Annotation of nuclear lncRNAs based on chromatin interactions

Annotation of nuclear lncRNAs based on chromatin interactions

<p dir="ltr">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...

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Main Author: Saumya Agrawal (3441386) (author)
Other Authors: Andrey Buyan (18510102) (author), Jessica Severin (178475) (author), Masaru Koido (14059995) (author), Tanvir Alam (638619) (author), Imad Abugessaisa (627440) (author), Howard Y. Chang (215450) (author), Josée Dostie (262897) (author), Masayoshi Itoh (15728) (author), Juha Kere (11900) (author), Naoto Kondo (32868) (author), Yunjing Li (644191) (author), Vsevolod J. Makeev (7592954) (author), Mickaël Mendez (3864016) (author), Yasushi Okazaki (3100) (author), Jordan A. Ramilowski (2259964) (author), Andrey I. Sigorskikh (18510105) (author), Lisa J. Strug (8293947) (author), Ken Yagi (246069) (author), Kayoko Yasuzawa (18510108) (author), Chi Wai Yip (15068455) (author), Chung Chau Hon (4520500) (author), Michael M. Hoffman (5846618) (author), Chikashi Terao (137128) (author), Ivan V. Kulakovskiy (7592957) (author), Takeya Kasukawa (3041) (author), Jay W. Shin (9030986) (author), Piero Carninci (3015) (author), Michiel J. L. de Hoon (11434447) (author)
Published: 2024
Subjects:
Biological sciences
Genetics
Human Genome
Long Non-Coding RNAs (lncRNAs)
RNA-Chromatin Interaction
Hi-C Chromatin Conformation
Chromatin 3D
Conformation Gene Regulation
RNA-Protein Interactions
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Summary:<p dir="ltr">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.</p><h2>Other Information</h2><p dir="ltr">Published in: PLOS ONE<br>License: <a href="http://creativecommons.org/licenses/by/4.0/" target="_blank">http://creativecommons.org/licenses/by/4.0/</a><br>See article on publisher's website: <a href="https://dx.doi.org/10.1371/journal.pone.0295971" target="_blank">https://dx.doi.org/10.1371/journal.pone.0295971</a></p>

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