RT Journal Article
SR Electronic
T1 Systematic identification of cis-interacting lncRNAs and their targets
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.01.13.426305
DO 10.1101/2021.01.13.426305
A1 Saumya Agrawal
A1 Ivan V. Kulakovskiy
A1 Jessica Severin
A1 Masaru Koido
A1 Tanvir Alam
A1 Imad Abugessaisa
A1 Andrey Buyan
A1 Howard Y. Chang
A1 Josee Dostie
A1 Masayoshi Itoh
A1 Juha Kere
A1 Naoto Kondo
A1 Yunjing Li
A1 Vsevolod J. Makeev
A1 Mickaël Mendez
A1 Yasushi Okazaki
A1 Jordan A. Ramilowski
A1 Andrey I. Sigorskikh
A1 Lisa J. Strug
A1 Ken Yagi
A1 Kayoko Yasuzawa
A1 Chi Wai Yip
A1 Chung Chau Hon
A1 Michael M. Hoffman
A1 Chikashi Terao
A1 Takeya Kasukawa
A1 Jay W. Shin
A1 Piero Carninci
A1 Michiel JL de Hoon
YR 2022
UL http://biorxiv.org/content/early/2022/07/12/2021.01.13.426305.abstract
AB 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. Studying lncRNAs is challenging due to their low expression level, cell type-specific occurrence, poor sequence conservation between orthologs, and lack of information about RNA domains. LncRNAs direct the regulatory factors in the locations that are in cis to their transcription sites. We designed a model to predict if an lncRNA acts in cis based on its features and trained it using RNA-chromatin interaction data. The trained model is cell type-independent and does not require RNA-chromatin data. Combining RNA-chromatin and Hi-C data, we showed that lncRNA-chromatin binding sites are determined by chromosome conformation. For each lncRNA, the spatially proximal genes were identified as their potential targets by combining Hi-C and Cap Analysis Gene Expression (CAGE) data in 18 human cell types. RNA-protein and RNA-chromatin interaction data suggested that lncRNAs act as scaffolds to recruit regulatory proteins to target promoters and enhancers. We provide the data through an interactive visualization web portal at https://fantom.gsc.riken.jp/zenbu/reports/#F6_3D_lncRNA.Competing Interest StatementThe authors have declared no competing interest.