RT Journal Article
SR Electronic
T1 Genome-wide analysis of repetitive elements associated with gene regulation Repetitive elements and gene regulation
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 142018
DO 10.1101/142018
A1 Lu Zeng
A1 Stephen M. Pederson
A1 Danfeng Cao
A1 Zhipeng Qu
A1 Zhiqiang Hu
A1 David L. Adelson
A1 Chaochun Wei
YR 2017
UL http://biorxiv.org/content/early/2017/05/25/142018.abstract
AB Nearly half of the human genome is made up of transposable elements (TEs) and evidence supports a possible role for TEs in gene regulation. Here, we have integrated publicly available genomic, epigenetic and transcriptomic data to investigate this potential function in a genome-wide manner. Results show that although most TE classes are primarily involved in reduced gene expression, Alu elements are associated with up regulated gene expression. This is consistent with our previously published work which showed that intronic Alu elements are capable of generating alternative splice variants in protein-coding genes, and further illustrates how Alu elements can alter protein function or gene expression level. Furthermore, non-coding regions were found to have a great density of TEs within regulatory sequences, most notably in repressors. Our exhaustive analysis of recent datasets has extended and updated our understanding of TEs in terms of their global impact on gene regulation, and indicates a significant association between repetitive elements and gene regulation.