101
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A long noncoding RNA distributed in both nucleus and cytoplasm operates in the PYCARD-regulated apoptosis by coordinating the epigenetic and translational regulation. PLoS Genet 2019; 15:e1008144. [PMID: 31086376 PMCID: PMC6534332 DOI: 10.1371/journal.pgen.1008144] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 05/24/2019] [Accepted: 04/17/2019] [Indexed: 02/05/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) participate in various biological processes such as apoptosis. The function of lncRNAs is closely correlated with their localization within the cell. While regulatory potential of many lncRNAs has been revealed at specific subcellular location, the biological significance of discrete distribution of an lncRNA in different cellular compartments remains largely unexplored. Here, we identified an lncRNA antisense to the pro-apoptotic gene PYCARD, named PYCARD-AS1, which exhibits a dual nuclear and cytoplasmic distribution and is required for the PYCARD silencing in breast cancer cells. The PYCARD-regulated apoptosis is controlled by PYCARD-AS1; moreover, PYCARD-AS1 regulates apoptosis in a PYCARD-dependent manner, indicating that PYCARD is a critical downstream target of PYCARD-AS1. Mechanistically, PYCARD-AS1 can localize to the PYCARD promoter, where it facilitates DNA methylation and H3K9me2 modification by recruiting the chromatin-suppressor proteins DNMT1 and G9a. Moreover, PYCARD-AS1 and PYCARD mRNA can interact with each other via their 5' overlapping region, leading to inhibition of ribosome assembly in the cytoplasm for PYCARD translation. This study reveals a mechanism whereby an lncRNA works at different cellular compartments to regulate the pro-apoptotic gene PYCARD at both the epigenetic and translational levels, contributing to the PYCARD-regulated apoptosis, and also sheds new light on the role of discretely distributed lncRNAs in diverse biological processes.
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102
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Caudron-Herger M, Rusin SF, Adamo ME, Seiler J, Schmid VK, Barreau E, Kettenbach AN, Diederichs S. R-DeeP: Proteome-wide and Quantitative Identification of RNA-Dependent Proteins by Density Gradient Ultracentrifugation. Mol Cell 2019; 75:184-199.e10. [PMID: 31076284 DOI: 10.1016/j.molcel.2019.04.018] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 01/07/2019] [Accepted: 04/11/2019] [Indexed: 12/16/2022]
Abstract
The comprehensive but specific identification of RNA-binding proteins as well as the discovery of RNA-associated protein functions remain major challenges in RNA biology. Here we adapt the concept of RNA dependence, defining a protein as RNA dependent when its interactome depends on RNA. We converted this concept into a proteome-wide, unbiased, and enrichment-free screen called R-DeeP (RNA-dependent proteins), based on density gradient ultracentrifugation. Quantitative mass spectrometry identified 1,784 RNA-dependent proteins, including 537 lacking known links to RNA. Exploiting the quantitative nature of R-DeeP, proteins were classified as not, partially, or completely RNA dependent. R-DeeP identified the transcription factor CTCF as completely RNA dependent, and we uncovered that RNA is required for the CTCF-chromatin association. Additionally, R-DeeP allows reconstruction of protein complexes based on co-segregation. The whole dataset is available at http://R-DeeP.dkfz.de, providing proteome-wide, specific, and quantitative identification of proteins with RNA-dependent interactions and aiming at future functional discovery of RNA-protein complexes.
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Affiliation(s)
- Maiwen Caudron-Herger
- Division of RNA Biology and Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
| | - Scott F Rusin
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Mark E Adamo
- Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Jeanette Seiler
- Division of RNA Biology and Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Vera K Schmid
- Division of RNA Biology and Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Elsa Barreau
- Division of RNA Biology and Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Arminja N Kettenbach
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA; Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Sven Diederichs
- Division of RNA Biology and Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Division of Cancer Research, Department of Thoracic Surgery, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, German Cancer Consortium (DKTK)- Partner Site Freiburg, 79106 Freiburg, Germany; National Center for Tumor Diseases (NCT), Partner Site Heidelberg, Heidelberg, Germany.
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103
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Endogenous interaction profiling identifies DDX5 as an oncogenic coactivator of transcription factor Fra-1. Oncogene 2019; 38:5725-5738. [PMID: 31015574 DOI: 10.1038/s41388-019-0824-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 03/11/2019] [Accepted: 04/02/2019] [Indexed: 01/06/2023]
Abstract
Fra-1, a member of the activator protein 1 (AP-1) family, is overexpressed in triple-negative breast cancer (TNBC) and plays crucial roles in tumor growth. Here we report the identification of 118 proteins interacting with endogenous chromatin-bound Fra-1 in TNBC cells, highlighting DDX5 as the most enriched Fra-1-interacting protein. DDX5, a previously unrecognized protein in the Fra-1 transcriptional network, shows extensive overlap with Fra-1 cistrome and transcriptome that are highly associated with the TNBC cell growth. We provide evidence that DDX5 expression enhances Fra-1 transcriptional activity and potentiates Fra-1-driven cell proliferation. Furthermore, we show that the DDX5 target gene signature predicts poor clinical outcome in breast cancer patients. DDX5 protein level was higher in triple-negative basal-like tumors than in non-basal-like tumors, including luminal A, luminal B, and HER2-enriched subtypes. Collectively, by combining proteomic and genomic approaches we reveal a role for DDX5 as a regulatory protein of Fra-1 signaling and suggest DDX5 as a potential therapeutic target for TNBC.
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104
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Tracey LJ, Brooke-Bisschop T, Jansen PWTC, Campos EI, Vermeulen M, Justice MJ. The Pluripotency Regulator PRDM14 Requires Hematopoietic Regulator CBFA2T3 to Initiate Leukemia in Mice. Mol Cancer Res 2019; 17:1468-1479. [PMID: 31015254 DOI: 10.1158/1541-7786.mcr-18-1327] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 02/07/2019] [Accepted: 04/19/2019] [Indexed: 12/20/2022]
Abstract
PR domain-containing 14 (Prdm14) is a pluripotency regulator central to embryonic stem cell identity and primordial germ cell specification. Genomic regions containing PRDM14 are often amplified leading to misexpression in human cancer. Prdm14 expression in mouse hematopoietic stem cells (HSC) leads to progenitor cell expansion prior to the development of T-cell acute lymphoblastic leukemia (T-ALL), consistent with PRDM14's role in cancer initiation. Here, we demonstrate mechanistic insight into PRDM14-driven leukemias in vivo. Mass spectrometry revealed novel PRDM14-protein interactions including histone H1, RNA-binding proteins, and the master hematopoietic regulator CBFA2T3. In mouse leukemic cells, CBFA2T3 and PRDM14 associate independently of the related ETO family member CBFA2T2, PRDM14's primary protein partner in pluripotent cells. CBFA2T3 plays crucial roles in HSC self-renewal and lineage commitment, and participates in oncogenic translocations in acute myeloid leukemia. These results suggest a model whereby PRDM14 recruits CBFA2T3 to DNA, leading to gene misregulation causing progenitor cell expansion and lineage perturbations preceding T-ALL development. Strikingly, Prdm14-induced T-ALL does not occur in mice deficient for Cbfa2t3, demonstrating that Cbfa2t3 is required for leukemogenesis. Moreover, T-ALL develops in Cbfa2t3 heterozygotes with a significantly longer latency, suggesting that PRDM14-associated T-ALL is sensitive to Cbfa2t3 levels. Our study highlights how an oncogenic protein uses a native protein in progenitor cells to initiate leukemia, providing insight into PRDM14-driven oncogenesis in other cell types. IMPLICATIONS: The pluripotency regulator PRDM14 requires the master hematopoietic regulator CBFA2T3 to initiate leukemia in progenitor cells, demonstrating an oncogenic role for CBFA2T3 and providing an avenue for targeting cancer-initiating cells.
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Affiliation(s)
- Lauren J Tracey
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Travis Brooke-Bisschop
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Pascal W T C Jansen
- Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Eric I Campos
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Michiel Vermeulen
- Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Monica J Justice
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada. .,Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
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105
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Michieletto D, Gilbert N. Role of nuclear RNA in regulating chromatin structure and transcription. Curr Opin Cell Biol 2019; 58:120-125. [PMID: 31009871 PMCID: PMC6694202 DOI: 10.1016/j.ceb.2019.03.007] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 03/10/2019] [Accepted: 03/13/2019] [Indexed: 12/31/2022]
Abstract
The importance of three-dimensional chromatin organisation in genome regulation has never been clearer. But in spite of the enormous technological advances to probe chromatin organisation in vivo, there is still a lack of mechanistic understanding of how such an arrangement is achieved. Here we review emerging evidence pointing to an intriguing role of nuclear RNA in shaping large-scale chromatin structure and regulating genome function. We suggest this role may be achieved through the formation of a dynamic nuclear mesh that can exploit ATP-driven processes and phase separation of RNA-binding proteins to tune its assembly and material properties.
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Affiliation(s)
- Davide Michieletto
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK; School of Physics and Astronomy, University of Edinburgh, EH9 3FD, UK
| | - Nick Gilbert
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK.
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106
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Han Y, Branon TC, Martell JD, Boassa D, Shechner D, Ellisman MH, Ting A. Directed Evolution of Split APEX2 Peroxidase. ACS Chem Biol 2019; 14:619-635. [PMID: 30848125 PMCID: PMC6548188 DOI: 10.1021/acschembio.8b00919] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
APEX is an engineered peroxidase that catalyzes the oxidation of a wide range of substrates, facilitating its use in a variety of applications from subcellular staining for electron microscopy to proximity biotinylation for spatial proteomics and transcriptomics. To further advance the capabilities of APEX, we used directed evolution to engineer a split APEX tool (sAPEX). A total of 20 rounds of fluorescence activated cell sorting (FACS)-based selections from yeast-displayed fragment libraries, using 3 different surface display configurations, produced a 200-amino-acid N-terminal fragment (with 9 mutations relative to APEX2) called "AP" and a 50-amino-acid C-terminal fragment called "EX". AP and EX fragments were each inactive on their own but were reconstituted to give peroxidase activity when driven together by a molecular interaction. We demonstrate sAPEX reconstitution in the mammalian cytosol, on engineered RNA motifs within a non-coding RNA scaffold, and at mitochondria-endoplasmic reticulum contact sites.
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Affiliation(s)
- Yisu Han
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Genetics, Stanford University, Stanford, California, USA
- Department of Biology, Stanford University, Stanford, California, USA
- Department of Chemistry, Stanford University, Stanford, California, USA
| | - Tess Caroline Branon
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Genetics, Stanford University, Stanford, California, USA
- Department of Biology, Stanford University, Stanford, California, USA
- Department of Chemistry, Stanford University, Stanford, California, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA
| | - Jeffrey D. Martell
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Chemistry, University of California, Berkeley, Berkeley, California, USA
| | - Daniela Boassa
- Department of Neuroscience, University of California San Diego, La Jolla, California, USA
| | - David Shechner
- Department of Pharmacology, University of Washington, Seattle, Washington, USA
| | - Mark H. Ellisman
- Department of Neuroscience, University of California San Diego, La Jolla, California, USA
| | - Alice Ting
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Genetics, Stanford University, Stanford, California, USA
- Department of Biology, Stanford University, Stanford, California, USA
- Department of Chemistry, Stanford University, Stanford, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
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107
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Shields EJ, Petracovici AF, Bonasio R. lncRedibly versatile: biochemical and biological functions of long noncoding RNAs. Biochem J 2019; 476:1083-1104. [PMID: 30971458 PMCID: PMC6745715 DOI: 10.1042/bcj20180440] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 02/28/2019] [Accepted: 03/19/2019] [Indexed: 02/07/2023]
Abstract
Long noncoding RNAs (lncRNAs) are transcripts that do not code for proteins, but nevertheless exert regulatory effects on various biochemical pathways, in part via interactions with proteins, DNA, and other RNAs. LncRNAs are thought to regulate transcription and other biological processes by acting, for example, as guides that target proteins to chromatin, scaffolds that facilitate protein-protein interactions and complex formation, and orchestrators of phase-separated compartments. The study of lncRNAs has reached an exciting time, as recent advances in experimental and computational methods allow for genome-wide interrogation of biochemical and biological mechanisms of these enigmatic transcripts. A better appreciation for the biochemical versatility of lncRNAs has allowed us to begin closing gaps in our knowledge of how they act in diverse cellular and organismal contexts, including development and disease.
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Affiliation(s)
- Emily J Shields
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, U.S.A
- Graduate Group in Genomics and Computational Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, U.S.A
| | - Ana F Petracovici
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, U.S.A
- Graduate Group in Genetics and Epigenetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, U.S.A
| | - Roberto Bonasio
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, U.S.A.
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, U.S.A
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108
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Post-transcriptional regulatory patterns revealed by protein-RNA interactions. Sci Rep 2019; 9:4302. [PMID: 30867517 PMCID: PMC6416249 DOI: 10.1038/s41598-019-40939-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 02/26/2019] [Indexed: 02/07/2023] Open
Abstract
The coordination of the synthesis of functionally-related proteins can be achieved at the post-transcriptional level by the action of common regulatory molecules, such as RNA–binding proteins (RBPs). Despite advances in the genome-wide identification of RBPs and their binding transcripts, the protein–RNA interaction space is still largely unexplored, thus hindering a broader understanding of the extent of the post-transcriptional regulation of related coding RNAs. Here, we propose a computational approach that combines protein–mRNA interaction networks and statistical analyses to provide an inferred regulatory landscape for more than 800 human RBPs and identify the cellular processes that can be regulated at the post-transcriptional level. We show that 10% of the tested sets of functionally-related mRNAs can be post-transcriptionally regulated. Moreover, we propose a classification of (i) the RBPs and (ii) the functionally-related mRNAs, based on their distinct behaviors in the functional landscape, hinting towards mechanistic regulatory hypotheses. In addition, we demonstrate the usefulness of the inferred functional landscape to investigate the cellular role of both well-characterized and novel RBPs in the context of human diseases.
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109
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Matveeva EA, Mathbout LF, Fondufe-Mittendorf YN. PARP1 is a versatile factor in the regulation of mRNA stability and decay. Sci Rep 2019; 9:3722. [PMID: 30842529 PMCID: PMC6403249 DOI: 10.1038/s41598-019-39969-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 02/01/2019] [Indexed: 12/30/2022] Open
Abstract
PARP1 is an abundant nuclear protein with many pleiotropic functions involved in epigenetic and transcriptional controls. Abundance of mRNA depends on the balance between synthesis and decay of a particular transcript. PARP1 binds RNA and its depletion results in increased expression of genes involved in nonsense-mediated decay, suggesting that PARP1 might be involved in mRNA stability. This is of interest considering RNA binding proteins play key roles in post-transcriptional processes in all eukaryotes. We tested the direct impact of PARP1 and PARylation on mRNA stability and decay. By measuring the half-lives of two PARP1-mRNA targets we found that the half-lives were significantly decreased in PARP1-depleted cells. PARP1 depletion impacted both the synthesis of nascent mRNA and the stability of mature mRNAs. PARylation impacted the production of nascent mRNA and the stability of mature mRNA, albeit to a lesser extent than PARP1 KD. PARylation enhanced the impact of PARP1 depletion. These studies provide the first direct comparative role of PARP1 and PARylation in RNA stability and decay, adding a new dimension as to how PARP1 regulates gene expression. These studies present a platform to begin to tease out the influence of PARP1 at each step of RNA biogenesis and decay to fine-tune gene expression.
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Affiliation(s)
- Elena A Matveeva
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
| | - Lein F Mathbout
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
- College of Medicine, Alfaisal University, Al Maather', Riyadh, Saudi Arabia
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110
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Nozawa RS, Gilbert N. RNA: Nuclear Glue for Folding the Genome. Trends Cell Biol 2019; 29:201-211. [DOI: 10.1016/j.tcb.2018.12.003] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 12/10/2018] [Accepted: 12/14/2018] [Indexed: 12/20/2022]
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111
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Jégu T, Blum R, Cochrane JC, Yang L, Wang CY, Gilles ME, Colognori D, Szanto A, Marr SK, Kingston RE, Lee JT. Xist RNA antagonizes the SWI/SNF chromatin remodeler BRG1 on the inactive X chromosome. Nat Struct Mol Biol 2019; 26:96-109. [PMID: 30664740 PMCID: PMC6421574 DOI: 10.1038/s41594-018-0176-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 12/03/2018] [Indexed: 02/08/2023]
Abstract
The noncoding RNA Xist recruits silencing factors to the inactive X chromosome (Xi) and facilitates re-organization of Xi structure. Here, we examine the mouse epigenomic landscape of Xi and assess how Xist alters chromatin accessibility. Interestingly, Xist deletion triggers a gain of accessibility of selective chromatin regions that is regulated by BRG1, an ATPase subunit of the SWI/SNF chromatin remodeling complex. In vitro, RNA binding inhibits nucleosome remodeling and ATPase activities of BRG1, while in cell culture Xist directly interacts with BRG1 and expels BRG1 from the Xi. Xist ablation leads to a selective return of BRG1 in cis, starting from pre-existing BRG1 sites that are free of Xist. BRG1 re-association correlates with cohesin binding and restoration of topologically associated domains (TADs), and results in formation of de novo Xi “superloops.” Thus, Xist binding inhibits BRG1’s nucleosome remodeling activity and results in expulsion of the SWI/SNF complex from the Xi.
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Affiliation(s)
- Teddy Jégu
- Howard Hughes Medical Institute, Boston, MA, USA.,Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Roy Blum
- Howard Hughes Medical Institute, Boston, MA, USA.,Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Jesse C Cochrane
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Lin Yang
- Howard Hughes Medical Institute, Boston, MA, USA.,Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Chen-Yu Wang
- Howard Hughes Medical Institute, Boston, MA, USA.,Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Maud-Emmanuelle Gilles
- Institute for RNA Medicine, Department of Pathology, Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - David Colognori
- Howard Hughes Medical Institute, Boston, MA, USA.,Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Attila Szanto
- Howard Hughes Medical Institute, Boston, MA, USA.,Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Sharon K Marr
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Robert E Kingston
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Jeannie T Lee
- Howard Hughes Medical Institute, Boston, MA, USA. .,Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA. .,Department of Genetics, Harvard Medical School, Boston, MA, USA.
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112
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Sauvageau M. Diverging RNPs: Toward Understanding lncRNA-Protein Interactions and Functions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1203:285-312. [PMID: 31811638 DOI: 10.1007/978-3-030-31434-7_10] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
RNA-protein interactions are essential to a variety of biological processes. The realization that mammalian genomes are pervasively transcribed brought a tidal wave of tens of thousands of newly identified long noncoding RNAs (lncRNAs) and raised questions about their purpose in cells. The vast majority of lncRNAs have yet to be studied, and it remains to be determined to how many of these transcripts a function can be ascribed. However, results gleaned from studying a handful of these macromolecules have started to reveal common themes of biological function and mechanism of action involving intricate RNA-protein interactions. Some lncRNAs were shown to regulate the chromatin and transcription of distant and neighboring genes in the nucleus, while others regulate the translation or localization of proteins in the cytoplasm. Some lncRNAs were found to be crucial during development, while mutations and aberrant expression of others have been associated with several types of cancer and a plethora of diseases. Over the last few years, the establishment of new technologies has been key in providing the tools to decode the rules governing lncRNA-protein interactions and functions. This chapter will highlight the general characteristics of lncRNAs, their function, and their mode of action, with a special focus on protein interactions. It will also describe the methods at the disposition of scientists to help them cross this next frontier in our understanding of lncRNA biology.
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Affiliation(s)
- Martin Sauvageau
- Montreal Clinical Research Institute (IRCM), Montréal, QC, Canada. .,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC, Canada.
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113
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Li L, Liang J, Luo H, Tam KM, Tse ECM, Li Y. A new chemical approach for proximity labelling of chromatin-associated RNAs and proteins with visible light irradiation. Chem Commun (Camb) 2019; 55:12340-12343. [DOI: 10.1039/c9cc06251c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new nucleus-localized singlet oxygen generator was designed and synthesized.
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Affiliation(s)
- Lan Li
- Department of Chemistry
- The University of Hong Kong
- Hong Kong, SAR
- Hong Kong
| | - Jiying Liang
- Department of Chemistry
- The University of Hong Kong
- Hong Kong, SAR
- Hong Kong
| | - Hao Luo
- Department of Chemistry
- The University of Hong Kong
- Hong Kong, SAR
- Hong Kong
| | - K. Ming Tam
- Department of Chemistry
- The University of Hong Kong
- Hong Kong, SAR
- Hong Kong
| | - Edmund C. M. Tse
- Department of Chemistry
- The University of Hong Kong
- Hong Kong, SAR
- Hong Kong
| | - Ying Li
- Department of Chemistry
- The University of Hong Kong
- Hong Kong, SAR
- Hong Kong
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114
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Smith KN, Starmer J, Magnuson T. Interactome determination of a Long Noncoding RNA implicated in Embryonic Stem Cell Self-Renewal. Sci Rep 2018; 8:17568. [PMID: 30514857 PMCID: PMC6279841 DOI: 10.1038/s41598-018-34864-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 10/25/2018] [Indexed: 12/18/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) constitute a significant fraction of mammalian transcriptomes and they have emerged as intricate regulators of many biological processes. Their broad capacity to adopt diverse structures facilitates their involvement in the transcriptional, translational and signaling processes that are central to embryonic stem (ES) cell self-renewal and pluripotency. While lncRNAs have been implicated in ES cell maintenance, detailed analyses of those that show significant expression in ES cells is largely absent. Moreover, cooperative molecular relationships that facilitate lncRNA action are poorly understood. Cyrano is a developmentally important lncRNA, and in ES cells, it supports gene expression network maintenance, cell adhesion and cell survival. We have interrogated the interactome of Cyrano to identify protein partners and find that Cyrano is involved in multiple protein networks. We identify a developmentally important cell-signaling hub and find STAT3 as a candidate through which Cyrano can function to reinforce self-renewal of ES cells. Based on commonalities between ES cells and cancer cells, we postulate such functional interactions may support cell proliferation, cell identity and adhesion characteristics in rapidly proliferating cell types. The interactome data will therefore provide a resource for further investigations into interactions that regulate Cyrano or mediate its function.
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Affiliation(s)
- Keriayn N Smith
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Joshua Starmer
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Terry Magnuson
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA.
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115
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SWI/SNF remains localized to chromatin in the presence of SCHLAP1. Nat Genet 2018; 51:26-29. [PMID: 30510238 PMCID: PMC6339527 DOI: 10.1038/s41588-018-0272-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 10/05/2018] [Indexed: 12/22/2022]
Abstract
SCHLAP1 is a long-noncoding RNA that is reported to function by depleting the SWI/SNF complex from the genome. We investigated the hypothesis that SCHLAP1 affects only specific compositions of SWI/SNF. Using several assays we found that SWI/SNF is not depleted from the genome by SCHLAP1, and that SWI/SNF is associated with many coding and non-coding RNAs, suggesting SCHLAP1 may function in a SWI/SNF independent manner.
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116
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Lesbirel S, Viphakone N, Parker M, Parker J, Heath C, Sudbery I, Wilson SA. The m 6A-methylase complex recruits TREX and regulates mRNA export. Sci Rep 2018; 8:13827. [PMID: 30218090 PMCID: PMC6138711 DOI: 10.1038/s41598-018-32310-8] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 09/04/2018] [Indexed: 11/09/2022] Open
Abstract
N6-methyladenosine (m6A) is the most abundant internal modification of eukaryotic mRNA. This modification has previously been shown to alter the export kinetics for mRNAs though the molecular details surrounding this phenomenon remain poorly understood. Recruitment of the TREX mRNA export complex to mRNA is driven by transcription, 5' capping and pre-mRNA splicing. Here we identify a fourth mechanism in human cells driving the association of TREX with mRNA involving the m6A methylase complex. We show that the m6A complex recruits TREX to m6A modified mRNAs and this process is essential for their efficient export. TREX also stimulates recruitment of the m6A reader protein YTHDC1 to the mRNA and the m6A complex influences the interaction of TREX with YTHDC1. Together our studies reveal a key role for TREX in the export of m6A modified mRNAs.
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Affiliation(s)
- Simon Lesbirel
- Sheffield Institute For Nucleic Acids (SInFoNiA), Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court Western Bank, Sheffield, S10 2TN, UK
| | - Nicolas Viphakone
- Sheffield Institute For Nucleic Acids (SInFoNiA), Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court Western Bank, Sheffield, S10 2TN, UK
| | - Matthew Parker
- Sheffield Institute For Nucleic Acids (SInFoNiA), Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court Western Bank, Sheffield, S10 2TN, UK
| | - Jacob Parker
- Sheffield Institute For Nucleic Acids (SInFoNiA), Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court Western Bank, Sheffield, S10 2TN, UK
| | - Catherine Heath
- Sheffield Institute For Nucleic Acids (SInFoNiA), Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court Western Bank, Sheffield, S10 2TN, UK
| | - Ian Sudbery
- Sheffield Institute For Nucleic Acids (SInFoNiA), Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court Western Bank, Sheffield, S10 2TN, UK
| | - Stuart A Wilson
- Sheffield Institute For Nucleic Acids (SInFoNiA), Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court Western Bank, Sheffield, S10 2TN, UK.
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117
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Maass PG, Barutcu AR, Rinn JL. Interchromosomal interactions: A genomic love story of kissing chromosomes. J Cell Biol 2018; 218:27-38. [PMID: 30181316 PMCID: PMC6314556 DOI: 10.1083/jcb.201806052] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 07/27/2018] [Accepted: 08/01/2018] [Indexed: 01/26/2023] Open
Abstract
Maass et al. review interchromosomal interactions, which, like intrachromosomal interactions, are emerging as important regulators of genome organization and gene expression. Nuclei require a precise three- and four-dimensional organization of DNA to establish cell-specific gene-expression programs. Underscoring the importance of DNA topology, alterations to the nuclear architecture can perturb gene expression and result in disease states. More recently, it has become clear that not only intrachromosomal interactions, but also interchromosomal interactions, a less studied feature of chromosomes, are required for proper physiological gene-expression programs. Here, we review recent studies with emerging insights into where and why cross-chromosomal communication is relevant. Specifically, we discuss how long noncoding RNAs (lncRNAs) and three-dimensional gene positioning are involved in genome organization and how low-throughput (live-cell imaging) and high-throughput (Hi-C and SPRITE) techniques contribute to understand the fundamental properties of interchromosomal interactions.
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Affiliation(s)
- Philipp G Maass
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA
| | - A Rasim Barutcu
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
| | - John L Rinn
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA .,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA.,Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA.,University of Colorado, BioFrontiers, Department of Biochemistry, Boulder, CO
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118
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Kaikkonen MU, Adelman K. Emerging Roles of Non-Coding RNA Transcription. Trends Biochem Sci 2018; 43:654-667. [DOI: 10.1016/j.tibs.2018.06.002] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 05/07/2018] [Accepted: 06/03/2018] [Indexed: 12/14/2022]
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119
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Kurup JT, Kidder BL. Identification of H4K20me3- and H3K4me3-associated RNAs using CARIP-Seq expands the transcriptional and epigenetic networks of embryonic stem cells. J Biol Chem 2018; 293:15120-15135. [PMID: 30115682 DOI: 10.1074/jbc.ra118.004974] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Indexed: 11/06/2022] Open
Abstract
RNA has been shown to interact with various proteins to regulate chromatin dynamics and gene expression. However, it is unknown whether RNAs associate with epigenetic marks such as post-translational modifications of histones, including histone 4 lysine 20 trimethylation (H4K20me3) or trimethylated histone 3 lysine 4 (H3K4me3), to regulate chromatin and gene expression. Here, we used chromatin-associated RNA immunoprecipitation (CARIP) followed by next-generation sequencing (CARIP-Seq) to survey RNAs associated with H4K20me3- and H3K4me3-marked chromatin on a global scale in embryonic stem (ES) cells. We identified thousands of mRNAs and noncoding RNAs that associate with H4K20me3- and H3K4me3-marked chromatin. H4K20me3- and H3K4me3-interacting RNAs are involved in chromatin organization and modification and RNA processing, whereas H4K20me3-only RNAs are involved in cell motility and differentiation, and H3K4me3-only RNAs are involved in metabolic processes and RNA processing. Expression of H3K4me3-associated RNAs is enriched in ES cells, whereas expression of H4K20me3-associated RNAs is enriched in ES cells and differentiated cells. H4K20me3- and H3K4me3-interacting RNAs originate from genes that co-localize with features of active chromatin, including transcriptional machinery and active promoter regions, and the histone modification H3K36me3 in gene body regions. We also found that H4K20me3 and H3K4me3 are associated with distinct gene features including transcripts of greater length and exon number relative to unoccupied transcripts. H4K20me3- and H3K4me3-marked chromatin is also associated with processed RNAs (exon transcripts) relative to unspliced pre-mRNA and ncRNA transcripts. In summary, our results provide evidence that H4K20me3- and H3K4me3-associated RNAs represent a distinct subnetwork of the ES cell transcriptional repertoire.
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Affiliation(s)
- Jiji T Kurup
- From the Department of Oncology and.,the Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, Michigan 48201
| | - Benjamin L Kidder
- From the Department of Oncology and .,the Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, Michigan 48201
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120
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Kachaev ZM, Lebedeva LA, Kozlov EN, Toropygin IY, Schedl P, Shidlovskii YV. Paip2 is localized to active promoters and loaded onto nascent mRNA in Drosophila. Cell Cycle 2018; 17:1708-1720. [PMID: 29995569 DOI: 10.1080/15384101.2018.1496738] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
Paip2 (Poly(A)-binding protein - interacting protein 2) is a conserved metazoan-specific protein that has been implicated in regulating the translation and stability of mRNAs. However, we have found that Paip2 is not restricted to the cytoplasm but is also found in the nucleus in Drosophila embryos, salivary glands, testes, and tissue culture cells. Nuclear Paip2 is associated with chromatin, and in chromatin immunoprecipitation experiments it maps to the promoter regions of active genes. However, this chromatin association is indirect, as it is RNA-dependent. Thus, Paip2 is one more item in the growing list of translation factors that are recruited to mRNAs co-transcriptionally.
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Affiliation(s)
- Zaur M Kachaev
- a Laboratory of Gene Expression Regulation in Development , Institute of Gene Biology, Russian Academy of Sciences , Moscow , Russia
| | - Lyubov A Lebedeva
- a Laboratory of Gene Expression Regulation in Development , Institute of Gene Biology, Russian Academy of Sciences , Moscow , Russia
| | - Eugene N Kozlov
- a Laboratory of Gene Expression Regulation in Development , Institute of Gene Biology, Russian Academy of Sciences , Moscow , Russia
| | - Ilya Y Toropygin
- d Center of Common Use "Human Proteome" , V.I. Orekhovich Research Institute of Biomedical Chemistry , Moscow , Russia
| | - Paul Schedl
- a Laboratory of Gene Expression Regulation in Development , Institute of Gene Biology, Russian Academy of Sciences , Moscow , Russia.,b Department of Molecular Biology , Princeton University , Princeton , NJ , USA
| | - Yulii V Shidlovskii
- a Laboratory of Gene Expression Regulation in Development , Institute of Gene Biology, Russian Academy of Sciences , Moscow , Russia.,c Department of Biology and General Genetics , I.M. Sechenov First Moscow State Medical University , Moscow , Russia
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121
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Yang S, Sun Z, Zhou Q, Wang W, Wang G, Song J, Li Z, Zhang Z, Chang Y, Xia K, Liu J, Yuan W. MicroRNAs, long noncoding RNAs, and circular RNAs: potential tumor biomarkers and targets for colorectal cancer. Cancer Manag Res 2018; 10:2249-2257. [PMID: 30100756 PMCID: PMC6065600 DOI: 10.2147/cmar.s166308] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Noncoding RNAs (ncRNAs) can be divided into microRNAs (miRNAs), long noncoding RNAs (lncRNAs), circular RNAs (circRNAs), pRNAs, and tRNAs. Traditionally, miRNAs exert their biological function mainly through the inhibition of translation via the induction of target RNA transcript degradation. lncRNAs and circRNAs were once considered to have no potential to code proteins. Here, we will review the current knowledge on ncRNAs in relation to their origins, characteristics, and functions. We will also review how ncRNAs work as competitive endogenous RNA, gene transcription and expression regulators, and RNA-binding protein sponges in colorectal cancer (CRC). Notably, except for the abovementioned mechanisms, recent advances revealed that lncRNAs can also act as the precursor of miRNAs, and a small portion of lncRNAs and circRNAs was verified to have the potential to code proteins, providing new evidence for the significance of ncRNAs in CRC tumorigenesis and development.
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Affiliation(s)
- Shuaixi Yang
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, People's Republic of China, ;
| | - Zhenqiang Sun
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, People's Republic of China, ;
| | - Quanbo Zhou
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, People's Republic of China, ;
| | - Weiwei Wang
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450001, People's Republic of China.,Department of Pathology, School of Basic Medicine, Zhengzhou University, Zhengzhou, Henan 450002, People's Republic of China
| | - Guixian Wang
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, People's Republic of China, ;
| | - Junmin Song
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, People's Republic of China, ;
| | - Zhen Li
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, People's Republic of China, ;
| | - Zhiyong Zhang
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, People's Republic of China, ;
| | - Yuan Chang
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, People's Republic of China, ;
| | - Kunkun Xia
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, People's Republic of China, ;
| | - Jinbo Liu
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, People's Republic of China, ;
| | - Weitang Yuan
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, People's Republic of China, ;
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122
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Albihlal WS, Gerber AP. Unconventional
RNA
‐binding proteins: an uncharted zone in
RNA
biology. FEBS Lett 2018; 592:2917-2931. [DOI: 10.1002/1873-3468.13161] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 06/04/2018] [Accepted: 06/06/2018] [Indexed: 01/25/2023]
Affiliation(s)
- Waleed S. Albihlal
- Department of Microbial Sciences School of Biosciences and Medicine Faculty of Health and Medical Sciences University of Surrey Guildford UK
| | - André P. Gerber
- Department of Microbial Sciences School of Biosciences and Medicine Faculty of Health and Medical Sciences University of Surrey Guildford UK
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123
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Zhao Z, Sentürk N, Song C, Grummt I. lncRNA PAPAS tethered to the rDNA enhancer recruits hypophosphorylated CHD4/NuRD to repress rRNA synthesis at elevated temperatures. Genes Dev 2018; 32:836-848. [PMID: 29907651 PMCID: PMC6049515 DOI: 10.1101/gad.311688.118] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 04/25/2018] [Indexed: 02/02/2023]
Abstract
Attenuation of pre-rRNA synthesis in response to elevated temperature is accompanied by increased levels of PAPAS ("promoter and pre-rRNA antisense"), a long noncoding RNA (lncRNA) that is transcribed in an orientation antisense to pre-rRNA. Here we show that PAPAS interacts directly with DNA, forming a DNA-RNA triplex structure that tethers PAPAS to a stretch of purines within the enhancer region, thereby guiding associated CHD4/NuRD (nucleosome remodeling and deacetylation) to the rDNA promoter. Protein-RNA interaction experiments combined with RNA secondary structure mapping revealed that the N-terminal part of CHD4 interacts with an unstructured A-rich region in PAPAS. Deletion or mutation of this sequence abolishes the interaction with CHD4. Stress-dependent up-regulation of PAPAS is accompanied by dephosphorylation of CHD4 at three serine residues, which enhances the interaction of CHD4/NuRD with RNA and reinforces repression of rDNA transcription. The results emphasize the function of lncRNAs in guiding chromatin remodeling complexes to specific genomic loci and uncover a phosphorylation-dependent mechanism of CHD4/NuRD-mediated transcriptional regulation.
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Affiliation(s)
- Zhongliang Zhao
- Division of Molecular Biology of the Cell II, German Cancer Research Center, Deutsches Krebsforschungszentrum-Zentrum für Molekulare Biologie der Universität Heidelberg Alliance, D-69120 Heidelberg, Germany
| | - Nevcin Sentürk
- Division of Molecular Biology of the Cell II, German Cancer Research Center, Deutsches Krebsforschungszentrum-Zentrum für Molekulare Biologie der Universität Heidelberg Alliance, D-69120 Heidelberg, Germany
| | - Chenlin Song
- Division of Molecular Biology of the Cell II, German Cancer Research Center, Deutsches Krebsforschungszentrum-Zentrum für Molekulare Biologie der Universität Heidelberg Alliance, D-69120 Heidelberg, Germany
| | - Ingrid Grummt
- Division of Molecular Biology of the Cell II, German Cancer Research Center, Deutsches Krebsforschungszentrum-Zentrum für Molekulare Biologie der Universität Heidelberg Alliance, D-69120 Heidelberg, Germany
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124
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Kidder BL. CARIP-Seq and ChIP-Seq: Methods to Identify Chromatin-Associated RNAs and Protein-DNA Interactions in Embryonic Stem Cells. J Vis Exp 2018. [PMID: 29889205 DOI: 10.3791/57481] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Embryonic stem (ES) cell self-renewal and differentiation is governed by extrinsic signals and intrinsic networks of transcription factors, epigenetic regulators, and post-translation modifications of histones that combinatorially influence the gene expression state of nearby genes. RNA has also been shown to interact with various proteins to regulate chromatin dynamics and gene expression. Chromatin-associated RNA immunoprecipitation (CARIP) followed by next-generation sequencing (CARIP-Seq) is a novel method to survey RNAs associated with chromatin proteins, while chromatin immunoprecipitation followed by next-generation sequencing (ChIP-Seq) is a powerful genomics technique to map the location of post-translational modification of histones, transcription factors, and epigenetic modifiers on a global-scale in ES cells. Here, we describe methods to perform CARIP-Seq and ChIP-Seq, including library construction for next-generation sequencing, to generate global chromatin-associated RNA and epigenomic maps in ES cells.
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Affiliation(s)
- Benjamin L Kidder
- Department of Oncology, Wayne State University School of Medicine; Karmanos Cancer Institute, Wayne State University School of Medicine;
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125
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Lu Z, Carter AC, Chang HY. Mechanistic insights in X-chromosome inactivation. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0356. [PMID: 28947655 DOI: 10.1098/rstb.2016.0356] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/09/2017] [Indexed: 11/12/2022] Open
Abstract
X-chromosome inactivation (XCI) is a critical epigenetic mechanism for balancing gene dosage between XY males and XX females in eutherian mammals. A long non-coding RNA (lncRNA), XIST, and its associated proteins orchestrate this multi-step process, resulting in the inheritable silencing of one of the two X-chromosomes in females. The XIST RNA is large and complex, exemplifying the unique challenges associated with the structural and functional analysis of lncRNAs. Recent technological advances in the analysis of macromolecular structure and interactions have enabled us to systematically dissect the XIST ribonucleoprotein complex, which is larger than the ribosome, and its place of action, the inactive X-chromosome. These studies shed light on key mechanisms of XCI, such as XIST coating of the X-chromosome, recruitment of DNA, RNA and histone modification enzymes, and compaction and compartmentalization of the inactive X. Here, we summarize recent studies on XCI, highlight the critical contributions of new technologies and propose a unifying model for XIST function in XCI where modular domains serve as the structural and functional units in both lncRNA-protein complexes and DNA-protein complexes in chromatin.This article is part of the themed issue 'X-chromosome inactivation: a tribute to Mary Lyon'.
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Affiliation(s)
- Zhipeng Lu
- Center for Dynamic Personal Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Ava C Carter
- Center for Dynamic Personal Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Howard Y Chang
- Center for Dynamic Personal Regulomes, Stanford University, Stanford, CA 94305, USA
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126
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Bifunctional cross-linking approaches for mass spectrometry-based investigation of nucleic acids and protein-nucleic acid assemblies. Methods 2018; 144:64-78. [PMID: 29753003 DOI: 10.1016/j.ymeth.2018.05.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 04/30/2018] [Accepted: 05/04/2018] [Indexed: 12/13/2022] Open
Abstract
With the goal of expanding the very limited toolkit of cross-linking agents available for nucleic acids and their protein complexes, we evaluated the merits of a wide range of bifunctional agents that may be capable of reacting with the functional groups characteristic of these types of biopolymers. The survey specifically focused on the ability of test reagents to produce desirable inter-molecular conjugates, which could reveal the identity of interacting components and the position of mutual contacts, while also considering a series of practical criteria for their utilization as viable nucleic acid probes. The survey employed models consisting of DNA, RNA, and corresponding protein complexes to mimic as close as possible typical applications. Denaturing polyacrylamide gel electrophoresis (PAGE) and mass spectrometric (MS) analyses were implemented in concert to monitor the formation of the desired conjugates. In particular, the former was used as a rapid and inexpensive tool for the efficient evaluation of cross-linker activity under a broad range of experimental conditions. The latter was applied after preliminary rounds of reaction optimization to enable full-fledged product characterization and, more significantly, differentiation between mono-functional and intra- versus inter-molecular conjugates. This information provided the feedback necessary to further optimize reaction conditions and explain possible outcomes. Among the reagents tested in the study, platinum complexes and nitrogen mustards manifested the most favorable characteristics for practical cross-linking applications, whereas other compounds provided inferior yields, or produced rather unstable conjugates that did not survive the selected analytical conditions. The observed outcomes will help guide the selection of the most appropriate cross-linking reagent for a specific task, whereas the experimental conditions described here will provide an excellent starting point for approaching these types of applications. As a whole, the results of the survey clearly emphasize that finding a universal reagent, which may afford excellent performance with all types of nucleic acid substrates, will require extending the exploration beyond the traditional chemistries employed to modify the constitutive functional groups of these vital biopolymers.
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127
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Chatterji P, Rustgi AK. RNA Binding Proteins in Intestinal Epithelial Biology and Colorectal Cancer. Trends Mol Med 2018; 24:490-506. [PMID: 29627433 DOI: 10.1016/j.molmed.2018.03.008] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 03/15/2018] [Accepted: 03/15/2018] [Indexed: 12/14/2022]
Abstract
The intestinal epithelium is highly proliferative and consists of crypt invaginations that house stem cells and villus projections with differentiated cells. There exists a dynamic equilibrium between proliferation, migration, differentiation, and senescence that is regulated by several factors. Among these are RNA binding proteins (RBPs) that bind their targets in a both context dependent and independent manner. RBP-RNA complexes act as rheostats by regulating expression of RNAs both co- and post-transcriptionally. This is important, especially in response to intestinal injury, to fuel regeneration. The manner in which these RBPs function in the intestine and their interactions with other pivotal pathways in colorectal cancer may provide a framework for new insights and potential therapeutic applications.
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Affiliation(s)
- Priya Chatterji
- Division of Gastroenterology, Departments of Medicine and Genetics, Abramson Cancer Center, University of Pennsylvania, Perelman School of Medicine, 421 Curie Blvd., Philadelphia, PA 19104, USA
| | - Anil K Rustgi
- Division of Gastroenterology, Departments of Medicine and Genetics, Abramson Cancer Center, University of Pennsylvania, Perelman School of Medicine, 421 Curie Blvd., Philadelphia, PA 19104, USA.
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128
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Köster T, Meyer K. Plant Ribonomics: Proteins in Search of RNA Partners. TRENDS IN PLANT SCIENCE 2018; 23:352-365. [PMID: 29429586 DOI: 10.1016/j.tplants.2018.01.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 01/08/2018] [Accepted: 01/15/2018] [Indexed: 06/08/2023]
Abstract
Research into the regulation of gene expression underwent a shift from focusing on DNA-binding proteins as key transcriptional regulators to RNA-binding proteins (RBPs) that come into play once transcription has been initiated. RBPs orchestrate all RNA-processing steps in the cell. To obtain a global view of in vivo targets, the RNA complement associated with particular RBPs is determined via immunoprecipitation of the RBP and subsequent identification of bound RNAs via RNA-seq. Here, we describe technical advances in identifying RBP in vivo targets and their binding motifs. We provide an up-to-date view of targets of nucleocytoplasmic RBPs collected in arabidopsis. We also discuss current experimental limitations and provide an outlook on how the approaches may advance our understanding of post-transcriptional networks.
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Affiliation(s)
- Tino Köster
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany.
| | - Katja Meyer
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
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129
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Li Y, Aggarwal MB, Ke K, Nguyen K, Spitale RC. Improved Analysis of RNA Localization by Spatially Restricted Oxidation of RNA-Protein Complexes. Biochemistry 2018; 57:1577-1581. [PMID: 29474061 PMCID: PMC6234203 DOI: 10.1021/acs.biochem.8b00053] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Recent analysis of transcriptomes has revealed that RNAs perform a myriad of functions beyond encoding proteins. Critical to RNA function is its transport to unique subcellular locations. Despite the importance of RNA localization, it is still very challenging to study in an unbiased manner. We recently described the ability to tag RNA molecules within subcellular locations through spatially restricted nucleobase oxidation. Herein, we describe a dramatic improvement of this protocol through the localized oxidation and tagging of proteins. Isolation of RNA-protein complexes enabled the enrichment of challenging RNA targets on chromatin and presented a considerably optimized protocol for the analysis of RNA subcellular localization within living cells.
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130
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Arun G, Diermeier SD, Spector DL. Therapeutic Targeting of Long Non-Coding RNAs in Cancer. Trends Mol Med 2018; 24:257-277. [PMID: 29449148 PMCID: PMC5840027 DOI: 10.1016/j.molmed.2018.01.001] [Citation(s) in RCA: 425] [Impact Index Per Article: 70.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 01/09/2018] [Accepted: 01/14/2018] [Indexed: 02/07/2023]
Abstract
Long non-coding RNAs (lncRNAs) represent a significant population of the human transcriptome. Many lncRNAs exhibit cell- and/or tissue/tumor-specific expression, making them excellent candidates for therapeutic applications. In this review we discuss examples of lncRNAs that demonstrate the diversity of their function in various cancer types. We also discuss recent advances in nucleic acid drug development with a focus on oligonucleotide-based therapies as a novel approach to inhibit tumor progression. The increased success rates of nucleic acid therapeutics provide an outstanding opportunity to explore lncRNAs as viable therapeutic targets to combat various aspects of cancer progression.
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Affiliation(s)
- Gayatri Arun
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; These authors contributed equally
| | - Sarah D Diermeier
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; These authors contributed equally
| | - David L Spector
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
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131
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Bierhoff H. Analysis of lncRNA-Protein Interactions by RNA-Protein Pull-Down Assays and RNA Immunoprecipitation (RIP). Methods Mol Biol 2018; 1686:241-250. [PMID: 29030825 DOI: 10.1007/978-1-4939-7371-2_17] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Long noncoding RNAs (lncRNAs) have important roles in shaping chromatin by targeting chromatin-modifying enzymes to distinct genomic sites. This section covers two methods to analyze lncRNA-protein interactions. The RNA-protein pull-down assays use either bead-bound proteins to capture in vitro transcripts, or immobilized synthetic RNAs to bind proteins from cell lysates. In the RNA immunoprecipitation (RIP) assay, endogenous RNAs are co-immunoprecipitated with a protein of interest. Both the methods can be applied to material from proliferating and quiescent cells, thus providing insights into how lncRNA-protein interactions are altered between these two cellular states.
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Affiliation(s)
- Holger Bierhoff
- Department of Biochemistry, Center for Molecular Biomedicine (CMB), Friedrich Schiller University Jena, Hans-Knöll-Str. 2, Jena, 07745, Germany.
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132
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Kaewsapsak P, Shechner DM, Mallard W, Rinn JL, Ting AY. Live-cell mapping of organelle-associated RNAs via proximity biotinylation combined with protein-RNA crosslinking. eLife 2017; 6:e29224. [PMID: 29239719 PMCID: PMC5730372 DOI: 10.7554/elife.29224] [Citation(s) in RCA: 124] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 11/06/2017] [Indexed: 12/18/2022] Open
Abstract
The spatial organization of RNA within cells is a crucial factor influencing a wide range of biological functions throughout all kingdoms of life. However, a general understanding of RNA localization has been hindered by a lack of simple, high-throughput methods for mapping the transcriptomes of subcellular compartments. Here, we develop such a method, termed APEX-RIP, which combines peroxidase-catalyzed, spatially restricted in situ protein biotinylation with RNA-protein chemical crosslinking. We demonstrate that, using a single protocol, APEX-RIP can isolate RNAs from a variety of subcellular compartments, including the mitochondrial matrix, nucleus, cytosol, and endoplasmic reticulum (ER), with specificity and sensitivity that rival or exceed those of conventional approaches. We further identify candidate RNAs localized to mitochondria-ER junctions and nuclear lamina, two compartments that are recalcitrant to classical biochemical purification. Since APEX-RIP is simple, versatile, and does not require special instrumentation, we envision its broad application in a variety of biological contexts.
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Affiliation(s)
- Pornchai Kaewsapsak
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeUnited States
- Department of GeneticsStanford UniversityStanfordUnited States
- Department of BiologyStanford UniversityStanfordUnited States
- Department of ChemistryStanford UniversityStanfordUnited States
| | - David Michael Shechner
- Department of Stem Cell and Regenerative BiologyHarvard UniversityCambridgeUnited States
- Department of Molecular and Cellular BiologyHarvard UniversityCambridgeUnited States
- Broad Institute of Massachusetts Institute of Technology and HarvardCambridgeUnited States
| | - William Mallard
- Department of Stem Cell and Regenerative BiologyHarvard UniversityCambridgeUnited States
- Department of Molecular and Cellular BiologyHarvard UniversityCambridgeUnited States
- Broad Institute of Massachusetts Institute of Technology and HarvardCambridgeUnited States
| | - John L Rinn
- Department of Stem Cell and Regenerative BiologyHarvard UniversityCambridgeUnited States
- Department of Molecular and Cellular BiologyHarvard UniversityCambridgeUnited States
- Broad Institute of Massachusetts Institute of Technology and HarvardCambridgeUnited States
| | - Alice Y Ting
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeUnited States
- Department of GeneticsStanford UniversityStanfordUnited States
- Department of BiologyStanford UniversityStanfordUnited States
- Department of ChemistryStanford UniversityStanfordUnited States
- Broad Institute of Massachusetts Institute of Technology and HarvardCambridgeUnited States
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133
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Chigi Y, Sasaki H, Sado T. The 5' region of Xist RNA has the potential to associate with chromatin through the A-repeat. RNA (NEW YORK, N.Y.) 2017; 23:1894-1901. [PMID: 28939698 PMCID: PMC5689009 DOI: 10.1261/rna.062158.117] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 09/10/2017] [Indexed: 06/07/2023]
Abstract
X inactive-specific transcript (Xist) is a long noncoding RNA that plays an essential role in X chromosome inactivation. Although Xist RNA, like common protein-coding mRNAs, is transcribed by RNA polymerase II, spliced and polyadenylated, it is retained in the nucleus and associates with the X chromosome it originates from. It has been assumed that Xist RNA recruits proteins involved in epigenetic modifications and chromatin compaction to the X chromosome. One of the major proteins constituting the nuclear matrix, hnRNP U, has been shown to be required for the association of Xist RNA with the inactive X chromosome (Xi). In this study, we found that the first 950-nt sequence of Xist RNA had the potential to associate with chromatin in a manner independent of hnRNP U. Furthermore, its chromatin association is apparently dependent on the presence of an intact A-repeat sequence, which is one of the repeats in Xist/XIST RNA conserved among many mammalian species, and has been shown to be important for Xist RNA-mediated silencing. Taking this unexpected finding and a previous study demonstrating the effect of Xist RNA lacking the A-repeat on the formation of the silent heterochromatin domain together, we suggest that the A-repeat captures chromatin near the initial loading site of Xist RNA and relocates it into the core of the heterochromatin domain.
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Affiliation(s)
- Yuta Chigi
- Department of Advanced Bioscience, Graduate School of Agriculture, Kindai University, 3327-204, Nakamachi, Nara 631-8505, Japan
| | - Hiroyuki Sasaki
- Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Takashi Sado
- Department of Advanced Bioscience, Graduate School of Agriculture, Kindai University, 3327-204, Nakamachi, Nara 631-8505, Japan
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134
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Long Y, Bolanos B, Gong L, Liu W, Goodrich KJ, Yang X, Chen S, Gooding AR, Maegley KA, Gajiwala KS, Brooun A, Cech TR, Liu X. Conserved RNA-binding specificity of polycomb repressive complex 2 is achieved by dispersed amino acid patches in EZH2. eLife 2017; 6. [PMID: 29185984 PMCID: PMC5706960 DOI: 10.7554/elife.31558] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 11/09/2017] [Indexed: 12/19/2022] Open
Abstract
Polycomb repressive complex 2 (PRC2) is a key chromatin modifier responsible for methylation of lysine 27 in histone H3. PRC2 has been shown to interact with thousands of RNA species in vivo, but understanding the physiological function of RNA binding has been hampered by the lack of separation-of-function mutants. Here, we use comprehensive mutagenesis and hydrogen deuterium exchange mass spectrometry (HDX-MS) to identify critical residues for RNA interaction in PRC2 core complexes from Homo sapiens and Chaetomium thermophilum, for which crystal structures are known. Preferential binding of G-quadruplex RNA is conserved, surprisingly using different protein elements. Key RNA-binding residues are spread out along the surface of EZH2, with other subunits including EED also contributing, and missense mutations of some of these residues have been found in cancer patients. The unusual nature of this protein-RNA interaction provides a paradigm for other epigenetic modifiers that bind RNA without canonical RNA-binding motifs.
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Affiliation(s)
- Yicheng Long
- Department of Chemistry and Biochemistry, BioFrontiers Institute, Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, United States
| | - Ben Bolanos
- Worldwide Medicinal Chemistry, Worldwide Research and Development, Pfizer Inc., San Diego, United States
| | - Lihu Gong
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Research, Department of Obstetrics and Gynecology, UT Southwestern Medical Center, Dallas, United States.,Department of Biophysics, UT Southwestern Medical Center, Dallas, United States
| | - Wei Liu
- Worldwide Medicinal Chemistry, Worldwide Research and Development, Pfizer Inc., San Diego, United States
| | - Karen J Goodrich
- Department of Chemistry and Biochemistry, BioFrontiers Institute, Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, United States
| | - Xin Yang
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Research, Department of Obstetrics and Gynecology, UT Southwestern Medical Center, Dallas, United States.,Department of Biophysics, UT Southwestern Medical Center, Dallas, United States
| | - Siming Chen
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Research, Department of Obstetrics and Gynecology, UT Southwestern Medical Center, Dallas, United States.,Department of Biophysics, UT Southwestern Medical Center, Dallas, United States
| | - Anne R Gooding
- Department of Chemistry and Biochemistry, BioFrontiers Institute, Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, United States
| | - Karen A Maegley
- Oncology Research Unit, Worldwide Research and Development, Pfizer Inc., San Diego, United States
| | - Ketan S Gajiwala
- Worldwide Medicinal Chemistry, Worldwide Research and Development, Pfizer Inc., San Diego, United States
| | - Alexei Brooun
- Worldwide Medicinal Chemistry, Worldwide Research and Development, Pfizer Inc., San Diego, United States
| | - Thomas R Cech
- Department of Chemistry and Biochemistry, BioFrontiers Institute, Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, United States
| | - Xin Liu
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Research, Department of Obstetrics and Gynecology, UT Southwestern Medical Center, Dallas, United States.,Department of Biophysics, UT Southwestern Medical Center, Dallas, United States
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135
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Melikishvili M, Chariker JH, Rouchka EC, Fondufe-Mittendorf YN. Transcriptome-wide identification of the RNA-binding landscape of the chromatin-associated protein PARP1 reveals functions in RNA biogenesis. Cell Discov 2017; 3:17043. [PMID: 29387452 PMCID: PMC5787697 DOI: 10.1038/celldisc.2017.43] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Accepted: 10/23/2017] [Indexed: 12/25/2022] Open
Abstract
Recent studies implicate Poly (ADP-ribose) polymerase 1 (PARP1) in alternative splicing regulation, and PARP1 may be an RNA-binding protein. However, detailed knowledge of RNA targets and the RNA-binding region for PARP1 are unknown. Here we report the first global study of PARP1–RNA interactions using PAR–CLIP in HeLa cells. We identified a largely overlapping set of 22 142 PARP1–RNA-binding peaks mapping to mRNAs, with 20 484 sites located in intronic regions. PARP1 preferentially bound RNA containing GC-rich sequences. Using a Bayesian model, we determined positional effects of PARP1 on regulated exon-skipping events: PARP1 binding upstream and downstream of the skipped exons generally promotes exon inclusion, whereas binding within the exon of interest and intronic regions closer to the skipped exon promotes exon skipping. Using truncation mutants, we show that removal of the Zn1Zn2 domain switches PARP1 from a DNA binder to an RNA binder. This study represents a first step into understanding the role of PARP1–RNA interaction. Continued identification and characterization of the functional interplay between PARPs and RNA may provide important insights into the role of PARPs in RNA regulation.
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Affiliation(s)
- Manana Melikishvili
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
| | - Julia H Chariker
- Department of Psychological and Brain Sciences, University of Louisville, Louisville, KY, USA.,Kentucky Biomedical Research Infrastructure Network Bioinformatics Core, 522 East Gray Street, Louisville, KY, USA
| | - Eric C Rouchka
- Kentucky Biomedical Research Infrastructure Network Bioinformatics Core, 522 East Gray Street, Louisville, KY, USA.,Department of Computer Engineering and Computer Science, University of Louisville, Louisville, KY, USA
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136
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Emerging Roles of MTG16 in Cell-Fate Control of Hematopoietic Stem Cells and Cancer. Stem Cells Int 2017; 2017:6301385. [PMID: 29358956 PMCID: PMC5735743 DOI: 10.1155/2017/6301385] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 10/12/2017] [Accepted: 10/23/2017] [Indexed: 12/13/2022] Open
Abstract
MTG16 (myeloid translocation gene on chromosome 16) and its related proteins, MTG8 and MTGR1, define a small family of transcriptional corepressors. These corepressors share highly conserved domain structures yet have distinct biological functions and tissue specificity. In vivo studies have shown that, of the three MTG corepressors, MTG16 is uniquely important for the regulation of hematopoietic stem/progenitor cell (HSPC) proliferation and differentiation. Apart from this physiological function, MTG16 is also involved in carcinomas and leukemias, acting as the genetic target of loss of heterozygosity (LOH) aberrations in breast cancer and recurrent translocations in leukemia. The frequent involvement of MTG16 in these disease etiologies implies an important developmental role for this transcriptional corepressor. Furthermore, mounting evidence suggests that MTG16 indirectly alters the disease course of several leukemias via its regulatory interactions with a variety of pathologic fusion proteins. For example, a recent study has shown that MTG16 can repress not only wild-type E2A-mediated transcription, but also leukemia fusion protein E2A-Pbx1-mediated transcription, suggesting that MTG16 may serve as a potential therapeutic target in acute lymphoblastic leukemia expressing the E2A-Pbx1 fusion protein. Given that leukemia stem cells share similar regulatory pathways with normal HSPCs, studies to further understand how MTG16 regulates cell proliferation and differentiation could lead to novel therapeutic approaches for leukemia treatment.
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137
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Auboeuf D. Alternative mRNA processing sites decrease genetic variability while increasing functional diversity. Transcription 2017; 9:75-87. [PMID: 29099315 PMCID: PMC5834221 DOI: 10.1080/21541264.2017.1373891] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Recent large-scale RNA sequencing efforts have revealed the extensive diversity of mRNA molecules produced from most eukaryotic coding genes, which arises from the usage of alternative, cryptic or non-canonical splicing and intronic polyadenylation sites. The prevailing view regarding the tremendous diversity of coding gene transcripts is that mRNA processing is a flexible and more-or-less noisy process leading to a diversity of proteins on which natural selection can act depending on protein-mediated cellular functions. However, this concept raises two main questions. First, do alternative mRNA processing pathways have a role other than generating mRNA and protein diversity? Second, is the cellular function of mRNA variants restricted to the biogenesis of functional protein isoforms? Here, I propose that the co-transcriptional use of alternative mRNA processing sites allows first, the resolution of co-transcriptional biophysical constraints that may otherwise result in DNA instability, and second, increases the diversity of cellular functions of mRNAs in a manner that is not restricted to protein synthesis.
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Affiliation(s)
- Didier Auboeuf
- a Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell , 46 Allée d'Italie Site Jacques Monod, Lyon , France
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138
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Bailey AS, Batista PJ, Gold RS, Chen YG, de Rooij DG, Chang HY, Fuller MT. The conserved RNA helicase YTHDC2 regulates the transition from proliferation to differentiation in the germline. eLife 2017; 6:e26116. [PMID: 29087293 PMCID: PMC5703642 DOI: 10.7554/elife.26116] [Citation(s) in RCA: 151] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 10/29/2017] [Indexed: 12/20/2022] Open
Abstract
The switch from mitosis to meiosis is the key event marking onset of differentiation in the germline stem cell lineage. In Drosophila, the translational repressor Bgcn is required for spermatogonia to stop mitosis and transition to meiotic prophase and the spermatocyte state. Here we show that the mammalian Bgcn homolog YTHDC2 facilitates a clean switch from mitosis to meiosis in mouse germ cells, revealing a conserved role for YTHDC2 in this critical cell fate transition. YTHDC2-deficient male germ cells enter meiosis but have a mixed identity, maintaining expression of Cyclin A2 and failing to properly express many meiotic markers. Instead of continuing through meiotic prophase, the cells attempt an abnormal mitotic-like division and die. YTHDC2 binds multiple transcripts including Ccna2 and other mitotic transcripts, binds specific piRNA precursors, and interacts with RNA granule components, suggesting that proper progression of germ cells through meiosis is licensed by YTHDC2 through post-transcriptional regulation.
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Affiliation(s)
- Alexis S Bailey
- Department of Developmental BiologyStanford University School of MedicineStanfordUnited States
| | - Pedro J Batista
- Center for Personal Dynamic RegulomesStanford University School of MedicineStanfordUnited States
| | - Rebecca S Gold
- Department of Developmental BiologyStanford University School of MedicineStanfordUnited States
| | - Y Grace Chen
- Center for Personal Dynamic RegulomesStanford University School of MedicineStanfordUnited States
| | - Dirk G de Rooij
- Center for Reproductive MedicineAcademic Medical Center, University of AmsterdamAmsterdamNetherlands
| | - Howard Y Chang
- Center for Personal Dynamic RegulomesStanford University School of MedicineStanfordUnited States
| | - Margaret T Fuller
- Department of Developmental BiologyStanford University School of MedicineStanfordUnited States
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139
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Abstract
A major shift in our understanding of genome regulation has emerged recently. It is now apparent that the majority of cellular transcripts do not code for proteins, and many of them are long noncoding RNAs (lncRNAs). Increasingly, studies suggest that lncRNAs regulate gene expression through diverse mechanisms. We review emerging mechanistic views of lncRNAs in gene regulation in the cell nucleus. We discuss the functional interactions that lncRNAs establish with other molecules as well as the relationship between lncRNA transcription and function. While some of these mechanisms are specific to lncRNAs, others might be shared with other types of genes.
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Affiliation(s)
- Francesco P Marchese
- University of Navarra, Center for Applied Medical Research (CIMA), Pamplona, 31008, Spain.,Institute of Health Research of Navarra (IdiSNA), Pamplona, 31008, Spain
| | - Ivan Raimondi
- University of Navarra, Center for Applied Medical Research (CIMA), Pamplona, 31008, Spain.,Institute of Health Research of Navarra (IdiSNA), Pamplona, 31008, Spain
| | - Maite Huarte
- University of Navarra, Center for Applied Medical Research (CIMA), Pamplona, 31008, Spain. .,Institute of Health Research of Navarra (IdiSNA), Pamplona, 31008, Spain.
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140
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Marín-Béjar O, Mas AM, González J, Martinez D, Athie A, Morales X, Galduroz M, Raimondi I, Grossi E, Guo S, Rouzaut A, Ulitsky I, Huarte M. The human lncRNA LINC-PINT inhibits tumor cell invasion through a highly conserved sequence element. Genome Biol 2017; 18:202. [PMID: 29078818 PMCID: PMC5660458 DOI: 10.1186/s13059-017-1331-y] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 10/04/2017] [Indexed: 01/16/2023] Open
Abstract
Background It is now obvious that the majority of cellular transcripts do not code for proteins, and a significant subset of them are long non-coding RNAs (lncRNAs). Many lncRNAs show aberrant expression in cancer, and some of them have been linked to cell transformation. However, the underlying mechanisms remain poorly understood and it is unknown how the sequences of lncRNA dictate their function. Results Here we characterize the function of the p53-regulated human lncRNA LINC-PINT in cancer. We find that LINC-PINT is downregulated in multiple types of cancer and acts as a tumor suppressor lncRNA by reducing the invasive phenotype of cancer cells. A cross-species analysis identifies a highly conserved sequence element in LINC-PINT that is essential for its function. This sequence mediates a specific interaction with PRC2, necessary for the LINC-PINT-dependent repression of a pro-invasion signature of genes regulated by the transcription factor EGR1. Conclusions Our findings support a conserved functional co-dependence between LINC-PINT and PRC2 and lead us to propose a new mechanism where the lncRNA regulates the availability of free PRC2 at the proximity of co-regulated genomic loci. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1331-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Oskar Marín-Béjar
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, 31008, Spain.,Institute of Health Research of Navarra (IdiSNA), Pamplona, Spain.,Present Address: Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Aina M Mas
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, 31008, Spain.,Institute of Health Research of Navarra (IdiSNA), Pamplona, Spain
| | - Jovanna González
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, 31008, Spain.,Institute of Health Research of Navarra (IdiSNA), Pamplona, Spain
| | - Dannys Martinez
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, 31008, Spain.,Institute of Health Research of Navarra (IdiSNA), Pamplona, Spain
| | - Alejandro Athie
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, 31008, Spain.,Institute of Health Research of Navarra (IdiSNA), Pamplona, Spain
| | - Xabier Morales
- Institute of Health Research of Navarra (IdiSNA), Pamplona, Spain.,Department of Immunology and Immunotherapy, Center for Applied Medical Research, University of Navarra, Pamplona, 31008, Spain
| | - Mikel Galduroz
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, 31008, Spain.,Institute of Health Research of Navarra (IdiSNA), Pamplona, Spain
| | - Ivan Raimondi
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, 31008, Spain.,Institute of Health Research of Navarra (IdiSNA), Pamplona, Spain
| | - Elena Grossi
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, 31008, Spain.,Institute of Health Research of Navarra (IdiSNA), Pamplona, Spain
| | - Shuling Guo
- Department of Antisense Drug Discovery and Clinical Development, Ionis Pharmaceuticals, Carlsbad, CA, USA
| | - Ana Rouzaut
- Institute of Health Research of Navarra (IdiSNA), Pamplona, Spain.,Department of Immunology and Immunotherapy, Center for Applied Medical Research, University of Navarra, Pamplona, 31008, Spain
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Maite Huarte
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, 31008, Spain. .,Institute of Health Research of Navarra (IdiSNA), Pamplona, Spain.
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141
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Condensin II and GAIT complexes cooperate to restrict LINE-1 retrotransposition in epithelial cells. PLoS Genet 2017; 13:e1007051. [PMID: 29028794 PMCID: PMC5656329 DOI: 10.1371/journal.pgen.1007051] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 10/25/2017] [Accepted: 10/03/2017] [Indexed: 12/15/2022] Open
Abstract
LINE-1 (L1) retrotransposons can mobilize (retrotranspose) within the human genome, and mutagenic de novo L1 insertions can lead to human diseases, including cancers. As a result, cells are actively engaged in preventing L1 retrotransposition. This work reveals that the human Condensin II complex restricts L1 retrotransposition in both non-transformed and transformed cell lines through inhibition of L1 transcription and translation. Condensin II subunits, CAP-D3 and CAP-H2, interact with members of the Gamma-Interferon Activated Inhibitor of Translation (GAIT) complex including the glutamyl-prolyl-tRNA synthetase (EPRS), the ribosomal protein L13a, Glyceraldehyde 3-phosphate dehydrogenase (GAPDH), and NS1 associated protein 1 (NSAP1). GAIT has been shown to inhibit translation of mRNAs encoding inflammatory proteins in myeloid cells by preventing the binding of the translation initiation complex, in response to Interferon gamma (IFN-γ). Excitingly, our data show that Condensin II promotes complexation of GAIT subunits. Furthermore, RNA-Immunoprecipitation experiments in epithelial cells demonstrate that Condensin II and GAIT subunits associate with L1 RNA in a co-dependent manner, independent of IFN-γ. These findings suggest that cooperation between the Condensin II and GAIT complexes may facilitate a novel mechanism of L1 repression, thus contributing to the maintenance of genome stability in somatic cells.
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142
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Tekel SJ, Haynes KA. Molecular structures guide the engineering of chromatin. Nucleic Acids Res 2017; 45:7555-7570. [PMID: 28609787 PMCID: PMC5570049 DOI: 10.1093/nar/gkx531] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 06/07/2017] [Indexed: 12/28/2022] Open
Abstract
Chromatin is a system of proteins, RNA, and DNA that interact with each other to organize and regulate genetic information within eukaryotic nuclei. Chromatin proteins carry out essential functions: packing DNA during cell division, partitioning DNA into sub-regions within the nucleus, and controlling levels of gene expression. There is a growing interest in manipulating chromatin dynamics for applications in medicine and agriculture. Progress in this area requires the identification of design rules for the chromatin system. Here, we focus on the relationship between the physical structure and function of chromatin proteins. We discuss key research that has elucidated the intrinsic properties of chromatin proteins and how this information informs design rules for synthetic systems. Recent work demonstrates that chromatin-derived peptide motifs are portable and in some cases can be customized to alter their function. Finally, we present a workflow for fusion protein design and discuss best practices for engineering chromatin to assist scientists in advancing the field of synthetic epigenetics.
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Affiliation(s)
- Stefan J Tekel
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
| | - Karmella A Haynes
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
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143
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The New RNA World: Growing Evidence for Long Noncoding RNA Functionality. Trends Genet 2017; 33:665-676. [DOI: 10.1016/j.tig.2017.08.002] [Citation(s) in RCA: 155] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 08/01/2017] [Accepted: 08/02/2017] [Indexed: 12/18/2022]
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144
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Bose DA, Berger SL. eRNA binding produces tailored CBP activity profiles to regulate gene expression. RNA Biol 2017; 14:1655-1659. [PMID: 28891741 DOI: 10.1080/15476286.2017.1353862] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
Enhancers are cis- regulatory genetic elements crucial for controlling temporal and cell-type specific patterns of gene expression. Active enhancers generate bi-directional non-coding RNA transcripts called enhancer RNAs (eRNAs). eRNAs are important for stimulating gene expression, but precise mechanisms for this ability remain unclear. Here we highlight recent findings that demonstrate a direct interaction between RNAs and the transcriptional co-activator Creb-binding protein (CBP). Notably, RNA binding could stimulate the core histone acetyltransferase activity of the enzyme, observable in cells as a link between eRNA production, CBP-dependent histone acetylation and expression of genes regulated by specific enhancers. Although RNA binding was independent of RNA sequence, specificity arises in a locus-specific manner at transcribed sites where CBP was bound to chromatin. The results suggest a functional role for eRNAs as regulatory molecules that are able to stimulate the activity of a key epigenetic regulatory enzyme, thereby promoting gene expression. Furthermore, they suggest an intriguing role for eRNAs: by modulating the activity of chromatin modifying enzymes, they could directly impact transcription by altering the chromatin environment.
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Affiliation(s)
- Daniel A Bose
- a Department of Molecular Biology and Biotechnology , Sheffield Institute for Nucleic Acids, University of Sheffield, Firth Court, Western Bank , Sheffield , UK.,b Departments of Cell and Developmental Biology, Genetics and Biology, Epigenetics Institute , University of Pennsylvania , Philadelphia, Pennsylvania , USA
| | - Shelley L Berger
- c Department of Cell and Developmental Biology, Genetics, Biology , University of Pennsylvania , Philadelphia , Pennsylvania , USA.,d Epigenetics Institute, Perelman School of Medicine , University of Pennsylvania , Philadelphia , Pennsylvania , USA
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145
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Capitanio JS, Montpetit B, Wozniak RW. Nucleoplasmic Nup98 controls gene expression by regulating a DExH/D-box protein. Nucleus 2017; 9:1-8. [PMID: 28934014 PMCID: PMC5973140 DOI: 10.1080/19491034.2017.1364826] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The nucleoporin Nup98 has been linked to the regulation of transcription and RNA metabolism, 1-3 but the mechanisms by which Nup98 contributes to these processes remains largely undefined. Recently, we uncovered interactions between Nup98 and several DExH/D-box proteins (DBPs), a protein family well-known for modulating gene expression and RNA metabolism. 4-6 Analysis of Nup98 and one of these DBPs, DHX9, showed that they directly interact, their association is facilitated by RNA, and Nup98 binding stimulates DHX9 ATPase activity. 7 Furthermore, these proteins were dependent on one another for their proper association with a subset of gene loci to control transcription and modulate mRNA splicing. 7 On the basis of these observations, we proposed that Nup98 functions to regulate DHX9 activity within the nucleoplasm. 7 Since Nup98 is associated with several DBPs, regulation of DHX9 by Nup98 may represent a paradigm for understanding how Nup98, and possibly other FG-Nup proteins, could direct the diverse cellular activities of multiple DBPs.
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Affiliation(s)
| | - Ben Montpetit
- a Department of Cell Biology , University of Alberta , Edmonton , Canada.,b Department of Viticulture and Enology , University of California at Davis , Davis , CA , USA
| | - Richard W Wozniak
- a Department of Cell Biology , University of Alberta , Edmonton , Canada
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146
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Stelloo S, Nevedomskaya E, Kim Y, Hoekman L, Bleijerveld OB, Mirza T, Wessels LFA, van Weerden WM, Altelaar AFM, Bergman AM, Zwart W. Endogenous androgen receptor proteomic profiling reveals genomic subcomplex involved in prostate tumorigenesis. Oncogene 2017; 37:313-322. [PMID: 28925401 DOI: 10.1038/onc.2017.330] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 07/10/2017] [Accepted: 08/06/2017] [Indexed: 12/13/2022]
Abstract
Androgen receptor (AR) is a key player in prostate cancer development and progression. Here we applied immunoprecipitation mass spectrometry of endogenous AR in LNCaP cells to identify components of the AR transcriptional complex. In total, 66 known and novel AR interactors were identified in the presence of synthetic androgen, most of which were critical for AR-driven prostate cancer cell proliferation. A subset of AR interactors required for LNCaP proliferation were profiled using chromatin immunoprecipitation assays followed by sequencing, identifying distinct genomic subcomplexes of AR interaction partners. Interestingly, three major subgroups of genomic subcomplexes were identified, where selective gain of function for AR genomic action in tumorigenesis was found, dictated by FOXA1 and HOXB13. In summary, by combining proteomic and genomic approaches we reveal subclasses of AR transcriptional complexes, differentiating normal AR behavior from the oncogenic state. In this process, the expression of AR interactors has key roles by reprogramming the AR cistrome and interactome in a genomic location-specific manner.
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Affiliation(s)
- S Stelloo
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - E Nevedomskaya
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Y Kim
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - L Hoekman
- Mass Spectrometry and Proteomics Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - O B Bleijerveld
- Mass Spectrometry and Proteomics Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - T Mirza
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - L F A Wessels
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Faculty of EEMCS, Delft University of Technology, Delft, The Netherlands
| | - W M van Weerden
- Department of Urology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - A F M Altelaar
- Mass Spectrometry and Proteomics Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, The Netherlands Proteomics Centre, Utrecht University, Utrecht, The Netherlands
| | - A M Bergman
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Division of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - W Zwart
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
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147
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Wang X, Goodrich KJ, Gooding AR, Naeem H, Archer S, Paucek RD, Youmans DT, Cech TR, Davidovich C. Targeting of Polycomb Repressive Complex 2 to RNA by Short Repeats of Consecutive Guanines. Mol Cell 2017; 65:1056-1067.e5. [PMID: 28306504 DOI: 10.1016/j.molcel.2017.02.003] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 12/20/2016] [Accepted: 02/01/2017] [Indexed: 11/18/2022]
Abstract
Polycomb repressive complex 2 (PRC2) is a histone methyltransferase that trimethylates H3K27, a mark of repressed chromatin. Mammalian PRC2 binds RNA promiscuously, with thousands of target transcripts in vivo. But what does PRC2 recognize in these RNAs? Here we show that purified human PRC2 recognizes G > C,U ≫ A in single-stranded RNA and has a high affinity for folded guanine quadruplex (G4) structures but little binding to duplex RNAs. Importantly, G-tract motifs are significantly enriched among PRC2-binding transcripts in vivo. DNA sequences coding for PRC2-binding RNA motifs are enriched at PRC2-binding sites on chromatin and H3K27me3-modified nucleosomes. Collectively, the abundance of PRC2-binding RNA motifs rationalizes the promiscuous RNA binding of PRC2, and their enrichment at Polycomb target genes provides a means for RNA-mediated regulation.
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Affiliation(s)
- Xueyin Wang
- Department of Chemistry & Biochemistry, BioFrontiers Institute and Howard Hughes Medical Institute, University of Colorado, Boulder, Boulder, CO 80309, USA
| | - Karen J Goodrich
- Department of Chemistry & Biochemistry, BioFrontiers Institute and Howard Hughes Medical Institute, University of Colorado, Boulder, Boulder, CO 80309, USA
| | - Anne R Gooding
- Department of Chemistry & Biochemistry, BioFrontiers Institute and Howard Hughes Medical Institute, University of Colorado, Boulder, Boulder, CO 80309, USA
| | - Haroon Naeem
- Monash Bioinformatics Platform, Monash University, Clayton, VIC 3800, Australia; Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Stuart Archer
- Monash Bioinformatics Platform, Monash University, Clayton, VIC 3800, Australia; Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Richard D Paucek
- Department of Chemistry & Biochemistry, BioFrontiers Institute and Howard Hughes Medical Institute, University of Colorado, Boulder, Boulder, CO 80309, USA
| | - Daniel T Youmans
- Department of Chemistry & Biochemistry, BioFrontiers Institute and Howard Hughes Medical Institute, University of Colorado, Boulder, Boulder, CO 80309, USA; University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Thomas R Cech
- Department of Chemistry & Biochemistry, BioFrontiers Institute and Howard Hughes Medical Institute, University of Colorado, Boulder, Boulder, CO 80309, USA.
| | - Chen Davidovich
- Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3800, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia; EMBL-Australia and the ARC Centre of Excellence in Advanced Molecular Imaging, Clayton, VIC 3800, Australia.
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148
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Li YE, Xiao M, Shi B, Yang YCT, Wang D, Wang F, Marcia M, Lu ZJ. Identification of high-confidence RNA regulatory elements by combinatorial classification of RNA-protein binding sites. Genome Biol 2017; 18:169. [PMID: 28886744 PMCID: PMC5591525 DOI: 10.1186/s13059-017-1298-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 08/14/2017] [Indexed: 12/20/2022] Open
Abstract
Crosslinking immunoprecipitation sequencing (CLIP-seq) technologies have enabled researchers to characterize transcriptome-wide binding sites of RNA-binding protein (RBP) with high resolution. We apply a soft-clustering method, RBPgroup, to various CLIP-seq datasets to group together RBPs that specifically bind the same RNA sites. Such combinatorial clustering of RBPs helps interpret CLIP-seq data and suggests functional RNA regulatory elements. Furthermore, we validate two RBP–RBP interactions in cell lines. Our approach links proteins and RNA motifs known to possess similar biochemical and cellular properties and can, when used in conjunction with additional experimental data, identify high-confidence RBP groups and their associated RNA regulatory elements.
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Affiliation(s)
- Yang Eric Li
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Mu Xiao
- Life Sciences Institute, Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Binbin Shi
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yu-Cheng T Yang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Dong Wang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Fei Wang
- Life Sciences Institute, Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Marco Marcia
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, Grenoble, 38042, France
| | - Zhi John Lu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
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149
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Han H, Braunschweig U, Gonatopoulos-Pournatzis T, Weatheritt RJ, Hirsch CL, Ha KCH, Radovani E, Nabeel-Shah S, Sterne-Weiler T, Wang J, O'Hanlon D, Pan Q, Ray D, Zheng H, Vizeacoumar F, Datti A, Magomedova L, Cummins CL, Hughes TR, Greenblatt JF, Wrana JL, Moffat J, Blencowe BJ. Multilayered Control of Alternative Splicing Regulatory Networks by Transcription Factors. Mol Cell 2017; 65:539-553.e7. [PMID: 28157508 DOI: 10.1016/j.molcel.2017.01.011] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 11/16/2016] [Accepted: 01/05/2017] [Indexed: 12/21/2022]
Abstract
Networks of coordinated alternative splicing (AS) events play critical roles in development and disease. However, a comprehensive knowledge of the factors that regulate these networks is lacking. We describe a high-throughput system for systematically linking trans-acting factors to endogenous RNA regulatory events. Using this system, we identify hundreds of factors associated with diverse regulatory layers that positively or negatively control AS events linked to cell fate. Remarkably, more than one-third of the regulators are transcription factors. Further analyses of the zinc finger protein Zfp871 and BTB/POZ domain transcription factor Nacc1, which regulate neural and stem cell AS programs, respectively, reveal roles in controlling the expression of specific splicing regulators. Surprisingly, these proteins also appear to regulate target AS programs via binding RNA. Our results thus uncover a large "missing cache" of splicing regulators among annotated transcription factors, some of which dually regulate AS through direct and indirect mechanisms.
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Affiliation(s)
- Hong Han
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | | | | | - Robert J Weatheritt
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Calley L Hirsch
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Kevin C H Ha
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Ernest Radovani
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Syed Nabeel-Shah
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | | | - Juli Wang
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Dave O'Hanlon
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Qun Pan
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Debashish Ray
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Hong Zheng
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Frederick Vizeacoumar
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Alessandro Datti
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Lilia Magomedova
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Carolyn L Cummins
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Timothy R Hughes
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Jack F Greenblatt
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Jeffrey L Wrana
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Jason Moffat
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Benjamin J Blencowe
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
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150
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Long Y, Wang X, Youmans DT, Cech TR. How do lncRNAs regulate transcription? SCIENCE ADVANCES 2017; 3:eaao2110. [PMID: 28959731 PMCID: PMC5617379 DOI: 10.1126/sciadv.aao2110] [Citation(s) in RCA: 466] [Impact Index Per Article: 66.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 09/12/2017] [Indexed: 05/11/2023]
Abstract
It has recently become apparent that RNA, itself the product of transcription, is a major regulator of the transcriptional process. In particular, long noncoding RNAs (lncRNAs), which are so numerous in eukaryotes, function in many cases as transcriptional regulators. These RNAs function through binding to histone-modifying complexes, to DNA binding proteins (including transcription factors), and even to RNA polymerase II. In other cases, it is the act of lncRNA transcription rather than the lncRNA product that appears to be regulatory. We review recent progress in elucidating the molecular mechanisms by which lncRNAs modulate gene expression and future opportunities in this research field.
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Affiliation(s)
- Yicheng Long
- Department of Chemistry and Biochemistry, University of Colorado BioFrontiers Institute, and Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80309, USA
| | - Xueyin Wang
- Department of Chemistry and Biochemistry, University of Colorado BioFrontiers Institute, and Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80309, USA
| | - Daniel T. Youmans
- Department of Chemistry and Biochemistry, University of Colorado BioFrontiers Institute, and Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80309, USA
- Anschutz Medical Campus, University of Colorado Denver, Aurora, CO 80045, USA
| | - Thomas R. Cech
- Department of Chemistry and Biochemistry, University of Colorado BioFrontiers Institute, and Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80309, USA
- Corresponding author.
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