediated reductions in LncRNA-HIT or p100 transcripts revealed a significant decrease in expression of many of the LncRNA-HIT-associated loci. LncRNA-HIT siRNA treatments also impacted the ability of the limb mesenchyme to form cartilage, reducing mesenchymal cell condensation and the formation of cartilage nodules. Mechanistically the LncRNA-HIT siRNA treatments impacted pro-chondrogenic gene expression by reducing H3K27ac or p100 activity, confirming that LncRNA-HIT is essential for chondrogenic differentiation in the limb mesenchyme. Taken together, these findings reveal a fundamental epigenetic mechanism functioning during early limb development, using LncRNA-HIT and its associated proteins to promote the expression of multiple genes whose products are necessary for the formation of cartilage. A fundamental problem studied by skeletal biologists is the development of regenerative therapies to replace cartilage tissues impacted by injury or disease, which for individuals affected by osteoarthritis represents nearly half of all of all adults over the age of sixty five. To date, no therapies exist to promote sustained cartilage regeneration, as we have not been able to recapitulate the programming events necessary to instruct cells to form articular cartilage without these cells continuing to differentiate into bone. Our analysis of the early programming events occurring during cartilage formation led to the identification of LncRNA-HIT a long noncoding RNA that is essential for the differentiation of the embryonic limb mesenchyme into cartilage. A genome wide analysis of LncRNA-HIT’s distribution in the mesenchyme revealed strong association between LncRNA-HIT and numerous genes whose products facilitate cartilage formation. In the absence of LncRNA-HIT, the expression of these chondrogenic genes is severely reduced, impacting the differentiation of these cells into cartilage. Mechanistically, LncRNA-HIT regulates these pro-chondrogenic genes by recruiting p100 and CBP to these loci, facilitating H3K27ac and transcriptional activation. LncRNA-HIT also appears to be present in most vertebrate species, suggesting that the epigenetic program regulated by this lncRNA may represent a fundamental mechanism used by many species to promote cartilage formation.
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Affiliation(s)
- Hanqian L. Carlson
- Skeletal Biology Program, Shriners Hospitals for Children, Portland, Oregon, United States of America
| | - Jeffrey J. Quinn
- Program in Epithelial Biology, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, United States of America
| | - Yul W. Yang
- Program in Epithelial Biology, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, United States of America
| | - Chelsea K. Thornburg
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Howard Y. Chang
- Program in Epithelial Biology, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, United States of America
| | - H. Scott Stadler
- Skeletal Biology Program, Shriners Hospitals for Children, Portland, Oregon, United States of America
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, Oregon, United States of America
- * E-mail:
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129
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Taylor DH, Chu ETJ, Spektor R, Soloway PD. Long non-coding RNA regulation of reproduction and development. Mol Reprod Dev 2015; 82:932-56. [PMID: 26517592 PMCID: PMC4762656 DOI: 10.1002/mrd.22581] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 09/03/2015] [Indexed: 12/13/2022]
Abstract
Noncoding RNAs (ncRNAs) have long been known to play vital roles in eukaryotic gene regulation. Studies conducted over a decade ago revealed that maturation of spliced, polyadenylated coding mRNA occurs by reactions involving small nuclear RNAs and small nucleolar RNAs; mRNA translation depends on activities mediated by transfer RNAs and ribosomal RNAs, subject to negative regulation by micro RNAs; transcriptional competence of sex chromosomes and some imprinted genes is regulated in cis by ncRNAs that vary by species; and both small-interfering RNAs and piwi-interacting RNAs bound to Argonaute-family proteins regulate post-translational modifications on chromatin and local gene expression states. More recently, gene-regulating noncoding RNAs have been identified, such as long intergenic and long noncoding RNAs (collectively referred to as lncRNAs)--a class totaling more than 100,000 transcripts in humans, which include some of the previously mentioned RNAs that regulate dosage compensation and imprinted gene expression. Here, we provide an overview of lncRNA activities, and then review the role of lncRNAs in processes vital to reproduction, such as germ cell specification, sex determination and gonadogenesis, sex hormone responses, meiosis, gametogenesis, placentation, non-genetic inheritance, and pathologies affecting reproductive tissues. Results from many species are presented to illustrate the evolutionarily conserved processes lncRNAs are involved in.
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Affiliation(s)
- David H. Taylor
- Field of Genetics, Genomics and Development, Cornell University, Ithaca, New York
| | - Erin Tsi-Jia Chu
- Field of Comparative Biomedical Sciences, Cornell University, Ithaca, New York
| | - Roman Spektor
- Field of Genetics, Genomics and Development, Cornell University, Ithaca, New York
| | - Paul D. Soloway
- Field of Genetics, Genomics and Development, Cornell University, Ithaca, New York
- Field of Comparative Biomedical Sciences, Cornell University, Ithaca, New York
- Division of Nutritional Sciences, Cornell University, Ithaca, New York
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130
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Long Noncoding RNA Regulation of Pluripotency. Stem Cells Int 2015; 2016:1797692. [PMID: 26697072 PMCID: PMC4677244 DOI: 10.1155/2016/1797692] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 07/07/2015] [Indexed: 02/05/2023] Open
Abstract
Pluripotent stem cells (PSCs) represent a unique kind of stem cell, as they are able to indefinitely self-renew and hold the potential to differentiate into any derivative of the three germ layers. As such, human Embryonic Stem Cells (hESCs) and human induced Pluripotent Stem Cells (hiPSCs) provide a unique opportunity for studying the earliest steps of human embryogenesis and, at the same time, are of great therapeutic interest. The molecular mechanisms underlying pluripotency represent a major field of research. Recent evidence suggests that a complex network of transcription factors, chromatin regulators, and noncoding RNAs exist in pluripotent cells to regulate the balance between self-renewal and multilineage differentiation. Regulatory noncoding RNAs come in two flavors: short and long. The first class includes microRNAs (miRNAs), which are involved in the posttranscriptional regulation of cell cycle and differentiation in PSCs. Instead, long noncoding RNAs (lncRNAs) represent a heterogeneous group of long transcripts that regulate gene expression at transcriptional and posttranscriptional levels. In this review, we focus on the role played by lncRNAs in the maintenance of pluripotency, emphasizing the interplay between lncRNAs and other pivotal regulators in PSCs.
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131
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Affiliation(s)
- Victoria H. Meller
- Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202; , ,
| | - Sonal S. Joshi
- Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202; , ,
| | - Nikita Deshpande
- Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202; , ,
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132
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Pervasive lncRNA binding by epigenetic modifying complexes--The challenges ahead. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:93-101. [PMID: 26463275 DOI: 10.1016/j.bbagrm.2015.10.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 10/01/2015] [Accepted: 10/08/2015] [Indexed: 02/08/2023]
Abstract
Epigenetic modifying factors are fundamental regulators of chromatin structure and gene expression during development and differentiation through the induction of chemical modifications on histones, DNA or via remodeling of the chromatin structure. Protein complexes involved in these three processes contain non-canonical RNA-binding components that interact with long non-coding RNAs, in many cases in the absence of any sequence or structural signatures. However, there is growing evidence of the role of such protein-lncRNA interactions in the regulation of the epigenetic landscape in vivo. This review summarizes the growing number of epigenetic modifying factors described to interact with lncRNAs in mouse and human, and then discusses the challenges that lay ahead in understanding lncRNAs as part of the intricate networks of epigenetic regulation. A combination of protein and RNA-centric approaches is required for this purpose. This article is part of a Special Issue entitled: Clues to long noncoding RNA taxonomy, edited by Dr. Tetsuro Hirose and Dr. Shinichi Nakagawa.
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133
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Sahu A, Singhal U, Chinnaiyan AM. Long noncoding RNAs in cancer: from function to translation. Trends Cancer 2015; 1:93-109. [PMID: 26693181 DOI: 10.1016/j.trecan.2015.08.010] [Citation(s) in RCA: 199] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
While our understanding of the molecular mechanisms underlying cancer has significantly improved, most of our knowledge focuses on protein-coding genes that make up a fraction of the genome. Recent studies have uncovered thousands of long noncoding RNAs (lncRNAs) that populate the cancer genome. A subset of these molecules shows striking cancer- and lineage-specific expression patterns, suggesting they may be potential drivers of cancer biology and have utility as clinical biomarkers. Here, we discuss emerging modalities of lncRNA biology and their interplay with cancer-associated concepts, including epigenetic regulation, DNA damage and cell cycle control, microRNA silencing, signal transduction pathways, and hormone-driven disease. Additionally, we highlight the translational impact of lncRNAs, tools for their mechanistic investigation, and directions for future lncRNA research.
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Affiliation(s)
- Anirban Sahu
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan USA. ; Department of Pathology, University of Michigan, Ann Arbor, Michigan USA
| | - Udit Singhal
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan USA. ; Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan USA
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan USA. ; Department of Pathology, University of Michigan, Ann Arbor, Michigan USA. ; Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan USA. ; Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan USA. ; Department of Urology, University of Michigan, Ann Arbor, Michigan USA
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134
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Thomas LR, Foshage AM, Weissmiller AM, Tansey WP. The MYC-WDR5 Nexus and Cancer. Cancer Res 2015; 75:4012-5. [PMID: 26383167 DOI: 10.1158/0008-5472.can-15-1216] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 06/10/2015] [Indexed: 02/05/2023]
Abstract
The MYC oncogenes encode a family of transcription factors that feature prominently in cancer. MYC proteins are overexpressed or deregulated in a majority of malignancies and drive tumorigenesis by inducing widespread transcriptional reprogramming that promotes cell proliferation, metabolism, and genomic instability. The ability of MYC to regulate transcription depends on its dimerization with MAX, which creates a DNA-binding domain that recognizes specific sequences in the regulatory elements of MYC target genes. Recently, we discovered that recognition of target genes by MYC also depends on its interaction with WDR5, a WD40-repeat protein that exists as part of several chromatin-regulatory complexes. Here, we discuss how interaction of MYC with WDR5 could create an avidity-based chromatin recognition mechanism that allows MYC to select its target genes in response to both genetic and epigenetic determinants. We rationalize how the MYC-WDR5 interaction provides plasticity in target gene selection by MYC and speculate on the biochemical and genomic contexts in which this interaction occurs. Finally, we discuss how properties of the MYC-WDR5 interface make it an attractive point for discovery of small-molecule inhibitors of MYC function in cancer cells.
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Affiliation(s)
- Lance R Thomas
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Audra M Foshage
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - April M Weissmiller
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - William P Tansey
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee.
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135
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Vallianatos CN, Iwase S. Disrupted intricacy of histone H3K4 methylation in neurodevelopmental disorders. Epigenomics 2015; 7:503-19. [PMID: 26077434 DOI: 10.2217/epi.15.1] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Methylation of histone H3 lysine 4 (H3K4me) is an intricately regulated posttranslational modification, which is broadly associated with enhancers and promoters of actively transcribed genomic loci. Recent advances in next-generation sequencing have identified a number of H3K4me regulators mutated in neurodevelopmental disorders including intellectual disabilities, autism spectrum disorders, and schizophrenia. Here, we aim to summarize the molecular function of H3K4me-regulating enzymes in brain development and function. We describe four H3K4me methyltransferases (KMT2A, KMT2C, KMT2D, KMT2F), four demethylases (KDM1A, KDM5A, KDM5B, KDM5C), and two reader proteins (PHF21A, PHF8) mutated in neurodevelopmental disorders. Understanding the role of these chromatin regulators in the development and maintenance of neural connections will advance therapeutic opportunities for prevention and treatment of these lifelong neurodevelopmental disorders.
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Affiliation(s)
- Christina N Vallianatos
- Department of Human Genetics, University of Michigan, 5815 Medical Science II, Ann Arbor, MI 48109, USA.,Predoctoral Training Program in Genetics, University of Michigan, 5815 Medical Science II, Ann Arbor, MI 48109, USA
| | - Shigeki Iwase
- Department of Human Genetics, University of Michigan, 5815 Medical Science II, Ann Arbor, MI 48109, USA
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136
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MINCR is a MYC-induced lncRNA able to modulate MYC's transcriptional network in Burkitt lymphoma cells. Proc Natl Acad Sci U S A 2015; 112:E5261-70. [PMID: 26351698 DOI: 10.1073/pnas.1505753112] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Despite the established role of the transcription factor MYC in cancer, little is known about the impact of a new class of transcriptional regulators, the long noncoding RNAs (lncRNAs), on MYC ability to influence the cellular transcriptome. Here, we have intersected RNA-sequencing data from two MYC-inducible cell lines and a cohort of 91 B-cell lymphomas with or without genetic variants resulting in MYC overexpression. We identified 13 lncRNAs differentially expressed in IG-MYC-positive Burkitt lymphoma and regulated in the same direction by MYC in the model cell lines. Among them, we focused on a lncRNA that we named MYC-induced long noncoding RNA (MINCR), showing a strong correlation with MYC expression in MYC-positive lymphomas. To understand its cellular role, we performed RNAi and found that MINCR knockdown is associated with an impairment in cell cycle progression. Differential gene expression analysis after RNAi showed a significant enrichment of cell cycle genes among the genes down-regulated after MINCR knockdown. Interestingly, these genes are enriched in MYC binding sites in their promoters, suggesting that MINCR acts as a modulator of the MYC transcriptional program. Accordingly, MINCR knockdown was associated with a reduction in MYC binding to the promoters of selected cell cycle genes. Finally, we show that down-regulation of Aurora kinases A and B and chromatin licensing and DNA replication factor 1 may explain the reduction in cellular proliferation observed on MINCR knockdown. We, therefore, suggest that MINCR is a newly identified player in the MYC transcriptional network able to control the expression of cell cycle genes.
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137
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Geisler SJ, Paro R. Trithorax and Polycomb group-dependent regulation: a tale of opposing activities. Development 2015; 142:2876-2887. [DOI: 10.1242/dev.120030] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
Abstract
Intricate layers of regulation determine the unique gene expression profiles of a given cell and, therefore, underlie the immense phenotypic diversity observed among cell types. Understanding the mechanisms that govern which genes are expressed and which genes are silenced is a fundamental focus in biology. The Polycomb and Trithorax group chromatin proteins play important roles promoting the stable and heritable repression and activation of gene expression, respectively. These proteins, which are conserved across metazoans, modulate post-translational modifications on histone tails and regulate nucleosomal structures. Here, we review recent advances that have shed light on the mechanisms by which these two classes of proteins act to maintain epigenetic memory and allow dynamic switches in gene expression during development.
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Affiliation(s)
- Sarah J. Geisler
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel 4058, Switzerland
| | - Renato Paro
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel 4058, Switzerland
- Faculty of Science, University of Basel, Klingelbergstrasse 50, Basel 4056, Switzerland
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138
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Shinsky SA, Cosgrove MS. Unique Role of the WD-40 Repeat Protein 5 (WDR5) Subunit within the Mixed Lineage Leukemia 3 (MLL3) Histone Methyltransferase Complex. J Biol Chem 2015; 290:25819-33. [PMID: 26324722 PMCID: PMC4646236 DOI: 10.1074/jbc.m115.684142] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Indexed: 12/29/2022] Open
Abstract
The MLL3 (mixed lineage leukemia 3) protein is a member of the human SET1 family of histone H3 lysine 4 methyltransferases and contains the conserved WDR5 interaction (Win) motif and the catalytic suppressor of variegation, enhancer of zeste, trithorax (SET) domain. The human SET1 family includes MLL1-4 and SETd1A/B, which all interact with a conserved subcomplex containing WDR5, RbBP5, Ash2L, and DPY-30 (WRAD) to form the minimal core complex required for full methyltransferase activity. However, recent evidence suggests that the WDR5 subunit may not be utilized in an identical manner within all SET1 family core complexes. Although the roles of WDR5 within the MLL1 core complex have been extensively studied, not much is known about the roles of WDR5 in other SET1 family core complexes. In this investigation, we set out to characterize the roles of the WDR5 subunit in the MLL3 core complex. We found that unlike MLL1, the MLL3 SET domain assembles with the RbBP5/Ash2L heterodimer independently of the Win motif-WDR5 interaction. Furthermore, we observed that WDR5 inhibits the monomethylation activity of the MLL3 core complex, which is dependent on the Win motif. We also found evidence suggesting that the WRAD subcomplex catalyzes weak H3K4 monomethylation within the context of the MLL3 core complex. Furthermore, solution structures of the MLL3 core complex assembled with and without WDR5 by small angle x-ray scattering show similar overall topologies. Together, this work demonstrates a unique role for WDR5 in modulating the enzymatic activity of the MLL3 core complex.
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Affiliation(s)
- Stephen A Shinsky
- From the Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, New York 13210
| | - Michael S Cosgrove
- From the Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, New York 13210
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139
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Qiu M, Xu Y, Wang J, Zhang E, Sun M, Zheng Y, Li M, Xia W, Feng D, Yin R, Xu L. A novel lncRNA, LUADT1, promotes lung adenocarcinoma proliferation via the epigenetic suppression of p27. Cell Death Dis 2015; 6:e1858. [PMID: 26291312 PMCID: PMC4558496 DOI: 10.1038/cddis.2015.203] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 06/17/2015] [Accepted: 06/24/2015] [Indexed: 12/15/2022]
Abstract
Long noncoding RNAs (lncRNAs) are known to regulate the development and progression of various cancers. However, few lncRNAs have been well characterized in lung adenocarcinoma (LUAD). Here, we identified the expression profile of lncRNAs and protein-coding genes via microarrays analysis of paired LUAD tissues and adjacent non-tumor tissues from five female non-smokes with LUAD. A total of 498 lncRNAs and 1691 protein-coding genes were differentially expressed between LUAD tissues and paired adjacent normal tissues. A novel lncRNA, LUAD transcript 1 (LUADT1), which is highly expressed in LUAD and correlates with T stage, was characterized. Both in vitro and in vivo data showed that LUADT1 knockdown significantly inhibited proliferation of LUAD cells and induced cell cycle arrest at the G0–G1 phase. Further analysis indicated that LUADT1 may regulate cell cycle progression by epigenetically inhibiting the expression of p27. RNA immunoprecipitation and chromatin immunoprecipitation assays confirmed that LUADT1 binds to SUZ12, a core component of polycomb repressive complex 2, and mediates the trimethylation of H3K27 at the promoter region of p27. The negative correlation between LUADT1 and p27 expression was confirmed in LUAD tissue samples. These data suggested that a set of lncRNAs and protein-coding genes were differentially expressed in LUAD. LUADT1 is an oncogenic lncRNA that regulates LUAD progression, suggesting that dysregulated lncRNAs may serve as key regulatory factors in LUAD progression.
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Affiliation(s)
- M Qiu
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Baiziting 42, Nanjing 210009, China.,The Fourth Clinical College of Nanjing Medical University, Nanjing, 210000, China
| | - Y Xu
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Baiziting 42, Nanjing 210009, China.,The First Clinical College of Nanjing Medical University, Nanjing 210000, China
| | - J Wang
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Baiziting 42, Nanjing 210009, China.,Department of Scientific Research, Nanjing Medical University Affiliated Cancer Hospital, Cancer Institute of Jiangsu Province, Nanjing 210009, China
| | - E Zhang
- Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing 210000, China
| | - M Sun
- Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing 210000, China
| | - Y Zheng
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Baiziting 42, Nanjing 210009, China.,Department of Nursing, Nanjing Medical University Affiliated Cancer Hospital, Cancer Institute of Jiangsu Province, Nanjing 210009, China
| | - M Li
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Baiziting 42, Nanjing 210009, China
| | - W Xia
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Baiziting 42, Nanjing 210009, China.,The Fourth Clinical College of Nanjing Medical University, Nanjing, 210000, China
| | - D Feng
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Baiziting 42, Nanjing 210009, China.,The Fourth Clinical College of Nanjing Medical University, Nanjing, 210000, China
| | - R Yin
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Baiziting 42, Nanjing 210009, China
| | - L Xu
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Baiziting 42, Nanjing 210009, China
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140
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Abstract
Histone-lysine N-methyltransferase 2 (KMT2) family proteins methylate lysine 4 on the histone H3 tail at important regulatory regions in the genome and thereby impart crucial functions through modulating chromatin structures and DNA accessibility. Although the human KMT2 family was initially named the mixed-lineage leukaemia (MLL) family, owing to the role of the first-found member KMT2A in this disease, recent exome-sequencing studies revealed KMT2 genes to be among the most frequently mutated genes in many types of human cancers. Efforts to integrate the molecular mechanisms of KMT2 with its roles in tumorigenesis have led to the development of first-generation inhibitors of KMT2 function, which could become novel cancer therapies.
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Affiliation(s)
- Rajesh C. Rao
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109
- Department of Ophthalmology & Visual Sciences, University of Michigan, Ann Arbor, MI 48109
| | - Yali Dou
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109
- Correspondence: , Tel: (734) 6151315, Fax: (734) 7636476
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141
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Grote P, Herrmann BG. Long noncoding RNAs in organogenesis: making the difference. Trends Genet 2015; 31:329-35. [DOI: 10.1016/j.tig.2015.02.002] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 02/03/2015] [Accepted: 02/03/2015] [Indexed: 01/06/2023]
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142
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Abstract
In recent years, long noncoding RNAs (lncRNAs) have emerged as an important class of regulators of gene expression. lncRNAs exhibit several distinctive features that confer unique regulatory functions, including exquisite cell- and tissue-specific expression and the capacity to transduce higher-order spatial information. Here we review evidence showing that lncRNAs exert critical functions in adult tissue stem cells, including skin, brain, and muscle, as well as in developmental patterning and pluripotency. We highlight new approaches for ascribing lncRNA functions and discuss mammalian dosage compensation as a classic example of an lncRNA network coupled to stem cell differentiation.
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Affiliation(s)
- Ryan A Flynn
- Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Howard Y Chang
- Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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143
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Paranjpe SS, Veenstra GJC. Establishing pluripotency in early development. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:626-36. [PMID: 25857441 DOI: 10.1016/j.bbagrm.2015.03.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 03/26/2015] [Accepted: 03/30/2015] [Indexed: 01/23/2023]
Abstract
The earliest steps of embryonic development involve important changes in chromatin and transcription factor networks, which are orchestrated to establish pluripotent cells that will form the embryo. DNA methylation, histone modifications, the pluripotency regulatory network of transcription factors, maternal factors and newly translated proteins all contribute to these transitions in dynamic ways. Moreover, these dynamics are linked to the onset of zygotic transcription. We will review recent progress in our understanding of chromatin state and regulation of gene expression in the context of embryonic development in vertebrates, in particular mouse, Xenopus and zebrafish. We include work on mouse embryonic stem cells and highlight work that illustrates how early embryonic dynamics establish gene regulatory networks and the state of pluripotency.
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Affiliation(s)
- Sarita S Paranjpe
- Radboud University, Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Gert Jan C Veenstra
- Radboud University, Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands.
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144
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Ucar D, Bayarsaihan D. Cell-specific gene promoters are marked by broader spans of H3K4me3 and are associated with robust gene expression patterns. Epigenomics 2015; 7:129-31. [DOI: 10.2217/epi.14.87] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Duygu Ucar
- Department of Bioinformatics & Computational Biology, The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032, USA
| | - Dashzeveg Bayarsaihan
- Department of Reconstructive Sciences, Institute for Systems Genomics & Center for Regenerative Medicine & Skeletal Development, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT 06030, USA
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145
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Trimarchi T, Bilal E, Ntziachristos P, Fabbri G, Dalla-Favera R, Tsirigos A, Aifantis I. Genome-wide mapping and characterization of Notch-regulated long noncoding RNAs in acute leukemia. Cell 2015; 158:593-606. [PMID: 25083870 DOI: 10.1016/j.cell.2014.05.049] [Citation(s) in RCA: 349] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Revised: 03/23/2014] [Accepted: 05/16/2014] [Indexed: 12/24/2022]
Abstract
Notch signaling is a key developmental pathway that is subject to frequent genetic and epigenetic perturbations in many different human tumors. Here we investigate whether long noncoding RNA (lncRNA) genes, in addition to mRNAs, are key downstream targets of oncogenic Notch1 in human T cell acute lymphoblastic leukemia (T-ALL). By integrating transcriptome profiles with chromatin state maps, we have uncovered many previously unreported T-ALL-specific lncRNA genes, a fraction of which are directly controlled by the Notch1/Rpbjκ activator complex. Finally we have shown that one specific Notch-regulated lncRNA, LUNAR1, is required for efficient T-ALL growth in vitro and in vivo due to its ability to enhance IGF1R mRNA expression and sustain IGF1 signaling. These results confirm that lncRNAs are important downstream targets of the Notch signaling pathway, and additionally they are key regulators of the oncogenic state in T-ALL.
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Affiliation(s)
- Thomas Trimarchi
- Howard Hughes Medical Institute, Laura and Isaac Perlmutter Cancer Center, and Helen L. and Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, 550 First Avenue, New York, NY 10016, USA; Department of Pathology, NYU School of Medicine, 550 First Avenue, New York, NY 10016, USA
| | - Erhan Bilal
- Computational Biology Center, IBM Thomas J. Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, NY 10598, USA
| | - Panagiotis Ntziachristos
- Howard Hughes Medical Institute, Laura and Isaac Perlmutter Cancer Center, and Helen L. and Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, 550 First Avenue, New York, NY 10016, USA; Department of Pathology, NYU School of Medicine, 550 First Avenue, New York, NY 10016, USA
| | - Giulia Fabbri
- Institute for Cancer Genetics and the Herbert Irving Comprehensive Cancer Center, Columbia University, 1130 St. Nicholas Avenue, New York, NY 10032, USA
| | - Riccardo Dalla-Favera
- Institute for Cancer Genetics and the Herbert Irving Comprehensive Cancer Center, Columbia University, 1130 St. Nicholas Avenue, New York, NY 10032, USA
| | - Aristotelis Tsirigos
- Department of Pathology, NYU School of Medicine, 550 First Avenue, New York, NY 10016, USA; Center for Health Informatics and Bioinformatics, NYU School of Medicine, 227 East 30(th) Street, New York, NY 10016, USA.
| | - Iannis Aifantis
- Howard Hughes Medical Institute, Laura and Isaac Perlmutter Cancer Center, and Helen L. and Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, 550 First Avenue, New York, NY 10016, USA; Department of Pathology, NYU School of Medicine, 550 First Avenue, New York, NY 10016, USA.
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146
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Sun M, Kraus WL. From discovery to function: the expanding roles of long noncoding RNAs in physiology and disease. Endocr Rev 2015; 36:25-64. [PMID: 25426780 PMCID: PMC4309736 DOI: 10.1210/er.2014-1034] [Citation(s) in RCA: 314] [Impact Index Per Article: 34.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Long noncoding RNAs (lncRNAs) are a relatively poorly understood class of RNAs with little or no coding capacity transcribed from a set of incompletely annotated genes. They have received considerable attention in the past few years and are emerging as potentially important players in biological regulation. Here we discuss the evolving understanding of this new class of molecular regulators that has emerged from ongoing research, which continues to expand our databases of annotated lncRNAs and provide new insights into their physical properties, molecular mechanisms of action, and biological functions. We outline the current strategies and approaches that have been employed to identify and characterize lncRNAs, which have been instrumental in revealing their multifaceted roles ranging from cis- to trans-regulation of gene expression and from epigenetic modulation in the nucleus to posttranscriptional control in the cytoplasm. In addition, we highlight the molecular and biological functions of some of the best characterized lncRNAs in physiology and disease, especially those relevant to endocrinology, reproduction, metabolism, immunology, neurobiology, muscle biology, and cancer. Finally, we discuss the tremendous diagnostic and therapeutic potential of lncRNAs in cancer and other diseases.
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Affiliation(s)
- Miao Sun
- 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, Texas 75390
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147
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Shinsky SA, Monteith KE, Viggiano S, Cosgrove MS. Biochemical reconstitution and phylogenetic comparison of human SET1 family core complexes involved in histone methylation. J Biol Chem 2015; 290:6361-75. [PMID: 25561738 DOI: 10.1074/jbc.m114.627646] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Mixed lineage leukemia protein-1 (MLL1) is a member of the SET1 family of histone H3 lysine 4 (H3K4) methyltransferases that are required for metazoan development. MLL1 is the best characterized human SET1 family member, which includes MLL1-4 and SETd1A/B. MLL1 assembles with WDR5, RBBP5, ASH2L, DPY-30 (WRAD) to form the MLL1 core complex, which is required for H3K4 dimethylation and transcriptional activation. Because all SET1 family proteins interact with WRAD in vivo, it is hypothesized they are regulated by similar mechanisms. However, recent evidence suggests differences among family members that may reflect unique regulatory inputs in the cell. Missing is an understanding of the intrinsic enzymatic activities of different SET1 family complexes under standard conditions. In this investigation, we reconstituted each human SET1 family core complex and compared subunit assembly and enzymatic activities. We found that in the absence of WRAD, all but one SET domain catalyzes at least weak H3K4 monomethylation. In the presence of WRAD, all SET1 family members showed stimulated monomethyltransferase activity but differed in their di- and trimethylation activities. We found that these differences are correlated with evolutionary lineage, suggesting these enzyme complexes have evolved to accomplish unique tasks within metazoan genomes. To understand the structural basis for these differences, we employed a "phylogenetic scanning mutagenesis" assay and identified a cluster of amino acid substitutions that confer a WRAD-dependent gain-of-function dimethylation activity on complexes assembled with the MLL3 or Drosophila trithorax proteins. These results form the basis for understanding how WRAD differentially regulates SET1 family complexes in vivo.
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Affiliation(s)
- Stephen A Shinsky
- From the Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, New York 13210
| | - Kelsey E Monteith
- From the Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, New York 13210
| | - Susan Viggiano
- From the Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, New York 13210
| | - Michael S Cosgrove
- From the Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, New York 13210
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148
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Abstract
Polycomb group (PcG) proteins are conserved chromatin regulators involved in the control of key developmental programs in eukaryotes. They collectively provide the transcriptional memory unique to each cell identity by maintaining transcriptional states of developmental genes. PcG proteins form multi-protein complexes, known as Polycomb repressive complex 1 (PRC1) and Polycomb repressive complex 2 (PRC2). PRC1 and PRC2 contribute to the stable gene silencing in part through catalyzing covalent histone modifications. Components of PRC1 and PRC2 are well conserved from plants to animals. PcG-mediated gene silencing has been extensively investigated in efforts to understand molecular mechanisms underlying developmental programs in eukaryotes. Here, we describe our current knowledge on PcG-mediated gene repression which dictates developmental programs by dynamic layers of regulatory activities, with an emphasis given to the model plant Arabidopsis thaliana.
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Affiliation(s)
- Dong-Hwan Kim
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712,
USA
| | - Sibum Sung
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712,
USA
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149
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Li Z, Rana TM. Decoding the noncoding: prospective of lncRNA-mediated innate immune regulation. RNA Biol 2014; 11:979-85. [PMID: 25482890 PMCID: PMC4615744 DOI: 10.4161/rna.29937] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The innate immune system is the first line of defense against microbial pathogens, but tight regulation of gene expression is necessary to prevent the detrimental effects of unrestrained activation. Although the functions of most long noncoding RNAs (lncRNAs; >200 nucleotides) are unknown, many have been shown to regulate diverse cellular activities. Recent reports by us and others have suggested that lncRNAs may also play critical roles in transcriptional regulation of gene expression during innate immune responses. Following engagement of Toll-like receptors, lncRNAs form functional RNA–protein complexes that recruit activators or remove repressors of transcription, leading to rapid expression of inflammatory mediators. These discoveries suggest that lncRNAs may contribute to the gene regulatory networks that govern host–pathogen interactions.
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Affiliation(s)
- Zhonghan Li
- a Program for RNA Biology; Sanford-Burnham Medical Research Institute ; La Jolla , CA USA
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150
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Long noncoding RNAs: an emerging link between gene regulation and nuclear organization. Trends Cell Biol 2014; 24:651-63. [PMID: 25441720 DOI: 10.1016/j.tcb.2014.08.009] [Citation(s) in RCA: 242] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 08/18/2014] [Accepted: 08/28/2014] [Indexed: 02/07/2023]
Abstract
Mammalian genomes encode thousands of long noncoding RNAs (lncRNAs) that play important roles in diverse biological processes. As a class, lncRNAs are generally enriched in the nucleus and, specifically, within the chromatin-associated fraction. Consistent with their localization, many lncRNAs have been implicated in the regulation of gene expression and in shaping 3D nuclear organization. In this review, we discuss the evidence that many nuclear-retained lncRNAs can interact with various chromatin regulatory proteins and recruit them to specific sites on DNA to regulate gene expression. Furthermore, we discuss the role of specific lncRNAs in shaping nuclear organization and their emerging mechanisms. Based on these examples, we propose a model that explains how lncRNAs may shape aspects of nuclear organization to regulate gene expression.
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