Associating divergent lncRNAs with target genes by integrating genome sequence, gene expression and chromatin accessibility data.

ABSTRACT: Recent RNA knockdown experiments revealed that a dozen divergent long noncoding RNAs (lncRNAs) positively regulate the transcription of genes in cis. Here, to understand the regulatory mechanism of divergent lncRNAs, we proposed a computational model IRDL (Identify the Regulatory Divergent LncRNAs) to associate divergent lncRNAs with target genes. IRDL took advantage of the cross-tissue paired expression and chromatin accessibility data in ENCODE and a dozen experimentally validated divergent lncRNA target genes. IRDL integrated sequence similarity, co-expression and co-accessibility features, battled the scarcity of gold standard datasets with an increasingly learning framework and identified 446 and 977 divergent lncRNA-gene regulatory associations for mouse a

SUBMITTER: Wang Y 

PROVIDER: S-EPMC7671357 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature