학술논문
Annotation of nuclear lncRNAs based on chromatin interactions.
Document Type
Academic Journal
Author
Agrawal S; RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.; Buyan A; Autosome.org, Russia.; FANTOM Consortium, Dolgoprudny, Russia.; Severin J; RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.; Koido M; RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.; Institute of Medical Science, The University of Tokyo, Tokyo, Japan.; Alam T; College of Science and Engineering, Hamad Bin Khalifa University, Doha, Qatar.; Abugessaisa I; RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.; Chang HY; Center for Personal Dynamic Regulome, Stanford University, Stanford, California, United States of America.; Dostie J; Department of Biochemistry, Rosalind and Morris Goodman Cancer Research Center, McGill University, Montréal, Québec, Canada.; Itoh M; RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.; RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Japan.; Kere J; Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.; Stem Cells and Metabolism Research Program, University of Helsinki and Folkhälsan Research Center, Helsinki, Finland.; Kondo N; RIKEN Center for Life Science Technologies, Yokohama, Japan.; Li Y; Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada.; Makeev VJ; FANTOM Consortium, Dolgoprudny, Russia.; Mendez M; Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.; Okazaki Y; RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.; Ramilowski JA; RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.; Advanced Medical Research Center, Yokohama City University, Yokohama, Japan.; Sigorskikh AI; FANTOM Consortium, Dolgoprudny, Russia.; Strug LJ; Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada.; Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.; Department of Statistical Sciences, University of Toronto, Ontario, Canada.; The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.; Yagi K; RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.; Yasuzawa K; RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.; Yip CW; RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.; Hon CC; RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.; Hoffman MM; Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.; Princess Margaret Cancer Centre, Toronto, Ontario, Canada.; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.; Vector Institute, Toronto, Ontario, Canada.; Terao C; RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.; Kulakovskiy IV; Autosome.org, Russia.; FANTOM Consortium, Dolgoprudny, Russia.; Kasukawa T; RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.; Shin JW; RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.; Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (ASTAR), Singapore, Republic of Singapore.; Carninci P; RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.; Human Technopole, Milan, Italy.; de Hoon MJL; RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
Source
Publisher: Public Library of Science Country of Publication: United States NLM ID: 101285081 Publication Model: eCollection Cited Medium: Internet ISSN: 1932-6203 (Electronic) Linking ISSN: 19326203 NLM ISO Abbreviation: PLoS One Subsets: MEDLINE
Subject
Language
English
Abstract
The human genome is pervasively transcribed and produces a wide variety of long non-coding RNAs (lncRNAs), constituting the majority of transcripts across human cell types. Some specific nuclear lncRNAs have been shown to be important regulatory components acting locally. As RNA-chromatin interaction and Hi-C chromatin conformation data showed that chromatin interactions of nuclear lncRNAs are determined by the local chromatin 3D conformation, we used Hi-C data to identify potential target genes of lncRNAs. RNA-protein interaction data suggested that nuclear lncRNAs act as scaffolds to recruit regulatory proteins to target promoters and enhancers. Nuclear lncRNAs may therefore play a role in directing regulatory factors to locations spatially close to the lncRNA gene. We provide the analysis results through an interactive visualization web portal at https://fantom.gsc.riken.jp/zenbu/reports/#F6_3D_lncRNA.
Competing Interests: The authors have declared that no competing interests exist.
(Copyright: © 2024 Agrawal et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
Competing Interests: The authors have declared that no competing interests exist.
(Copyright: © 2024 Agrawal et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)