101
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Bylino OV, Ibragimov AN, Pravednikova AE, Shidlovskii YV. Investigation of the Basic Steps in the Chromosome Conformation Capture Procedure. Front Genet 2021; 12:733937. [PMID: 34616432 PMCID: PMC8488379 DOI: 10.3389/fgene.2021.733937] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/16/2021] [Indexed: 12/05/2022] Open
Abstract
A constellation of chromosome conformation capture methods (С-methods) are an important tool for biochemical analysis of the spatial interactions between DNA regions that are separated in the primary sequence. All these methods are based on the long sequence of basic steps of treating cells, nuclei, chromatin, and finally DNA, thus representing a significant technical challenge. Here, we present an in-depth study of the basic steps in the chromatin conformation capture procedure (3С), which was performed using Drosophila Schneider 2 cells as a model. We investigated the steps of cell lysis, nuclei washing, nucleoplasm extraction, chromatin treatment with SDS/Triton X-100, restriction enzyme digestion, chromatin ligation, reversion of cross-links, DNA extraction, treatment of a 3C library with RNases, and purification of the 3C library. Several options were studied, and optimal conditions were found. Our work contributes to the understanding of the 3C basic steps and provides a useful guide to the 3C procedure.
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Affiliation(s)
- Oleg V. Bylino
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Airat N. Ibragimov
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Anna E. Pravednikova
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Yulii V. Shidlovskii
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- Department of Biology and General Genetics, I.M. Sechenov First Moscow State Medical University, Moscow, Russia
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102
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Elizarova A, Ozturk M, Guler R, Medvedeva YA. MIREyA: a computational approach to detect miRNA-directed gene activation. F1000Res 2021; 10:249. [PMID: 34527215 PMCID: PMC8411277 DOI: 10.12688/f1000research.28142.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/04/2021] [Indexed: 11/20/2022] Open
Abstract
Emerging studies demonstrate the ability of microRNAs (miRNAs) to activate genes via different mechanisms. Specifically, miRNAs may trigger an enhancer promoting chromatin remodelling in the enhancer region, thus activating the enhancer and its target genes. Here we present MIREyA, a pipeline developed to predict such miRNA-gene-enhancer trios based on an expression dataset which obviates the need to write custom scripts. We applied our pipeline to primary murine macrophages infected by Mycobacterium tuberculosis (HN878 strain) and detected Mir22, Mir221, Mir222, Mir155 and Mir1956, which could up-regulate genes related to immune responses. We believe that MIREyA is a useful tool for detecting putative miRNA-directed gene activation cases. MIREyA is available from: https://github.com/veania/MIREyA.
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Affiliation(s)
- Anna Elizarova
- Group of Regulatory Transcriptomics and Epigenomics, Research Center of Biotechnology, Institute of Bioengineering, Russian Academy of Sciences, Moscow, 117312, Russian Federation.,Department of Biological and Medical Physics, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, 141701, Russian Federation
| | - Mumin Ozturk
- International Centre for Genetic Engineering and Biotechnology, Cape Town, Cape Town, 7925, South Africa.,Department of Pathology, University of Cape Town, Institute of Infectious Diseases and Molecular Medicine (IDM), Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, Cape Town, 7925, South Africa
| | - Reto Guler
- International Centre for Genetic Engineering and Biotechnology, Cape Town, Cape Town, 7925, South Africa.,Department of Pathology, University of Cape Town, Institute of Infectious Diseases and Molecular Medicine (IDM), Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, Cape Town, 7925, South Africa.,Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Institute of Infectious Disease and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa
| | - Yulia A Medvedeva
- Group of Regulatory Transcriptomics and Epigenomics, Research Center of Biotechnology, Institute of Bioengineering, Russian Academy of Sciences, Moscow, 117312, Russian Federation.,Department of Biological and Medical Physics, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, 141701, Russian Federation
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103
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Subramaniam N, Nair R, Marsden PA. Epigenetic Regulation of the Vascular Endothelium by Angiogenic LncRNAs. Front Genet 2021; 12:668313. [PMID: 34512715 PMCID: PMC8427604 DOI: 10.3389/fgene.2021.668313] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 05/17/2021] [Indexed: 12/15/2022] Open
Abstract
The functional properties of the vascular endothelium are diverse and heterogeneous between vascular beds. This is especially evident when new blood vessels develop from a pre-existing closed cardiovascular system, a process termed angiogenesis. Endothelial cells are key drivers of angiogenesis as they undergo a highly choreographed cascade of events that has both exogenous (e.g., hypoxia and VEGF) and endogenous regulatory inputs. Not surprisingly, angiogenesis is critical in health and disease. Diverse therapeutics target proteins involved in coordinating angiogenesis with varying degrees of efficacy. It is of great interest that recent work on non-coding RNAs, especially long non-coding RNAs (lncRNAs), indicates that they are also important regulators of the gene expression paradigms that underpin this cellular cascade. The protean effects of lncRNAs are dependent, in part, on their subcellular localization. For instance, lncRNAs enriched in the nucleus can act as epigenetic modifiers of gene expression in the vascular endothelium. Of great interest to genetic disease, they are undergoing rapid evolution and show extensive inter- and intra-species heterogeneity. In this review, we describe endothelial-enriched lncRNAs that have robust effects in angiogenesis.
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Affiliation(s)
- Noeline Subramaniam
- Marsden Lab, Institute of Medical Sciences, University of Toronto, Toronto, ON, Canada
- Marsden Lab, Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael’s Hospital, Toronto, ON, Canada
| | - Ranju Nair
- Marsden Lab, Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael’s Hospital, Toronto, ON, Canada
- Marsden Lab, Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Philip A. Marsden
- Marsden Lab, Institute of Medical Sciences, University of Toronto, Toronto, ON, Canada
- Marsden Lab, Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael’s Hospital, Toronto, ON, Canada
- Marsden Lab, Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Department of Medicine, University of Toronto, Toronto, ON, Canada
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104
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Feng Y, Huang W, Paul C, Liu X, Sadayappan S, Wang Y, Pauklin S. Mitochondrial nucleoid in cardiac homeostasis: bidirectional signaling of mitochondria and nucleus in cardiac diseases. Basic Res Cardiol 2021; 116:49. [PMID: 34392401 PMCID: PMC8364536 DOI: 10.1007/s00395-021-00889-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 07/20/2021] [Indexed: 01/11/2023]
Abstract
Metabolic function and energy production in eukaryotic cells are regulated by mitochondria, which have been recognized as the intracellular 'powerhouses' of eukaryotic cells for their regulation of cellular homeostasis. Mitochondrial function is important not only in normal developmental and physiological processes, but also in a variety of human pathologies, including cardiac diseases. An emerging topic in the field of cardiovascular medicine is the implication of mitochondrial nucleoid for metabolic reprogramming. This review describes the linear/3D architecture of the mitochondrial nucleoid (e.g., highly organized protein-DNA structure of nucleoid) and how it is regulated by a variety of factors, such as noncoding RNA and its associated R-loop, for metabolic reprogramming in cardiac diseases. In addition, we highlight many of the presently unsolved questions regarding cardiac metabolism in terms of bidirectional signaling of mitochondrial nucleoid and 3D chromatin structure in the nucleus. In particular, we explore novel techniques to dissect the 3D structure of mitochondrial nucleoid and propose new insights into the mitochondrial retrograde signaling, and how it regulates the nuclear (3D) chromatin structures in mitochondrial diseases.
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Affiliation(s)
- Yuliang Feng
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Old Road, University of Oxford, Oxford, OX3 7LD, UK
| | - Wei Huang
- Department of Pathology and Laboratory Medicine, Regenerative Medicine Research, University of Cincinnati College of Medicine, 231 Albert Sabin Way, CincinnatiCincinnati, OH, 45267-0529, USA
| | - Christian Paul
- Department of Pathology and Laboratory Medicine, Regenerative Medicine Research, University of Cincinnati College of Medicine, 231 Albert Sabin Way, CincinnatiCincinnati, OH, 45267-0529, USA
| | - Xingguo Liu
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Hefei Institute of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Hefei Institute of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Guangzhou, 510530, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Institute for Stem Cell and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Sakthivel Sadayappan
- Heart, Lung and Vascular Institute, Division of Cardiovascular Health and Disease, Department of Internal Medicine, University of Cincinnati, Cincinnati, OH, 45267, USA
| | - Yigang Wang
- Department of Pathology and Laboratory Medicine, Regenerative Medicine Research, University of Cincinnati College of Medicine, 231 Albert Sabin Way, CincinnatiCincinnati, OH, 45267-0529, USA.
| | - Siim Pauklin
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Old Road, University of Oxford, Oxford, OX3 7LD, UK.
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105
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Boltsis I, Grosveld F, Giraud G, Kolovos P. Chromatin Conformation in Development and Disease. Front Cell Dev Biol 2021; 9:723859. [PMID: 34422840 PMCID: PMC8371409 DOI: 10.3389/fcell.2021.723859] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 07/16/2021] [Indexed: 01/23/2023] Open
Abstract
Chromatin domains and loops are important elements of chromatin structure and dynamics, but much remains to be learned about their exact biological role and nature. Topological associated domains and functional loops are key to gene expression and hold the answer to many questions regarding developmental decisions and diseases. Here, we discuss new findings, which have linked chromatin conformation with development, differentiation and diseases and hypothesized on various models while integrating all recent findings on how chromatin architecture affects gene expression during development, evolution and disease.
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Affiliation(s)
- Ilias Boltsis
- Department of Cell Biology, Erasmus Medical Centre, Rotterdam, Netherlands
| | - Frank Grosveld
- Department of Cell Biology, Erasmus Medical Centre, Rotterdam, Netherlands
| | - Guillaume Giraud
- Department of Cell Biology, Erasmus Medical Centre, Rotterdam, Netherlands
- Cancer Research Center of Lyon – INSERM U1052, Lyon, France
| | - Petros Kolovos
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
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106
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Lange M, Begolli R, Giakountis A. Non-Coding Variants in Cancer: Mechanistic Insights and Clinical Potential for Personalized Medicine. Noncoding RNA 2021; 7:47. [PMID: 34449663 PMCID: PMC8395730 DOI: 10.3390/ncrna7030047] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 07/26/2021] [Accepted: 08/01/2021] [Indexed: 12/11/2022] Open
Abstract
The cancer genome is characterized by extensive variability, in the form of Single Nucleotide Polymorphisms (SNPs) or structural variations such as Copy Number Alterations (CNAs) across wider genomic areas. At the molecular level, most SNPs and/or CNAs reside in non-coding sequences, ultimately affecting the regulation of oncogenes and/or tumor-suppressors in a cancer-specific manner. Notably, inherited non-coding variants can predispose for cancer decades prior to disease onset. Furthermore, accumulation of additional non-coding driver mutations during progression of the disease, gives rise to genomic instability, acting as the driving force of neoplastic development and malignant evolution. Therefore, detection and characterization of such mutations can improve risk assessment for healthy carriers and expand the diagnostic and therapeutic toolbox for the patient. This review focuses on functional variants that reside in transcribed or not transcribed non-coding regions of the cancer genome and presents a collection of appropriate state-of-the-art methodologies to study them.
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Affiliation(s)
- Marios Lange
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece; (M.L.); (R.B.)
| | - Rodiola Begolli
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece; (M.L.); (R.B.)
| | - Antonis Giakountis
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece; (M.L.); (R.B.)
- Institute for Fundamental Biomedical Research, B.S.R.C “Alexander Fleming”, 34 Fleming Str., 16672 Vari, Greece
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107
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Enhancer RNA: biogenesis, function, and regulation. Essays Biochem 2021; 64:883-894. [PMID: 33034351 DOI: 10.1042/ebc20200014] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/02/2020] [Accepted: 09/23/2020] [Indexed: 12/30/2022]
Abstract
Enhancers are noncoding DNA elements that are present upstream or downstream of a gene to control its spatial and temporal expression. Specific histone modifications, such as monomethylation on histone H3 lysine 4 (H3K4me1) and H3K27ac, have been widely used to assign enhancer regions in mammalian genomes. In recent years, emerging evidence suggests that active enhancers are bidirectionally transcribed to produce enhancer RNAs (eRNAs). This finding not only adds a new reliable feature to define enhancers but also raises a fundamental question of how eRNAs function to activate transcription. Although some believe that eRNAs are merely transcriptional byproducts, many studies have demonstrated that eRNAs execute crucial tasks in regulating chromatin conformation and transcription activation. In this review, we summarize the current understanding of eRNAs from their biogenesis, functions, and regulation to their pathological significance. Additionally, we discuss the challenges and possible mechanisms of eRNAs in regulated transcription.
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108
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Dhoondia Z, Elewa H, Malik M, Arif Z, Pique-Regi R, Ansari A. A termination-independent role of Rat1 in cotranscriptional splicing. Nucleic Acids Res 2021; 49:5520-5536. [PMID: 33978753 PMCID: PMC8191773 DOI: 10.1093/nar/gkab339] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 04/12/2021] [Accepted: 04/19/2021] [Indexed: 01/18/2023] Open
Abstract
Rat1 is a 5′→3′ exoribonuclease in budding yeast. It is a highly conserved protein with homologs being present in fission yeast, flies, worms, mice and humans. Rat1 and its human homolog Xrn2 have been implicated in multiple nuclear processes. Here we report a novel role of Rat1 in mRNA splicing. We observed an increase in the level of unspliced transcripts in mutants of Rat1. Accumulation of unspliced transcripts was not due to the surveillance role of Rat1 in degrading unspliced mRNA, or an indirect effect of Rat1 function in termination of transcription or on the level of splicing factors in the cell, or due to an increased elongation rate in Rat1 mutants. ChIP-Seq analysis revealed Rat1 crosslinking to the introns of a subset of yeast genes. Mass spectrometry and coimmunoprecipitation revealed an interaction of Rat1 with the Clf1, Isy1, Yju2, Prp43 and Sub2 splicing factors. Furthermore, recruitment of splicing factors on the intron was compromised in the Rat1 mutant. Based on these findings we propose that Rat1 has a novel role in splicing of mRNA in budding yeast. Rat1, however, is not a general splicing factor as it crosslinks to only long introns with an average length of 400 nucleotides.
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Affiliation(s)
- Zuzer Dhoondia
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
| | - Hesham Elewa
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
| | - Marva Malik
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
| | - Zahidur Arif
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
| | - Roger Pique-Regi
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, 540 East Canfield, Detroit, MI 48201, USA
| | - Athar Ansari
- To whom correspondence should be addressed. Tel: +1 313 577 9251; Fax: +1 313 571 6891;
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109
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Razin SV, Gavrilov AA. Non-coding RNAs in chromatin folding and nuclear organization. Cell Mol Life Sci 2021; 78:5489-5504. [PMID: 34117518 PMCID: PMC11072467 DOI: 10.1007/s00018-021-03876-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/24/2021] [Accepted: 06/05/2021] [Indexed: 12/19/2022]
Abstract
One of the most intriguing questions facing modern biology concerns how the genome directs the construction of cells, tissues, and whole organisms. It is tempting to suggest that the part of the genome that does not encode proteins contains architectural plans. We are still far from understanding how these plans work at the level of building tissues and the body as a whole. However, the results of recent studies demonstrate that at the cellular level, special non-coding RNAs serve as scaffolds for the construction of various intracellular structures. The term "architectural RNAs" was proposed to designate this subset of non-coding RNAs. In this review, we discuss the role of architectural RNAs in the construction of the cell nucleus and maintenance of the three-dimensional organization of the genome.
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Affiliation(s)
- Sergey V Razin
- Institute of Gene Biology, Russian Academy of Sciences, 119334, Moscow, Russia.
- Faculty of Biology, M. V. Lomonosov Moscow State University, 119234, Moscow, Russia.
| | - Alexey A Gavrilov
- Institute of Gene Biology, Russian Academy of Sciences, 119334, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 119334, Moscow, Russia
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110
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Yamazaki T, Yamamoto T, Yoshino H, Souquere S, Nakagawa S, Pierron G, Hirose T. Paraspeckles are constructed as block copolymer micelles. EMBO J 2021; 40:e107270. [PMID: 33885174 PMCID: PMC8204865 DOI: 10.15252/embj.2020107270] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 03/14/2021] [Accepted: 03/18/2021] [Indexed: 01/20/2023] Open
Abstract
Paraspeckles are constructed by NEAT1_2 architectural long noncoding RNAs. Their characteristic cylindrical shapes, with highly ordered internal organization, distinguish them from typical liquid-liquid phase-separated condensates. We experimentally and theoretically investigated how the shape and organization of paraspeckles are determined. We identified the NEAT1_2 RNA domains responsible for shell localization of the NEAT1_2 ends, which determine the characteristic internal organization. Using the soft matter physics, we then applied a theoretical framework to understand the principles that determine NEAT1_2 organization as well as shape, number, and size of paraspeckles. By treating paraspeckles as amphipathic block copolymer micelles, we could explain and predict the experimentally observed behaviors of paraspeckles upon NEAT1_2 domain deletions or transcriptional modulation. Thus, we propose that paraspeckles are block copolymer micelles assembled through a type of microphase separation, micellization. This work provides an experiment-based theoretical framework for the concept that ribonucleoprotein complexes (RNPs) can act as block copolymers to form RNA-scaffolding biomolecular condensates with optimal sizes and structures in cells.
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Affiliation(s)
| | - Tetsuya Yamamoto
- Institute for Chemical Reaction Design and DiscoveryHokkaido UniversitySapporoJapan
| | - Hyura Yoshino
- Institute for Genetic MedicineHokkaido UniversitySapporoJapan
| | | | | | - Gerard Pierron
- Centre National de la Recherche ScientifiqueUMR‐9196Gustave RoussyVillejuifFrance
| | - Tetsuro Hirose
- Graduate School of Frontier BiosciencesOsaka UniversitySuitaJapan
- Institute for Genetic MedicineHokkaido UniversitySapporoJapan
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111
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Feng Y, Liu X, Pauklin S. 3D chromatin architecture and epigenetic regulation in cancer stem cells. Protein Cell 2021; 12:440-454. [PMID: 33453053 PMCID: PMC8160035 DOI: 10.1007/s13238-020-00819-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 12/05/2020] [Indexed: 12/29/2022] Open
Abstract
Dedifferentiation of cell identity to a progenitor-like or stem cell-like state with increased cellular plasticity is frequently observed in cancer formation. During this process, a subpopulation of cells in tumours acquires a stem cell-like state partially resembling to naturally occurring pluripotent stem cells that are temporarily present during early embryogenesis. Such characteristics allow these cancer stem cells (CSCs) to give rise to the whole tumour with its entire cellular heterogeneity and thereby support metastases formation while being resistant to current cancer therapeutics. Cancer development and progression are demarcated by transcriptional dysregulation. In this article, we explore the epigenetic mechanisms shaping gene expression during tumorigenesis and cancer stem cell formation, with an emphasis on 3D chromatin architecture. Comparing the pluripotent stem cell state and epigenetic reprogramming to dedifferentiation in cellular transformation provides intriguing insight to chromatin dynamics. We suggest that the 3D chromatin architecture could be used as a target for re-sensitizing cancer stem cells to therapeutics.
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Affiliation(s)
- Yuliang Feng
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences Old Road, University of Oxford, Oxford, OX3 7LD, UK
| | - Xingguo Liu
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Hefei Institute of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences; Guangzhou Medical University, Guangzhou, 510530, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Institute for Stem Cell and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Siim Pauklin
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences Old Road, University of Oxford, Oxford, OX3 7LD, UK.
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112
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He K, Cao X, Deng X. Histone methylation in epigenetic regulation and temperature responses. CURRENT OPINION IN PLANT BIOLOGY 2021; 61:102001. [PMID: 33508540 DOI: 10.1016/j.pbi.2021.102001] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/21/2020] [Accepted: 01/04/2021] [Indexed: 05/26/2023]
Abstract
Methylation of histones on different lysine residues is dynamically added by distinct writer enzymes, interpreted by reader proteins, and removed by eraser enzymes. This epigenetic mark has widespread, dynamic roles in plant development and environmental responses. For example, histone methylation plays a key role in mediating plant responses to temperature, including alterations of flowering time. In this review, we summarize recent advances in understanding the mechanism by which histone methylation regulates these processes, and discuss the role of histone methylation in temperature responses, based on data from Arabidopsis thaliana.
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Affiliation(s)
- Kaixuan He
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Xian Deng
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
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113
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Decoding LncRNAs. Cancers (Basel) 2021; 13:cancers13112643. [PMID: 34072257 PMCID: PMC8199187 DOI: 10.3390/cancers13112643] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 05/23/2021] [Accepted: 05/25/2021] [Indexed: 02/07/2023] Open
Abstract
Non-coding RNAs (ncRNAs) have been considered as unimportant additions to the transcriptome. Yet, in light of numerous studies, it has become clear that ncRNAs play important roles in development, health and disease. Long-ignored, long non-coding RNAs (lncRNAs), ncRNAs made of more than 200 nucleotides have gained attention due to their involvement as drivers or suppressors of a myriad of tumours. The detailed understanding of some of their functions, structures and interactomes has been the result of interdisciplinary efforts, as in many cases, new methods need to be created or adapted to characterise these molecules. Unlike most reviews on lncRNAs, we summarize the achievements on lncRNA studies by taking into consideration the approaches for identification of lncRNA functions, interactomes, and structural arrangements. We also provide information about the recent data on the involvement of lncRNAs in diseases and present applications of these molecules, especially in medicine.
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114
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Cao H, Xu D, Cai Y, Han X, Tang L, Gao F, Qi Y, Cai D, Wang H, Ri M, Antonets D, Vyatkin Y, Chen Y, You X, Wang F, Nicolas E, Kapranov P. Very long intergenic non-coding (vlinc) RNAs directly regulate multiple genes in cis and trans. BMC Biol 2021; 19:108. [PMID: 34016118 PMCID: PMC8139166 DOI: 10.1186/s12915-021-01044-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 05/01/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The majority of the human genome is transcribed in the form of long non-coding (lnc) RNAs. While these transcripts have attracted considerable interest, their molecular mechanisms of function and biological significance remain controversial. One of the main reasons behind this lies in the significant challenges posed by lncRNAs requiring the development of novel methods and concepts to unravel their functionality. Existing methods often lack cross-validation and independent confirmation by different methodologies and therefore leave significant ambiguity as to the authenticity of the outcomes. Nonetheless, despite all the caveats, it appears that lncRNAs may function, at least in part, by regulating other genes via chromatin interactions. Therefore, the function of a lncRNA could be inferred from the function of genes it regulates. In this work, we present a genome-wide functional annotation strategy for lncRNAs based on identification of their regulatory networks via the integration of three distinct types of approaches: co-expression analysis, mapping of lncRNA-chromatin interactions, and assaying molecular effects of lncRNA knockdowns obtained using an inducible and highly specific CRISPR/Cas13 system. RESULTS We applied the strategy to annotate 407 very long intergenic non-coding (vlinc) RNAs belonging to a novel widespread subclass of lncRNAs. We show that vlincRNAs indeed appear to regulate multiple genes encoding proteins predominantly involved in RNA- and development-related functions, cell cycle, and cellular adhesion via a mechanism involving proximity between vlincRNAs and their targets in the nucleus. A typical vlincRNAs can be both a positive and negative regulator and regulate multiple genes both in trans and cis. Finally, we show vlincRNAs and their regulatory networks potentially represent novel components of DNA damage response and are functionally important for the ability of cancer cells to survive genotoxic stress. CONCLUSIONS This study provides strong evidence for the regulatory role of the vlincRNA class of lncRNAs and a potentially important role played by these transcripts in the hidden layer of RNA-based regulation in complex biological systems.
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Affiliation(s)
- Huifen Cao
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Dongyang Xu
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Ye Cai
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Xueer Han
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Lu Tang
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Fan Gao
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Yao Qi
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - DingDing Cai
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Huifang Wang
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Maxim Ri
- AcademGene Ltd., 6, Acad. Lavrentjev ave, Novosibirsk, 630090, Russia
| | - Denis Antonets
- AcademGene Ltd., 6, Acad. Lavrentjev ave, Novosibirsk, 630090, Russia
- SRC VB "Vector" Rospotrebnadzor, Novosibirsk, Koltsovo, 630559, Russia
| | - Yuri Vyatkin
- AcademGene Ltd., 6, Acad. Lavrentjev ave, Novosibirsk, 630090, Russia
| | - Yue Chen
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Xiang You
- School of Medicine, Xiamen University, Xiang'an Southern Road, Xiamen, 361102, China
| | - Fang Wang
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Estelle Nicolas
- LBCMCP, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Philipp Kapranov
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China.
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115
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Cai D, Han JDJ. Aging-associated lncRNAs are evolutionarily conserved and participate in NFκB signaling. NATURE AGING 2021; 1:438-453. [PMID: 37118014 DOI: 10.1038/s43587-021-00056-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 03/10/2021] [Indexed: 04/30/2023]
Abstract
The transcriptome undergoes global changes during aging, including both protein-coding and noncoding RNAs. Using comparative genomics, we identify aging-associated long noncoding RNAs (lncRNAs) that are under evolutionary constraint and are more conserved than lncRNAs that do not change with age. Aging-associated lncRNAs are enriched for functional elements, including binding sites for RNA-binding proteins and transcription factors, in particular nuclear factor kappa B (NFκB). Using CRISPR screening, we discovered that 13 of the aging-associated lncRNAs were regulators of the NFκB pathway, and we named this family 'NFκB modulating aging-related lncRNAs (NFKBMARLs)'. Further characterization of NFκBMARL-1 reveals it can be traced to 29 Ma before humans and is induced by NFκB during aging, inflammation and senescence. Reciprocally, NFκBMARL-1 directly regulates transcription of the NFκB inhibitor NFKBIZ in cis within the same topologically associated domain by binding to the NFKBIZ enhancer and recruiting RELA to the NFKBIZ promoter. These findings reveal many aging-associated lncRNAs are evolutionarily conserved components of the NFκB pathway.
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Affiliation(s)
- Donghong Cai
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jing-Dong J Han
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, China.
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116
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Liu S, Zhao K. The Toolbox for Untangling Chromosome Architecture in Immune Cells. Front Immunol 2021; 12:670884. [PMID: 33995409 PMCID: PMC8120992 DOI: 10.3389/fimmu.2021.670884] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 04/06/2021] [Indexed: 12/19/2022] Open
Abstract
The code of life is not only encrypted in the sequence of DNA but also in the way it is organized into chromosomes. Chromosome architecture is gradually being recognized as an important player in regulating cell activities (e.g., controlling spatiotemporal gene expression). In the past decade, the toolbox for elucidating genome structure has been expanding, providing an opportunity to explore this under charted territory. In this review, we will introduce the recent advancements in approaches for mapping spatial organization of the genome, emphasizing applications of these techniques to immune cells, and trying to bridge chromosome structure with immune cell activities.
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Affiliation(s)
- Shuai Liu
- Laboratory of Epigenome Biology, Systems Biology Center, NHLBI, NIH, Bethesda, MD, United States
| | - Keji Zhao
- Laboratory of Epigenome Biology, Systems Biology Center, NHLBI, NIH, Bethesda, MD, United States
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117
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Panigrahi A, O'Malley BW. Mechanisms of enhancer action: the known and the unknown. Genome Biol 2021; 22:108. [PMID: 33858480 PMCID: PMC8051032 DOI: 10.1186/s13059-021-02322-1] [Citation(s) in RCA: 128] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 03/23/2021] [Indexed: 12/13/2022] Open
Abstract
Differential gene expression mechanisms ensure cellular differentiation and plasticity to shape ontogenetic and phylogenetic diversity of cell types. A key regulator of differential gene expression programs are the enhancers, the gene-distal cis-regulatory sequences that govern spatiotemporal and quantitative expression dynamics of target genes. Enhancers are widely believed to physically contact the target promoters to effect transcriptional activation. However, our understanding of the full complement of regulatory proteins and the definitive mechanics of enhancer action is incomplete. Here, we review recent findings to present some emerging concepts on enhancer action and also outline a set of outstanding questions.
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Affiliation(s)
- Anil Panigrahi
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Bert W O'Malley
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
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118
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Functional annotation of lncRNA in high-throughput screening. Essays Biochem 2021; 65:761-773. [PMID: 33835127 PMCID: PMC8564734 DOI: 10.1042/ebc20200061] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/25/2021] [Accepted: 03/15/2021] [Indexed: 12/17/2022]
Abstract
Recent efforts on the characterization of long non-coding RNAs (lncRNAs) revealed their functional roles in modulating diverse cellular processes. These include pluripotency maintenance, lineage commitment, carcinogenesis, and pathogenesis of various diseases. By interacting with DNA, RNA and protein, lncRNAs mediate multifaceted mechanisms to regulate transcription, RNA processing, RNA interference and translation. Of more than 173000 discovered lncRNAs, the majority remain functionally unknown. The cell type-specific expression and localization of the lncRNA also suggest potential distinct functions of lncRNAs across different cell types. This highlights the niche of identifying functional lncRNAs in different biological processes and diseases through high-throughput (HTP) screening. This review summarizes the current work performed and perspectives on HTP screening of functional lncRNAs where different technologies, platforms, cellular responses and the downstream analyses are discussed. We hope to provide a better picture in applying different technologies to facilitate functional annotation of lncRNA efficiently.
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119
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Vasudeva K, Dutta A, Munshi A. Role of lncRNAs in the Development of Ischemic Stroke and Their Therapeutic Potential. Mol Neurobiol 2021; 58:3712-3728. [PMID: 33818737 DOI: 10.1007/s12035-021-02359-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 03/11/2021] [Indexed: 12/20/2022]
Abstract
Stroke is a major cause of premature mortality and disability around the world. Therefore, identification of cellular and molecular processes implicated in the pathogenesis and progression of ischemic stroke has become a priority. Long non-coding RNAs (lncRNAs) are emerging as significant players in the pathophysiology of cerebral ischemia. They are involved in different signalling pathways of cellular processes like cell apoptosis, autophagy, angiogenesis, inflammation, and cell death, impacting the progression of cerebral damage. Exploring the functions of these lncRNAs and their mechanism of action may help in the development of promising treatment strategies. In this review, the current knowledge of lncRNAs in ischemic stroke, focusing on the mechanism by which they cause cellular apoptosis, inflammation, and microglial activation, has been summarized. Very few lncRNAs have been functionally annotated. Therefore, the therapies based on lncRNAs still face many hurdles since the potential targets are likely to increase with the identification of new ones. Majority of experiments involving the identification and function of lncRNAs have been carried out in animal models, and the role of lncRNAs in human stroke presents a challenge. However, mitigating these issues through more rational experimental design might lead to the development of lncRNA-based stroke therapies to treat ischemic stroke.
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Affiliation(s)
- Kanika Vasudeva
- Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, 151001, India
| | - Anyeasha Dutta
- Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, 151001, India
| | - Anjana Munshi
- Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, 151001, India.
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120
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METTL3 regulates heterochromatin in mouse embryonic stem cells. Nature 2021; 591:317-321. [PMID: 33505026 DOI: 10.1038/s41586-021-03210-1] [Citation(s) in RCA: 181] [Impact Index Per Article: 60.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 12/14/2020] [Indexed: 02/07/2023]
Abstract
METTL3 (methyltransferase-like 3) mediates the N6-methyladenosine (m6A) methylation of mRNA, which affects the stability of mRNA and its translation into protein1. METTL3 also binds chromatin2-4, but the role of METTL3 and m6A methylation in chromatin is not fully understood. Here we show that METTL3 regulates mouse embryonic stem-cell heterochromatin, the integrity of which is critical for silencing retroviral elements and for mammalian development5. METTL3 predominantly localizes to the intracisternal A particle (IAP)-type family of endogenous retroviruses. Knockout of Mettl3 impairs the deposition of multiple heterochromatin marks onto METTL3-targeted IAPs, and upregulates IAP transcription, suggesting that METTL3 is important for the integrity of IAP heterochromatin. We provide further evidence that RNA transcripts derived from METTL3-bound IAPs are associated with chromatin and are m6A-methylated. These m6A-marked transcripts are bound by the m6A reader YTHDC1, which interacts with METTL3 and in turn promotes the association of METTL3 with chromatin. METTL3 also interacts physically with the histone 3 lysine 9 (H3K9) tri-methyltransferase SETDB1 and its cofactor TRIM28, and is important for their localization to IAPs. Our findings demonstrate that METTL3-catalysed m6A modification of RNA is important for the integrity of IAP heterochromatin in mouse embryonic stem cells, revealing a mechanism of heterochromatin regulation in mammals.
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121
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The RNA m 6A reader YTHDC1 silences retrotransposons and guards ES cell identity. Nature 2021; 591:322-326. [PMID: 33658714 DOI: 10.1038/s41586-021-03313-9] [Citation(s) in RCA: 168] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 01/29/2021] [Indexed: 02/07/2023]
Abstract
The RNA modification N6-methyladenosine (m6A) has critical roles in many biological processes1,2. However, the function of m6A in the early phase of mammalian development remains poorly understood. Here we show that the m6A reader YT521-B homology-domain-containing protein 1 (YTHDC1) is required for the maintenance of mouse embryonic stem (ES) cells in an m6A-dependent manner, and that its deletion initiates cellular reprogramming to a 2C-like state. Mechanistically, YTHDC1 binds to the transcripts of retrotransposons (such as intracisternal A particles, ERVK and LINE1) in mouse ES cells and its depletion results in the reactivation of these silenced retrotransposons, accompanied by a global decrease in SETDB1-mediated trimethylation at lysine 9 of histone H3 (H3K9me3). We further demonstrate that YTHDC1 and its target m6A RNAs act upstream of SETDB1 to repress retrotransposons and Dux, the master inducer of the two-cell stage (2C)-like program. This study reveals an essential role for m6A RNA and YTHDC1 in chromatin modification and retrotransposon repression.
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122
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Abstract
Long noncoding RNAs (lncRNAs) are involved in many regulatory mechanisms in practically every step of the RNA cycle, from transcription to RNA stability and translation. They are a highly heterogeneous class of molecules in terms of site of production, interaction networks, and functions. More and more databases are available on the web with the aim to make public information about lncRNA accessible to the scientific community. Here we review the most interesting resources with the purpose to organize a compendium of useful tools to interrogate before studying a lncRNA of interest.
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123
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Abstract
Evidence accumulated over the past decade shows that long non-coding RNAs (lncRNAs) are widely expressed and have key roles in gene regulation. Recent studies have begun to unravel how the biogenesis of lncRNAs is distinct from that of mRNAs and is linked with their specific subcellular localizations and functions. Depending on their localization and their specific interactions with DNA, RNA and proteins, lncRNAs can modulate chromatin function, regulate the assembly and function of membraneless nuclear bodies, alter the stability and translation of cytoplasmic mRNAs and interfere with signalling pathways. Many of these functions ultimately affect gene expression in diverse biological and physiopathological contexts, such as in neuronal disorders, immune responses and cancer. Tissue-specific and condition-specific expression patterns suggest that lncRNAs are potential biomarkers and provide a rationale to target them clinically. In this Review, we discuss the mechanisms of lncRNA biogenesis, localization and functions in transcriptional, post-transcriptional and other modes of gene regulation, and their potential therapeutic applications.
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124
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Wu SK, Roberts JT, Balas MM, Johnson AM. RNA matchmaking in chromatin regulation. Biochem Soc Trans 2020; 48:2467-2481. [PMID: 33245317 PMCID: PMC7888525 DOI: 10.1042/bst20191225] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/05/2020] [Accepted: 10/07/2020] [Indexed: 01/12/2023]
Abstract
Beyond being the product of gene expression, RNA can also influence the regulation of chromatin. The majority of the human genome has the capacity to be transcribed and the majority of the non-protein-coding transcripts made by RNA Polymerase II are enriched in the nucleus. Many chromatin regulators can bind to these ncRNAs in the nucleus; in some cases, there are clear examples of direct RNA-mediated chromatin regulation mechanisms stemming from these interactions, while others have yet to be determined. Recent studies have highlighted examples of chromatin regulation via RNA matchmaking, a term we use broadly here to describe intermolecular base-pairing interactions between one RNA molecule and an RNA or DNA match. This review provides examples of RNA matchmaking that regulates chromatin processes and summarizes the technical approaches used to capture these events.
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Affiliation(s)
- Stephen K. Wu
- Molecular Biology Program, University of Colorado Denver Anschutz Medical Campus 12801 East 17 Ave., Aurora, CO, United States
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver Anschutz Medical Campus 12801 East 17 Ave., Aurora, CO, United States
| | - Justin T. Roberts
- Molecular Biology Program, University of Colorado Denver Anschutz Medical Campus 12801 East 17 Ave., Aurora, CO, United States
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver Anschutz Medical Campus 12801 East 17 Ave., Aurora, CO, United States
| | - Maggie M. Balas
- Molecular Biology Program, University of Colorado Denver Anschutz Medical Campus 12801 East 17 Ave., Aurora, CO, United States
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver Anschutz Medical Campus 12801 East 17 Ave., Aurora, CO, United States
| | - Aaron M. Johnson
- Molecular Biology Program, University of Colorado Denver Anschutz Medical Campus 12801 East 17 Ave., Aurora, CO, United States
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver Anschutz Medical Campus 12801 East 17 Ave., Aurora, CO, United States
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125
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Ramírez-Colmenero A, Oktaba K, Fernandez-Valverde SL. Evolution of Genome-Organizing Long Non-coding RNAs in Metazoans. Front Genet 2020; 11:589697. [PMID: 33329735 PMCID: PMC7734150 DOI: 10.3389/fgene.2020.589697] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/09/2020] [Indexed: 12/28/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) have important regulatory functions across eukarya. It is now clear that many of these functions are related to gene expression regulation through their capacity to recruit epigenetic modifiers and establish chromatin interactions. Several lncRNAs have been recently shown to participate in modulating chromatin within the spatial organization of the genome in the three-dimensional space of the nucleus. The identification of lncRNA candidates is challenging, as it is their functional characterization. Conservation signatures of lncRNAs are different from those of protein-coding genes, making identifying lncRNAs under selection a difficult task, and the homology between lncRNAs may not be readily apparent. Here, we review the evidence for these higher-order genome organization functions of lncRNAs in animals and the evolutionary signatures they display.
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Affiliation(s)
- América Ramírez-Colmenero
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, México
| | - Katarzyna Oktaba
- Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, México
| | - Selene L Fernandez-Valverde
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, México
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126
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Antonov I, Medvedeva Y. Direct Interactions with Nascent Transcripts Is Potentially a Common Targeting Mechanism of Long Non-Coding RNAs. Genes (Basel) 2020; 11:genes11121483. [PMID: 33321875 PMCID: PMC7764144 DOI: 10.3390/genes11121483] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 12/03/2020] [Accepted: 12/04/2020] [Indexed: 11/16/2022] Open
Abstract
Although thousands of mammalian long non-coding RNAs (lncRNAs) have been reported in the last decade, their functional annotation remains limited. A wet-lab approach to detect functions of a novel lncRNA usually includes its knockdown followed by RNA sequencing and identification of the deferentially expressed genes. However, identification of the molecular mechanism(s) used by the lncRNA to regulate its targets frequently becomes a challenge. Previously, we developed the ASSA algorithm that detects statistically significant inter-molecular RNA-RNA interactions. Here we designed a workflow that uses ASSA predictions to estimate the ability of an lncRNA to function via direct base pairing with the target transcripts (co- or post-transcriptionally). The workflow was applied to 300+ lncRNA knockdown experiments from the FANTOM6 pilot project producing statistically significant predictions for 71 unique lncRNAs (104 knockdowns). Surprisingly, the majority of these lncRNAs were likely to function co-transcriptionally, i.e., hybridize with the nascent transcripts of the target genes. Moreover, a number of the obtained predictions were supported by independent iMARGI experimental data on co-localization of lncRNA and chromatin. We detected an evolutionarily conserved lncRNA CHASERR (AC013394.2 or LINC01578) that could regulate target genes co-transcriptionally via interaction with a nascent transcript by directing CHD2 helicase. The obtained results suggested that this nuclear lncRNA may be able to activate expression of the target genes in trans by base-pairing with the nascent transcripts and directing the CHD2 helicase to the regulated promoters leading to open the chromatin and active transcription. Our study highlights the possible importance of base-pairing between nuclear lncRNAs and nascent transcripts for the regulation of gene expression.
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Affiliation(s)
- Ivan Antonov
- Research Center of Biotechnology, Institute of Bioengineering, Russian Academy of Science, 119071 Moscow, Russia;
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, 141701 Moscow Region, Russia
| | - Yulia Medvedeva
- Research Center of Biotechnology, Institute of Bioengineering, Russian Academy of Science, 119071 Moscow, Russia;
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, 141701 Moscow Region, Russia
- Correspondence:
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127
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Grosch M, Ittermann S, Shaposhnikov D, Drukker M. Chromatin-Associated Membraneless Organelles in Regulation of Cellular Differentiation. Stem Cell Reports 2020; 15:1220-1232. [PMID: 33217325 PMCID: PMC7724471 DOI: 10.1016/j.stemcr.2020.10.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 10/22/2020] [Accepted: 10/23/2020] [Indexed: 12/12/2022] Open
Abstract
Membrane-free intracellular biocondensates are enclosures of proteins and nucleic acids that form by phase separation. Extensive ensembles of nuclear "membraneless organelles" indicate their involvement in genome regulation. Indeed, nuclear bodies have been linked to regulation of gene expression by formation of condensates made of chromatin and RNA processing factors. Important questions pertain to the involvement of membraneless organelles in determining cell identity through their cell-type-specific composition and function. Paraspeckles provide a prism to these questions because they exhibit striking cell-type-specific patterns and since they are crucial in embryogenesis. Here, we outline known interactions between paraspeckles and chromatin, and postulate how such interactions may be important in regulation of cell fate transitions. Moreover, we propose long non-coding RNAs (lncRNAs) as candidates for similar regulation because many form foci that resemble biocondensates and exhibit dynamic patterns during differentiation. Finally, we outline approaches that could ascertain how chromatin-associated membraneless organelles regulate cellular differentiation.
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Affiliation(s)
- Markus Grosch
- Institute of Stem Cell Research, Helmholtz Center Munich, Neuherberg, Germany
| | - Sebastian Ittermann
- Institute of Stem Cell Research, Helmholtz Center Munich, Neuherberg, Germany
| | - Dmitry Shaposhnikov
- Institute of Stem Cell Research, Helmholtz Center Munich, Neuherberg, Germany
| | - Micha Drukker
- Institute of Stem Cell Research, Helmholtz Center Munich, Neuherberg, Germany; Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Gorlaeus Building, Einsteinweg 55, 2333 CC RA Leiden, The Netherlands.
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128
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An emerging role of chromatin-interacting RNA-binding proteins in transcription regulation. Essays Biochem 2020; 64:907-918. [PMID: 33034346 DOI: 10.1042/ebc20200004] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/08/2020] [Accepted: 09/15/2020] [Indexed: 01/01/2023]
Abstract
Transcription factors (TFs) are well-established key factors orchestrating gene transcription, and RNA-binding proteins (RBPs) are mainly thought to participate in post-transcriptional control of gene. In fact, these two steps are functionally coupled, offering a possibility for reciprocal communications between transcription and regulatory RNAs and RBPs. Recently, a series of exploratory studies, utilizing functional genomic strategies, have revealed that RBPs are prevalently involved in transcription control genome-wide through their interactions with chromatin. Here, we present a refined census of RBPs to grope for such an emerging role and discuss the global view of RBP-chromatin interactions and their functional diversities in transcription regulation.
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129
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Ouyang W, Xiong D, Li G, Li X. Unraveling the 3D Genome Architecture in Plants: Present and Future. MOLECULAR PLANT 2020; 13:1676-1693. [PMID: 33065269 DOI: 10.1016/j.molp.2020.10.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 08/09/2020] [Accepted: 10/08/2020] [Indexed: 05/02/2023]
Abstract
The eukaryotic genome has a hierarchical three-dimensional (3D) organization with functional implications for DNA replication, DNA repair, and transcriptional regulation. Over the past decade, scientists have endeavored to elucidate the spatial characteristics and functions of plant genome architecture using high-throughput chromatin conformation capturing technologies such as Hi-C, ChIA-PET, and HiChIP. Here, we systematically review current understanding of chromatin organization in plants at multiple scales. We also discuss the emerging opinions and concepts in 3D genome research, focusing on state-of-the-art 3D genome techniques, RNA-chromatin interactions, liquid-liquid phase separation, and dynamic chromatin alterations. We propose the application of single-cell/single-molecule multi-omics, multiway (DNA-DNA, DNA-RNA, and RNA-RNA interactions) chromatin conformation capturing methods, and proximity ligation-independent 3D genome-mapping technologies to explore chromatin organization structure and function in plants. Such methods could reveal the spatial interactions between trait-related SNPs and their target genes at various spatiotemporal resolutions, and elucidate the molecular mechanisms of the interactions among DNA elements, RNA molecules, and protein factors during the formation of key traits in plants.
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Affiliation(s)
- Weizhi Ouyang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Dan Xiong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Guoliang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, Huazhong Agricultural University, Wuhan 430070, China.
| | - Xingwang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
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130
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Feng Y, Pauklin S. Revisiting 3D chromatin architecture in cancer development and progression. Nucleic Acids Res 2020; 48:10632-10647. [PMID: 32941624 PMCID: PMC7641747 DOI: 10.1093/nar/gkaa747] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/21/2020] [Accepted: 09/03/2020] [Indexed: 12/17/2022] Open
Abstract
Cancer development and progression are demarcated by transcriptional dysregulation, which is largely attributed to aberrant chromatin architecture. Recent transformative technologies have enabled researchers to examine the genome organization at an unprecedented dimension and precision. In particular, increasing evidence supports the essential roles of 3D chromatin architecture in transcriptional homeostasis and proposes its alterations as prominent causes of human cancer. In this article, we will discuss the recent findings on enhancers, enhancer-promoter interaction, chromatin topology, phase separation and explore their potential mechanisms in shaping transcriptional dysregulation in cancer progression. In addition, we will propose our views on how to employ state-of-the-art technologies to decode the unanswered questions in this field. Overall, this article motivates the study of 3D chromatin architecture in cancer, which allows for a better understanding of its pathogenesis and develop novel approaches for diagnosis and treatment of cancer.
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Affiliation(s)
- Yuliang Feng
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Old Road, University of Oxford, Oxford OX3 7LD, U.K
| | - Siim Pauklin
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Old Road, University of Oxford, Oxford OX3 7LD, U.K
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131
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Hao Y, Wang D, Wu S, Li X, Shao C, Zhang P, Chen JY, Lim DH, Fu XD, Chen R, He S. Active retrotransposons help maintain pericentromeric heterochromatin required for faithful cell division. Genome Res 2020; 30:1570-1582. [PMID: 33060173 PMCID: PMC7605247 DOI: 10.1101/gr.256131.119] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 09/22/2020] [Indexed: 12/20/2022]
Abstract
Retrotransposons are populated in vertebrate genomes, and when active, are thought to cause genome instability with potential benefit to genome evolution. Retrotransposon-derived RNAs are also known to give rise to small endo-siRNAs to help maintain heterochromatin at their sites of transcription; however, as not all heterochromatic regions are equally active in transcription, it remains unclear how heterochromatin is maintained across the genome. Here, we address these problems by defining the origins of repeat-derived RNAs and their specific chromatin locations in Drosophila S2 cells. We demonstrate that repeat RNAs are predominantly derived from active gypsy elements and processed by Dcr-2 into small RNAs to help maintain pericentromeric heterochromatin. We also show in cultured S2 cells that synthetic repeat-derived endo-siRNA mimics are sufficient to rescue Dcr-2-deficiency-induced defects in heterochromatin formation in interphase and chromosome segregation during mitosis, demonstrating that active retrotransposons are required for stable genetic inheritance.
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Affiliation(s)
- Yajing Hao
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093-0651, USA
| | - Dongpeng Wang
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuheng Wu
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao Li
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093-0651, USA
| | - Changwei Shao
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093-0651, USA
| | - Peng Zhang
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, 100101, China
| | - Jia-Yu Chen
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093-0651, USA
| | - Do-Hwan Lim
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093-0651, USA
| | - Xiang-Dong Fu
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093-0651, USA
| | - Runsheng Chen
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Guangdong Geneway Decoding Bio-Tech Corporation Limited, Foshan 528316, China
| | - Shunmin He
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
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132
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Stress-induced RNA-chromatin interactions promote endothelial dysfunction. Nat Commun 2020; 11:5211. [PMID: 33060583 PMCID: PMC7566596 DOI: 10.1038/s41467-020-18957-w] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 09/11/2020] [Indexed: 01/06/2023] Open
Abstract
Chromatin-associated RNA (caRNA) has been proposed as a type of epigenomic modifier. Here, we test whether environmental stress can induce cellular dysfunction through modulating RNA-chromatin interactions. We induce endothelial cell (EC) dysfunction with high glucose and TNFα (H + T), that mimic the common stress in diabetes mellitus. We characterize the H + T-induced changes in gene expression by single cell (sc)RNA-seq, DNA interactions by Hi-C, and RNA-chromatin interactions by iMARGI. H + T induce inter-chromosomal RNA-chromatin interactions, particularly among the super enhancers. To test the causal relationship between H + T-induced RNA-chromatin interactions and the expression of EC dysfunction-related genes, we suppress the LINC00607 RNA. This suppression attenuates the expression of SERPINE1, a critical pro-inflammatory and pro-fibrotic gene. Furthermore, the changes of the co-expression gene network between diabetic and healthy donor-derived ECs corroborate the H + T-induced RNA-chromatin interactions. Taken together, caRNA-mediated dysregulation of gene expression modulates EC dysfunction, a crucial mechanism underlying numerous diseases. Global interaction of chromatin-associated RNAs and DNA can be identified in situ. Here the authors report the genome-wide increase of interchromosomal RNA-DNA interactions and demonstrate the importance of such RNA-DNA contacts exemplified by LINC00607 RNA and SERPINE1 gene’s super enhancer in dysfunctional endothelial cell models.
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133
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Yan P, Lu JY, Niu J, Gao J, Zhang MQ, Yin Y, Shen X. LncRNA Platr22 promotes super-enhancer activity and stem cell pluripotency. J Mol Cell Biol 2020; 13:295-313. [PMID: 33049031 PMCID: PMC8339366 DOI: 10.1093/jmcb/mjaa056] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 08/17/2020] [Accepted: 09/14/2020] [Indexed: 12/13/2022] Open
Abstract
Super-enhancers (SEs) comprise large clusters of enhancers, which are co-occupied by multiple lineage-specific and master transcription factors, and play pivotal roles in regulating gene expression and cell fate determination. However, it is still largely unknown whether and how SEs are regulated by the noncoding portion of the genome. Here, through genome-wide analysis, we found that long noncoding RNA (lncRNA) genes preferentially lie next to SEs. In mouse embryonic stem cells (mESCs), depletion of SE-associated lncRNA transcripts dysregulated the activity of their nearby SEs. Specifically, we revealed a critical regulatory role of the lncRNA gene Platr22 in modulating the activity of a nearby SE and the expression of the nearby pluripotency regulator ZFP281. Through these regulatory events, Platr22 contributes to pluripotency maintenance and proper differentiation of mESCs. Mechanistically, Platr22 transcripts coat chromatin near the SE region and interact with DDX5 and hnRNP-L. DDX5 further recruits p300 and other factors related to active transcription. We propose that these factors assemble into a transcription hub, thus promoting an open and active epigenetic chromatin state. Our study highlights an unanticipated role for a class of lncRNAs in epigenetically controlling the activity and vulnerability to perturbation of nearby SEs for cell fate determination.
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Affiliation(s)
- Pixi Yan
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, China
| | - J Yuyang Lu
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, China
| | - Jing Niu
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, China
| | - Juntao Gao
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, China
| | - Michael Q Zhang
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, China
| | - Yafei Yin
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, China
| | - Xiaohua Shen
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, China
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134
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Ouyang W, Cao Z, Xiong D, Li G, Li X. Decoding the plant genome: From epigenome to 3D organization. J Genet Genomics 2020; 47:425-435. [PMID: 33023833 DOI: 10.1016/j.jgg.2020.06.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 05/25/2020] [Accepted: 06/01/2020] [Indexed: 12/25/2022]
Abstract
The linear genome of eukaryotes is partitioned into diverse chromatin states and packaged into a three-dimensional (3D) structure, which has functional implications in DNA replication, DNA repair, and transcriptional regulation. Over the past decades, research on plant functional genomics and epigenomics has made great progress, with thousands of genes cloned and molecular mechanisms of diverse biological processes elucidated. Recently, 3D genome research has gradually attracted great attention of many plant researchers. Herein, we briefly review the progress in genomic and epigenomic research in plants, with a focus on Arabidopsis and rice, and summarize the currently used technologies and advances in plant 3D genome organization studies. We also discuss the relationships between one-dimensional linear genome sequences, epigenomic states, and the 3D chromatin architecture. This review provides basis for future research on plant 3D genomics.
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Affiliation(s)
- Weizhi Ouyang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhilin Cao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China; Department of Resources and Environment, Henan University of Engineering, Zhengzhou, 451191, China
| | - Dan Xiong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guoliang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China; Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Xingwang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
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135
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Kantidze OL, Razin SV. Weak interactions in higher-order chromatin organization. Nucleic Acids Res 2020; 48:4614-4626. [PMID: 32313950 PMCID: PMC7229822 DOI: 10.1093/nar/gkaa261] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/30/2020] [Accepted: 04/03/2020] [Indexed: 12/20/2022] Open
Abstract
The detailed principles of the hierarchical folding of eukaryotic chromosomes have been revealed during the last two decades. Along with structures composing three-dimensional (3D) genome organization (chromatin compartments, topologically associating domains, chromatin loops, etc.), the molecular mechanisms that are involved in their establishment and maintenance have been characterized. Generally, protein-protein and protein-DNA interactions underlie the spatial genome organization in eukaryotes. However, it is becoming increasingly evident that weak interactions, which exist in biological systems, also contribute to the 3D genome. Here, we provide a snapshot of our current understanding of the role of the weak interactions in the establishment and maintenance of the 3D genome organization. We discuss how weak biological forces, such as entropic forces operating in crowded solutions, electrostatic interactions of the biomolecules, liquid-liquid phase separation, DNA supercoiling, and RNA environment participate in chromosome segregation into structural and functional units and drive intranuclear functional compartmentalization.
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Affiliation(s)
- Omar L Kantidze
- Institute of Gene Biology Russian Academy of Sciences, 119334 Moscow, Russia
| | - Sergey V Razin
- Institute of Gene Biology Russian Academy of Sciences, 119334 Moscow, Russia
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136
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Gavrilov AA, Zharikova AA, Galitsyna AA, Luzhin A, Rubanova NM, Golov AK, Petrova NV, Logacheva M, Kantidze OL, Ulianov SV, Magnitov MD, Mironov AA, Razin SV. Studying RNA-DNA interactome by Red-C identifies noncoding RNAs associated with various chromatin types and reveals transcription dynamics. Nucleic Acids Res 2020; 48:6699-6714. [PMID: 32479626 PMCID: PMC7337940 DOI: 10.1093/nar/gkaa457] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 05/13/2020] [Accepted: 05/18/2020] [Indexed: 12/15/2022] Open
Abstract
Non-coding RNAs (ncRNAs) participate in various biological processes, including regulating transcription and sustaining genome 3D organization. Here, we present a method termed Red-C that exploits proximity ligation to identify contacts with the genome for all RNA molecules present in the nucleus. Using Red-C, we uncovered the RNA-DNA interactome of human K562 cells and identified hundreds of ncRNAs enriched in active or repressed chromatin, including previously undescribed RNAs. Analysis of the RNA-DNA interactome also allowed us to trace the kinetics of messenger RNA production. Our data support the model of co-transcriptional intron splicing, but not the hypothesis of the circularization of actively transcribed genes.
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Affiliation(s)
- Alexey A Gavrilov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Anastasiya A Zharikova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- National Medical Research Center for Preventive Medicine, Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Aleksandra A Galitsyna
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Russia
| | - Artem V Luzhin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | | | - Arkadiy K Golov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- Mental Health Research Center, Moscow, Russia
| | | | | | - Omar L Kantidze
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Sergey V Ulianov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Mikhail D Magnitov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Andrey A Mironov
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- Faculty of Computer Science, Higher School of Economics, Moscow, Russia
| | - Sergey V Razin
- To whom correspondence should be addressed. Tel: +7 499 135 3092; Fax: +7 499 135 4105;
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137
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Fort V, Khelifi G, Hussein SMI. Long non-coding RNAs and transposable elements: A functional relationship. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1868:118837. [PMID: 32882261 DOI: 10.1016/j.bbamcr.2020.118837] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 07/29/2020] [Accepted: 08/27/2020] [Indexed: 12/30/2022]
Abstract
Long non-coding RNAs (lncRNAs) have become increasingly important in the past decade. They are known to regulate gene expression and to interact with chromatin, proteins and other coding and non-coding RNAs. The study of lncRNAs has been challenging due to their low expression and the lack of tools developed to adapt to their particular features. Studies on lncRNAs performed to date have largely focused on cellular functions, whereas details on the mechanism of action has only been thoroughly investigated for a small number of lncRNAs. Nevertheless, some studies have highlighted the potential of these transcripts to contain functional domains, following the same accepted trend as proteins. Interestingly, many of these identified "domains" are attributed to functional units derived from transposable elements. Here, we review several types of functions of lncRNAs and relate these functions to lncRNA-embedded transposable elements.
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Affiliation(s)
- Victoire Fort
- Laval University Cancer Research Centre, Canada; Research Center of the CHU of Québec, Laval University, Québec G1R 3S3, Canada
| | - Gabriel Khelifi
- Laval University Cancer Research Centre, Canada; Research Center of the CHU of Québec, Laval University, Québec G1R 3S3, Canada
| | - Samer M I Hussein
- Laval University Cancer Research Centre, Canada; Research Center of the CHU of Québec, Laval University, Québec G1R 3S3, Canada.
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138
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Sun YM, Chen YQ. Principles and innovative technologies for decrypting noncoding RNAs: from discovery and functional prediction to clinical application. J Hematol Oncol 2020; 13:109. [PMID: 32778133 PMCID: PMC7416809 DOI: 10.1186/s13045-020-00945-8] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 07/27/2020] [Indexed: 12/20/2022] Open
Abstract
Noncoding RNAs (ncRNAs) are a large segment of the transcriptome that do not have apparent protein-coding roles, but they have been verified to play important roles in diverse biological processes, including disease pathogenesis. With the development of innovative technologies, an increasing number of novel ncRNAs have been uncovered; information about their prominent tissue-specific expression patterns, various interaction networks, and subcellular locations will undoubtedly enhance our understanding of their potential functions. Here, we summarized the principles and innovative methods for identifications of novel ncRNAs that have potential functional roles in cancer biology. Moreover, this review also provides alternative ncRNA databases based on high-throughput sequencing or experimental validation, and it briefly describes the current strategy for the clinical translation of cancer-associated ncRNAs to be used in diagnosis.
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Affiliation(s)
- Yu-Meng Sun
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275 People’s Republic of China
| | - Yue-Qin Chen
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275 People’s Republic of China
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139
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140
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Ramilowski JA, Yip CW, Agrawal S, Chang JC, Ciani Y, Kulakovskiy IV, Mendez M, Ooi JLC, Ouyang JF, Parkinson N, Petri A, Roos L, Severin J, Yasuzawa K, Abugessaisa I, Akalin A, Antonov IV, Arner E, Bonetti A, Bono H, Borsari B, Brombacher F, Cameron CJF, Cannistraci CV, Cardenas R, Cardon M, Chang H, Dostie J, Ducoli L, Favorov A, Fort A, Garrido D, Gil N, Gimenez J, Guler R, Handoko L, Harshbarger J, Hasegawa A, Hasegawa Y, Hashimoto K, Hayatsu N, Heutink P, Hirose T, Imada EL, Itoh M, Kaczkowski B, Kanhere A, Kawabata E, Kawaji H, Kawashima T, Kelly ST, Kojima M, Kondo N, Koseki H, Kouno T, Kratz A, Kurowska-Stolarska M, Kwon ATJ, Leek J, Lennartsson A, Lizio M, López-Redondo F, Luginbühl J, Maeda S, Makeev VJ, Marchionni L, Medvedeva YA, Minoda A, Müller F, Muñoz-Aguirre M, Murata M, Nishiyori H, Nitta KR, Noguchi S, Noro Y, Nurtdinov R, Okazaki Y, Orlando V, Paquette D, Parr CJC, Rackham OJL, Rizzu P, Sánchez Martinez DF, Sandelin A, Sanjana P, Semple CAM, Shibayama Y, Sivaraman DM, Suzuki T, Szumowski SC, Tagami M, Taylor MS, Terao C, Thodberg M, Thongjuea S, Tripathi V, Ulitsky I, Verardo R, Vorontsov IE, Yamamoto C, Young RS, Baillie JK, Forrest ARR, Guigó R, Hoffman MM, Hon CC, Kasukawa T, Kauppinen S, Kere J, Lenhard B, Schneider C, Suzuki H, Yagi K, de Hoon MJL, Shin JW, Carninci P. Functional annotation of human long noncoding RNAs via molecular phenotyping. Genome Res 2020; 30:1060-1072. [PMID: 32718982 PMCID: PMC7397864 DOI: 10.1101/gr.254219.119] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 06/24/2020] [Indexed: 12/12/2022]
Abstract
Long noncoding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian genomes, and yet, their functions remain largely unknown. As part of the FANTOM6 project, we systematically knocked down the expression of 285 lncRNAs in human dermal fibroblasts and quantified cellular growth, morphological changes, and transcriptomic responses using Capped Analysis of Gene Expression (CAGE). Antisense oligonucleotides targeting the same lncRNAs exhibited global concordance, and the molecular phenotype, measured by CAGE, recapitulated the observed cellular phenotypes while providing additional insights on the affected genes and pathways. Here, we disseminate the largest-to-date lncRNA knockdown data set with molecular phenotyping (over 1000 CAGE deep-sequencing libraries) for further exploration and highlight functional roles for ZNF213-AS1 and lnc-KHDC3L-2.
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Affiliation(s)
- Jordan A Ramilowski
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Chi Wai Yip
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Saumya Agrawal
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Jen-Chien Chang
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Yari Ciani
- Laboratorio Nazionale Consorzio Interuniversitario Biotecnologie (CIB), Trieste 34127, Italy
| | - Ivan V Kulakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia.,Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Russia
| | - Mickaël Mendez
- Department of Computer Science, University of Toronto, Toronto, Ontario M5S 1A1, Canada
| | | | - John F Ouyang
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore 169857, Singapore
| | - Nick Parkinson
- Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, United Kingdom
| | - Andreas Petri
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, Copenhagen 9220, Denmark
| | - Leonie Roos
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom.,Computational Regulatory Genomics, MRC London Institute of Medical Sciences, London W12 0NN, United Kingdom
| | - Jessica Severin
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Kayoko Yasuzawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Imad Abugessaisa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Altuna Akalin
- Berlin Institute for Medical Systems Biology, Max Delbrük Center for Molecular Medicine in the Helmholtz Association, Berlin 13125, Germany
| | - Ivan V Antonov
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow 117312, Russia
| | - Erik Arner
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Alessandro Bonetti
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Hidemasa Bono
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima City 739-0046, Japan
| | - Beatrice Borsari
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08003, Spain
| | - Frank Brombacher
- International Centre for Genetic Engineering and Biotechnology (ICGEB), University of Cape Town, Cape Town 7925, South Africa.,Institute of Infectious Diseases and Molecular Medicine (IDM), Department of Pathology, Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Christopher JF Cameron
- School of Computer Science, McGill University, Montréal, Québec H3G 1Y6, Canada.,Department of Biochemistry, Rosalind and Morris Goodman Cancer Research Center, McGill University, Montréal, Québec H3G 1Y6, Canada.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06510, USA
| | - Carlo Vittorio Cannistraci
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Center for Systems Biology Dresden (CSBD), Cluster of Excellence Physics of Life (PoL), Department of Physics, Technische Universität Dresden, Dresden 01062, Germany.,Center for Complex Network Intelligence (CCNI) at the Tsinghua Laboratory of Brain and Intelligence (THBI), Department of Bioengineering, Tsinghua University, Beijing 100084, China
| | - Ryan Cardenas
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Melissa Cardon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Howard Chang
- Center for Personal Dynamic Regulome, Stanford University, Stanford, California 94305, USA
| | - Josée Dostie
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Research Center, McGill University, Montréal, Québec H3G 1Y6, Canada
| | - Luca Ducoli
- Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology, Zurich 8093, Switzerland
| | - Alexander Favorov
- Department of Computational Systems Biology, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia.,Department of Oncology, Johns Hopkins University, Baltimore, Maryland 21287, USA
| | - Alexandre Fort
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Diego Garrido
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08003, Spain
| | - Noa Gil
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Juliette Gimenez
- Epigenetics and Genome Reprogramming Laboratory, IRCCS Fondazione Santa Lucia, Rome 00179, Italy
| | - Reto Guler
- International Centre for Genetic Engineering and Biotechnology (ICGEB), University of Cape Town, Cape Town 7925, South Africa.,Institute of Infectious Diseases and Molecular Medicine (IDM), Department of Pathology, Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Lusy Handoko
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Jayson Harshbarger
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Akira Hasegawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Yuki Hasegawa
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Kosuke Hashimoto
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Norihito Hayatsu
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Peter Heutink
- Genome Biology of Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Tübingen 72076, Germany
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
| | - Eddie L Imada
- Department of Oncology, Johns Hopkins University, Baltimore, Maryland 21287, USA
| | - Masayoshi Itoh
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program (PMI), Saitama 351-0198, Japan
| | - Bogumil Kaczkowski
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Aditi Kanhere
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Emily Kawabata
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Hideya Kawaji
- RIKEN Preventive Medicine and Diagnosis Innovation Program (PMI), Saitama 351-0198, Japan
| | - Tsugumi Kawashima
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - S Thomas Kelly
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Miki Kojima
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Naoto Kondo
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Haruhiko Koseki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Tsukasa Kouno
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Anton Kratz
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Mariola Kurowska-Stolarska
- Institute of Infection, Immunity, and Inflammation, University of Glasgow, Glasgow, Scotland G12 8QQ, United Kingdom
| | - Andrew Tae Jun Kwon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Jeffrey Leek
- Department of Oncology, Johns Hopkins University, Baltimore, Maryland 21287, USA
| | - Andreas Lennartsson
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge 14157, Sweden
| | - Marina Lizio
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Fernando López-Redondo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Joachim Luginbühl
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Shiori Maeda
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Vsevolod J Makeev
- Department of Computational Systems Biology, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Luigi Marchionni
- Department of Oncology, Johns Hopkins University, Baltimore, Maryland 21287, USA
| | - Yulia A Medvedeva
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow 117312, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Aki Minoda
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Ferenc Müller
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Manuel Muñoz-Aguirre
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08003, Spain
| | - Mitsuyoshi Murata
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Hiromi Nishiyori
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Kazuhiro R Nitta
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Shuhei Noguchi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Yukihiko Noro
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Ramil Nurtdinov
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08003, Spain
| | - Yasushi Okazaki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Valerio Orlando
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Denis Paquette
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Research Center, McGill University, Montréal, Québec H3G 1Y6, Canada
| | - Callum J C Parr
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Owen J L Rackham
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore 169857, Singapore
| | - Patrizia Rizzu
- Genome Biology of Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Tübingen 72076, Germany
| | | | - Albin Sandelin
- Department of Biology and BRIC, University of Copenhagen, Denmark, Copenhagen N DK2200, Denmark
| | - Pillay Sanjana
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Colin A M Semple
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Youtaro Shibayama
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Divya M Sivaraman
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Takahiro Suzuki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | | | - Michihira Tagami
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Martin S Taylor
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Chikashi Terao
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Malte Thodberg
- Department of Biology and BRIC, University of Copenhagen, Denmark, Copenhagen N DK2200, Denmark
| | - Supat Thongjuea
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Vidisha Tripathi
- National Centre for Cell Science, Pune, Maharashtra 411007, India
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Roberto Verardo
- Laboratorio Nazionale Consorzio Interuniversitario Biotecnologie (CIB), Trieste 34127, Italy
| | - Ilya E Vorontsov
- Department of Computational Systems Biology, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia
| | - Chinatsu Yamamoto
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Robert S Young
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh EH8 9AG, United Kingdom
| | - J Kenneth Baillie
- Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, United Kingdom
| | - Alistair R R Forrest
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan.,Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, Perth, Western Australia 6009, Australia
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08003, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Catalonia 08002, Spain
| | | | - Chung Chau Hon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Takeya Kasukawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Sakari Kauppinen
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, Copenhagen 9220, Denmark
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge 14157, Sweden.,Stem Cells and Metabolism Research Program, University of Helsinki and Folkhälsan Research Center, 00290 Helsinki, Finland
| | - Boris Lenhard
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom.,Computational Regulatory Genomics, MRC London Institute of Medical Sciences, London W12 0NN, United Kingdom.,Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen N-5008, Norway
| | - Claudio Schneider
- Laboratorio Nazionale Consorzio Interuniversitario Biotecnologie (CIB), Trieste 34127, Italy.,Department of Medicine and Consorzio Interuniversitario Biotecnologie p.zle Kolbe 1 University of Udine, Udine 33100, Italy
| | - Harukazu Suzuki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Ken Yagi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Michiel J L de Hoon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Jay W Shin
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
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141
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Chen Q, Meng X, Liao Q, Chen M. Versatile interactions and bioinformatics analysis of noncoding RNAs. Brief Bioinform 2020; 20:1781-1794. [PMID: 29939215 DOI: 10.1093/bib/bby050] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 05/02/2018] [Indexed: 02/07/2023] Open
Abstract
Advances in RNA sequencing technologies and computational methodologies have provided a huge impetus to noncoding RNA (ncRNA) study. Once regarded as inconsequential results of transcriptional promiscuity, ncRNAs were later found to exert great roles in various aspects of biological functions. They are emerging as key players in gene regulatory networks by interacting with other biomolecules (DNA, RNA or protein). Here, we provide an overview of ncRNA repertoire and highlight recent discoveries of their versatile interactions. To better investigate the ncRNA-mediated regulation, it is necessary to make full use of innovative sequencing techniques and computational tools. We further describe a comprehensive workflow for in silico ncRNA analysis, providing up-to-date platforms, databases and tools dedicated to ncRNA identification and functional annotation.
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Affiliation(s)
- Qi Chen
- Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China
| | - Xianwen Meng
- Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China
| | - Qi Liao
- Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China
| | - Ming Chen
- Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, Medical School of Ningbo University, Ningbo, Zhejiang, P. R. China
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142
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Mapping Transcriptome-Wide and Genome-Wide RNA-DNA Contacts with Chromatin-Associated RNA Sequencing (ChAR-seq). Methods Mol Biol 2020. [PMID: 32681510 DOI: 10.1007/978-1-0716-0680-3_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2023]
Abstract
RNAs play key roles in the cell as molecular intermediates for protein synthesis and as regulators of nuclear processes such as splicing, posttranscriptional regulation, or chromatin remodeling. Various classes of non-coding RNAs, including long non-coding RNAs (lncRNAs), can bind chromatin either directly or via interaction with chromatin binding proteins. It has been proposed that lncRNAs regulate cell-state-specific genes by coordinating the locus-dependent activity of chromatin-modifying complexes. Yet, the vast majority of lncRNAs have unknown functions, and we know little about the specific loci they regulate. A key step toward understanding chromatin regulation by RNAs is to map the genomic loci with which every nuclear RNA interacts and, reciprocally, to identify all RNAs that target a given locus. Our ability to generate such data has been limited, until recently, by the lack of methods to probe the genomic localization of more than a few RNAs at a time. Here, we describe a protocol for ChAR-seq, an RNA-DNA proximity ligation method that maps the binding loci for thousands of RNAs at once and without the need for specific RNA or DNA probe sequences. The ChAR-seq approach generates chimeric RNA-DNA molecules in situ and then converts those chimeras to DNA for next-generation sequencing. Using ChAR-seq we detect many types of chromatin-associated RNA, both coding and non-coding. Understanding the RNA-DNA interactome and its changes during differentiation or disease with ChAR-seq will likely provide key insights into chromatin and RNA biology.
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143
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Khelifi G, Hussein SMI. A New View of Genome Organization Through RNA Directed Interactions. Front Cell Dev Biol 2020; 8:517. [PMID: 32760716 PMCID: PMC7371936 DOI: 10.3389/fcell.2020.00517] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 06/02/2020] [Indexed: 12/30/2022] Open
Affiliation(s)
- Gabriel Khelifi
- Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Québec, QC, Canada.,Université Laval Cancer Research Center, Université Laval, Québec, QC, Canada.,Oncology Division, Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Québec, QC, Canada
| | - Samer M I Hussein
- Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Québec, QC, Canada.,Université Laval Cancer Research Center, Université Laval, Québec, QC, Canada.,Oncology Division, Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Québec, QC, Canada
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144
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Jiang Y, Huang J, Lun K, Li B, Zheng H, Li Y, Zhou R, Duan W, Wang C, Feng Y, Yao H, Li C, Ji X. Genome-wide analyses of chromatin interactions after the loss of Pol I, Pol II, and Pol III. Genome Biol 2020; 21:158. [PMID: 32616013 PMCID: PMC7331254 DOI: 10.1186/s13059-020-02067-3] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 06/08/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The relationship between transcription and the 3D chromatin structure is debated. Multiple studies have shown that transcription affects global Cohesin binding and 3D genome structures. However, several other studies have indicated that inhibited transcription does not alter chromatin conformations. RESULTS We provide the most comprehensive evidence to date to demonstrate that transcription plays a relatively modest role in organizing the local, small-scale chromatin structures in mammalian cells. We show degraded Pol I, Pol II, and Pol III proteins in mESCs cause few or no changes in large-scale 3D chromatin structures, selected RNA polymerases with a high abundance of binding sites or active promoter-associated interactions appear to be relatively more affected after the degradation, transcription inhibition alters local, small loop domains, as indicated by high-resolution chromatin interaction maps, and loops with bound Pol II but without Cohesin or CTCF are identified and found to be largely unchanged after transcription inhibition. Interestingly, Pol II depletion for a longer time significantly affects the chromatin accessibility and Cohesin occupancy, suggesting that RNA polymerases are capable of affecting the 3D genome indirectly. These direct and indirect effects explain the previous inconsistent findings on the influence of transcription inhibition on the 3D genome. CONCLUSIONS We conclude that Pol I, Pol II, and Pol III loss alters local, small-scale chromatin interactions in mammalian cells, suggesting that the 3D chromatin structures are pre-established and relatively stable.
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Affiliation(s)
- Yongpeng Jiang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Jie Huang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Kehuan Lun
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Boyuan Li
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Haonan Zheng
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Yuanjun Li
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Rong Zhou
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Wenjia Duan
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Chenlu Wang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Yuanqing Feng
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Hong Yao
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Cheng Li
- Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Center for Statistical Science, Center for Bioinformatics, Peking University, Beijing, 100871, China
| | - Xiong Ji
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
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145
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Papanicolaou N, Bonetti A. The New Frontier of Functional Genomics: From Chromatin Architecture and Noncoding RNAs to Therapeutic Targets. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2020; 25:568-580. [PMID: 32486876 PMCID: PMC7309355 DOI: 10.1177/2472555220926158] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 04/21/2020] [Accepted: 04/22/2020] [Indexed: 12/11/2022]
Abstract
Common diseases are complex, multifactorial disorders whose pathogenesis is influenced by the interplay of genetic predisposition and environmental factors. Genome-wide association studies have interrogated genetic polymorphisms across genomes of individuals to test associations between genotype and susceptibility to specific disorders, providing insights into the genetic architecture of several complex disorders. However, genetic variants associated with the susceptibility to common diseases are often located in noncoding regions of the genome, such as tissue-specific enhancers or long noncoding RNAs, suggesting that regulatory elements might play a relevant role in human diseases. Enhancers are cis-regulatory genomic sequences that act in concert with promoters to regulate gene expression in a precise spatiotemporal manner. They can be located at a considerable distance from their cognate target promoters, increasing the difficulty of their identification. Genomes are organized in domains of chromatin folding, namely topologically associating domains (TADs). Identification of enhancer-promoter interactions within TADs has revealed principles of cell-type specificity across several organisms and tissues. The vast majority of mammalian genomes are pervasively transcribed, accounting for a previously unappreciated complexity of the noncoding RNA fraction. Particularly, long noncoding RNAs have emerged as key players for the establishment of chromatin architecture and regulation of gene expression. In this perspective, we describe the new advances in the fields of transcriptomics and genome organization, focusing on the role of noncoding genomic variants in the predisposition of common diseases. Finally, we propose a new framework for the identification of the next generation of pharmacological targets for common human diseases.
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Affiliation(s)
- Natali Papanicolaou
- Division of Biomaterials, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Alessandro Bonetti
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
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146
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Arun G, Aggarwal D, Spector DL. MALAT1 Long Non-Coding RNA: Functional Implications. Noncoding RNA 2020; 6:E22. [PMID: 32503170 PMCID: PMC7344863 DOI: 10.3390/ncrna6020022] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 05/27/2020] [Accepted: 05/29/2020] [Indexed: 12/13/2022] Open
Abstract
The mammalian genome is pervasively transcribed and the functional significance of many long non-coding RNA (lncRNA) transcripts are gradually being elucidated. Metastasis Associated Lung Adenocarcinoma Transcript 1 (MALAT1) is one of the most well-studied lncRNAs. MALAT1 is a highly conserved nuclear retained lncRNA that is abundantly expressed in cells and tissues and has been shown to play a role in regulating genes at both the transcriptional and post-transcriptional levels in a context-dependent manner. However, Malat1 has been shown to be dispensable for normal development and viability in mice. Interestingly, accumulating evidence suggests that MALAT1 plays an important role in numerous diseases including cancer. Here, we discuss the current state-of-knowledge in regard to MALAT1 with respect to its function, role in diseases, and the potential therapeutic opportunities for targeting MALAT1 using antisense oligonucleotides and small molecules.
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Affiliation(s)
- Gayatri Arun
- Envisagenics, 101 Avenue of the Americas, New York, NY 10013, USA;
| | - Disha Aggarwal
- Graduate Program in Genetics, Stony Brook University, Stony Brook, New York, NY 11794, USA;
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY 11724, USA
| | - David L. Spector
- Graduate Program in Genetics, Stony Brook University, Stony Brook, New York, NY 11794, USA;
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY 11724, USA
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147
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Kato M, Carninci P. Genome-Wide Technologies to Study RNA-Chromatin Interactions. Noncoding RNA 2020; 6:ncrna6020020. [PMID: 32471183 PMCID: PMC7345514 DOI: 10.3390/ncrna6020020] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 05/23/2020] [Accepted: 05/25/2020] [Indexed: 12/21/2022] Open
Abstract
An increasing number of studies have revealed that long non-coding RNAs (lncRNAs) play important roles in gene regulation and nuclear organization. Although the mechanisms are still largely unknown, many lncRNAs have been shown to interact with chromatin. Thus, one approach to understanding the function of these lncRNAs is to identify their sites of genomic interaction. Hybridization capture methods using oligonucleotide probes have been used for years to study chromatin-associated RNA. Recently, several groups have developed novel methods based on proximity ligation to investigate RNA–chromatin interactions at a genome-wide scale. This review discusses these technologies and highlights their advantages and disadvantages for the consideration of potential users.
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Affiliation(s)
- Masaki Kato
- Correspondence: (M.K.); (P.C.); Tel.: +81-045-503-9111 (M.K.)
| | - Piero Carninci
- Correspondence: (M.K.); (P.C.); Tel.: +81-045-503-9111 (M.K.)
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148
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Cai Z, Cao C, Ji L, Ye R, Wang D, Xia C, Wang S, Du Z, Hu N, Yu X, Chen J, Wang L, Yang X, He S, Xue Y. RIC-seq for global in situ profiling of RNA-RNA spatial interactions. Nature 2020; 582:432-437. [PMID: 32499643 DOI: 10.1038/s41586-020-2249-1] [Citation(s) in RCA: 155] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 03/02/2020] [Indexed: 01/23/2023]
Abstract
Highly structured RNA molecules usually interact with each other, and associate with various RNA-binding proteins, to regulate critical biological processes. However, RNA structures and interactions in intact cells remain largely unknown. Here, by coupling proximity ligation mediated by RNA-binding proteins with deep sequencing, we report an RNA in situ conformation sequencing (RIC-seq) technology for the global profiling of intra- and intermolecular RNA-RNA interactions. This technique not only recapitulates known RNA secondary structures and tertiary interactions, but also facilitates the generation of three-dimensional (3D) interaction maps of RNA in human cells. Using these maps, we identify noncoding RNA targets globally, and discern RNA topological domains and trans-interacting hubs. We reveal that the functional connectivity of enhancers and promoters can be assigned using their pairwise-interacting RNAs. Furthermore, we show that CCAT1-5L-a super-enhancer hub RNA-interacts with the RNA-binding protein hnRNPK, as well as RNA derived from the MYC promoter and enhancer, to boost MYC transcription by modulating chromatin looping. Our study demonstrates the power and applicability of RIC-seq in discovering the 3D structures, interactions and regulatory roles of RNA.
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Affiliation(s)
- Zhaokui Cai
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Changchang Cao
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Lei Ji
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Rong Ye
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Di Wang
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Cong Xia
- School of Life Sciences, Henan Normal University, Xinxiang, China
| | - Sui Wang
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Zongchang Du
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Naijing Hu
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiaohua Yu
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Juan Chen
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Lei Wang
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Xianguang Yang
- School of Life Sciences, Henan Normal University, Xinxiang, China
| | - Shunmin He
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yuanchao Xue
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China. .,University of Chinese Academy of Sciences, Beijing, China.
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149
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RNA-mediated regulation of chromatin structures. Genes Genomics 2020; 42:609-617. [PMID: 32297146 DOI: 10.1007/s13258-020-00929-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 03/27/2020] [Indexed: 12/26/2022]
Abstract
It is now evident that transcriptional gene regulation usually requires the re-organization of chromatin architecture. Increasing evidence suggested various kinds of RNAs are involved in this process. Especially the nascent RNAs retained at their site of transcription can serve as a scaffold for organizing transcriptionally either favorable or unfavorable chromatin structures. An emerging concept of phase separation explains how these chromatin structures can be maintained as physically discrete subcompartments within membrane-less nucleoplasm. Evidences that support the crucial role of nascent RNAs in the formation of phase-separated condensates are now rapidly growing.
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150
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Guh CY, Hsieh YH, Chu HP. Functions and properties of nuclear lncRNAs-from systematically mapping the interactomes of lncRNAs. J Biomed Sci 2020; 27:44. [PMID: 32183863 PMCID: PMC7079490 DOI: 10.1186/s12929-020-00640-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 03/06/2020] [Indexed: 02/07/2023] Open
Abstract
Protein and DNA have been considered as the major components of chromatin. But beyond that, an increasing number of studies show that RNA occupies a large amount of chromatin and acts as a regulator of nuclear architecture. A significant fraction of long non-coding RNAs (lncRNAs) prefers to stay in the nucleus and cooperate with protein complexes to modulate epigenetic regulation, phase separation, compartment formation, and nuclear organization. An RNA strand also can invade into double-stranded DNA to form RNA:DNA hybrids (R-loops) in living cells, contributing to the regulation of gene expression and genomic instability. In this review, we discuss how nuclear lncRNAs orchestrate cellular processes through their interactions with proteins and DNA and summarize the recent genome-wide techniques to study the functions of lncRNAs by revealing their interactomes in vivo.
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Affiliation(s)
- Chia-Yu Guh
- Institute of Molecular and Cellular Biology, National Taiwan University, No. 1 Sec. 4 Roosevelt Road, Taipei, Taiwan, Republic of China
| | - Yu-Hung Hsieh
- Institute of Molecular and Cellular Biology, National Taiwan University, No. 1 Sec. 4 Roosevelt Road, Taipei, Taiwan, Republic of China
| | - Hsueh-Ping Chu
- Institute of Molecular and Cellular Biology, National Taiwan University, No. 1 Sec. 4 Roosevelt Road, Taipei, Taiwan, Republic of China.
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