LncRNA/DNA binding analysis reveals losses and gains and lineage specificity of genomic imprinting in mammals

• DOI: 10.1093/bioinformatics/btw818
• Publication Date: 2016-12-20T20:06:34Z
• Authors: Haihua Liu; Xiaoxiao Shang; Hao Zhu
• Keywords: Mammals; 0301 basic medicine; 0303 health sciences; Binding Sites; Computational Biology; DNA; Genomic Imprinting; Mice; 03 medical and health sciences; Animals; Humans; RNA, Long Noncoding; Promoter Regions, Genetic; Software

Abstract

Motivation Genomic imprinting is regulated by lncRNAs and is important for embryogenesis, physiology and behaviour in mammals. Aberrant imprinting causes diseases and disorders. Experimental studies have examined genomic imprinting primarily in humans and mice, thus leaving some fundamental issues poorly addressed. The cost of experimentally examining imprinted genes in many tissues in diverse species makes computational analysis of lncRNAs’ DNA binding sites valuable.

Results We performed lncRNA/DNA binding analysis in imprinting clusters from multiple mammalian clades and discovered the following: (i) lncRNAs and imprinting sites show significant losses and gains and distinct lineage-specificity; (ii) binding of lncRNAs to promoters of imprinted genes may occur widely throughout the genome; (iii) a considerable number of imprinting sites occur in only evolutionarily more derived species; and (iv) multiple lncRNAs may bind to the same imprinting sites, and some lncRNAs have multiple DNA binding motifs. These results suggest that the occurrence of abundant lncRNAs in mammalian genomes makes genomic imprinting a mechanism of adaptive evolution at the epigenome level.

Availability and Implementation The data and program are available at the database LongMan at lncRNA.smu.edu.cn.

Supplementary information Supplementary data are available at Bioinformatics online.