Deciphering the complexity of human non-coding promoter-proximal transcriptome.

Details

Serval ID
serval:BIB_3084C6B239C8
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Deciphering the complexity of human non-coding promoter-proximal transcriptome.
Journal
Bioinformatics
Author(s)
Mapelli S.N., Napoli S., Pisignano G., Garcia-Escudero R., Carbone G.M., Catapano C.V.
ISSN
1367-4811 (Electronic)
ISSN-L
1367-4803
Publication state
Published
Issued date
01/08/2019
Peer-reviewed
Oui
Volume
35
Number
15
Pages
2529-2534
Language
english
Notes
Publication types: Journal Article ; Research Support, Non-U.S. Gov't
Publication Status: ppublish
Abstract
Long non-coding RNAs (lncRNAs) have gained increasing relevance in epigenetic regulation and nuclear functional organization. High-throughput sequencing approaches have revealed frequent non-coding transcription in promoter-proximal regions. However, a comprehensive catalogue of promoter-associated RNAs (paRNAs) and an analysis of the possible interactions with neighboring genes and genomic regulatory elements are missing.
Integrating data from multiple cell types and experimental platforms we identified thousands of paRNAs in the human genome. paRNAs are transcribed in both sense and antisense orientation, are mostly non-polyadenylated and retained in the cell nucleus. Transcriptional regulators, epigenetic effectors and activating chromatin marks are enriched in paRNA-positive promoters. Furthermore, paRNA-positive promoters exhibit chromatin signatures of both active promoters and enhancers. Promoters with paRNAs reside preferentially at chromatin loop boundaries, suggesting an involvement in anchor site recognition and chromatin looping. Importantly, these features are independent of the transcriptional state of neighboring genes. Thus, paRNAs may act as cis-regulatory modules with an impact on local recruitment of transcription factors, epigenetic state and chromatin loop organization. This study provides a comprehensive analysis of the promoter-proximal transcriptome and offers novel insights into the roles of paRNAs in epigenetic processes and human diseases.
Genomic coordinates of predicted paRNAs are available at https://figshare.com: https://doi.org/10.6084/m9.figshare.7392791.v1 and https://doi.org/10.6084/m9.figshare.4856630.v2.
Supplementary data are available at Bioinformatics online.
Keywords
Chromatin, Epigenesis, Genetic, Humans, Promoter Regions, Genetic, RNA, Long Noncoding/genetics, Transcriptome
Pubmed
Web of science
Open Access
Yes
Create date
05/01/2019 16:52
Last modification date
07/07/2020 6:20
Usage data