Kuo, Chao-Chung ORCID: 0000-0001-8879-4754, Haenzelmann, Sonja, Cetin, Nevcin Sentuerk, Frank, Stefan, Zajzon, Barna, Derks, Jens-Peter, Akhade, Vijay Suresh, Ahuja, Gaurav ORCID: 0000-0002-2837-9361, Kanduri, Chandrasekhar, Grummt, Ingrid, Kurian, Leo ORCID: 0000-0001-7466-5169 and Costa, Ivan G. ORCID: 0000-0003-2890-8697 (2019). Detection of RNA-DNA binding sites in long noncoding RNAs. Nucleic Acids Res., 47 (6). OXFORD: OXFORD UNIV PRESS. ISSN 1362-4962

Full text not available from this repository.

Abstract

Long non-coding RNAs (lncRNAs) can act as scaffolds that promote the interaction of proteins, RNA, and DNA. There is increasing evidence of sequence-specific interactions of lncRNAs with DNA via triple-helix (triplex) formation. This process allows lncRNAs to recruit protein complexes to specific genomic regions and regulate gene expression. Here we propose a computational method called Triplex Domain Finder (TDF) to detect triplexes and characterize DNA-binding domains and DNA targets statistically. Case studies showed that this approach can detect the known domains of lncRNAs Fendrr, HOTAIR and MEG3. Moreover, we validated a novel DNA-binding domain in MEG3 by a genome-wide sequencing method. We used TDF to perform a systematic analysis of the triplex-forming potential of lncRNAs relevant to human cardiac differentiation. We demonstrated that the lncRNA with the highest triplex-forming potential, GATA6-AS, forms triple helices in the promoter of genes relevant to cardiac development. Moreover, down-regulation of GATA6-AS impairs GATA6 expression and cardiac development. These data indicate the unique ability of our computational tool to identify novel triplex-forming lncRNAs and their target genes.

Item Type: Journal Article
Creators:
CreatorsEmailORCIDORCID Put Code
Kuo, Chao-ChungUNSPECIFIEDorcid.org/0000-0001-8879-4754UNSPECIFIED
Haenzelmann, SonjaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Cetin, Nevcin SentuerkUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Frank, StefanUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Zajzon, BarnaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Derks, Jens-PeterUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Akhade, Vijay SureshUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Ahuja, GauravUNSPECIFIEDorcid.org/0000-0002-2837-9361UNSPECIFIED
Kanduri, ChandrasekharUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Grummt, IngridUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Kurian, LeoUNSPECIFIEDorcid.org/0000-0001-7466-5169UNSPECIFIED
Costa, Ivan G.UNSPECIFIEDorcid.org/0000-0003-2890-8697UNSPECIFIED
URN: urn:nbn:de:hbz:38-150880
DOI: 10.1093/nar/gkz037
Journal or Publication Title: Nucleic Acids Res.
Volume: 47
Number: 6
Date: 2019
Publisher: OXFORD UNIV PRESS
Place of Publication: OXFORD
ISSN: 1362-4962
Language: English
Faculty: Unspecified
Divisions: Unspecified
Subjects: no entry
Uncontrolled Keywords:
KeywordsLanguage
PRINCIPLES; ELEMENTSMultiple languages
Biochemistry & Molecular BiologyMultiple languages
Refereed: Yes
URI: http://kups.ub.uni-koeln.de/id/eprint/15088

Downloads

Downloads per month over past year

Altmetric

Export

Actions (login required)

View Item View Item