Annotation of nuclear lncRNAs based on chromatin interactions.
Saumya AgrawalAndrey BuyanJessica SeverinMasaru KoidoTanvir AlamImad AbugessaisaHoward Y ChangJosée DostieMasayoshi ItohJuha KereNaoto KondoYunjing LiVsevolod J MakeevMickaël MendezYasushi OkazakiJordan A RamilowskiAndrey I SigorskikhLisa J StrugKen YagiKayoko YasuzawaChi Wai YipChung Chau HonMichael M HoffmanChikashi C TeraoIvan V KulakovskiyTakeya KasukawaJay W ShinPiero CarninciMichiel J L de HoonPublished in: PloS one (2024)
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.
Keyphrases
- genome wide identification
- transcription factor
- genome wide
- genome wide analysis
- long non coding rna
- dna damage
- gene expression
- network analysis
- endothelial cells
- electronic health record
- big data
- dna methylation
- emergency department
- long noncoding rna
- molecular dynamics simulations
- copy number
- oxidative stress
- data analysis
- crystal structure
- amino acid
- nucleic acid