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- Title
Annotation of nuclear lncRNAs based on chromatin interactions.
- Authors
Agrawal, Saumya; Buyan, Andrey; Severin, Jessica; Koido, Masaru; Alam, Tanvir; Abugessaisa, Imad; Chang, Howard Y.; Dostie, Josée; Itoh, Masayoshi; Kere, Juha; Kondo, Naoto; Li, Yunjing; Makeev, Vsevolod J.; Mendez, Mickaël; Okazaki, Yasushi; Ramilowski, Jordan A.; Sigorskikh, Andrey I.; Strug, Lisa J.; Yagi, Ken; Yasuzawa, Kayoko
- 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.
- Subjects
RNA-protein interactions; LINCRNA; CHROMATIN; GENE enhancers; WEB portals; HUMAN genome
- Publication
PLoS ONE, 2024, Vol 19, Issue 5, p1
- ISSN
1932-6203
- Publication type
Article
- DOI
10.1371/journal.pone.0295971