scholarly journals Genome-Wide Analysis of the Association of Transposable Elements with Gene Regulation Suggests that Alu Elements Have the Largest Overall Regulatory Impact

2018 ◽  
Vol 25 (6) ◽  
pp. 551-562 ◽  
Author(s):  
Lu Zeng ◽  
Stephen M. Pederson ◽  
Danfeng Cao ◽  
Zhipeng Qu ◽  
Zhiqiang Hu ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Transposable Elements ◽  
Alu Elements ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Regulatory Impact

scholarly journals Genome-wide analysis of the association of transposable elements with gene regulation suggests that Alu elements have the largest overall regulatory impact

2017 ◽  
Author(s):  
Lu Zeng ◽  
Stephen M. Pederson ◽  
Danfeng Cao ◽  
Zhipeng Qu ◽  
Zhiqiang Hu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Transposable Elements ◽  
Regulatory Sequences ◽  
Alu Elements ◽  
Genome Wide ◽  
A Genome ◽  
Regulatory Impact ◽  
Species Specific ◽  
Regulated Gene Expression

ABSTRACTNearly half of the human genome is made up of transposable elements (TEs) and there is evidence that TEs are involved in gene regulation. Here, we have integrated publicly available genomic, epigenetic and transcriptomic data to investigate this in a genome-wide manner. A bootstrapping statistical method was applied to minimize the confounder effects from different repeat types. Our results show that although most TE classes are primarily associated with reduced gene expression, Alu elements are associated with up regulated gene expression. Furthermore, Alu elements had the highest probability of any TE class of contributing to regulatory regions of any type defined by chromatin state. This suggests a general model where clade specific SINEs may contribute more to gene regulation than ancient/ancestral TEs. Finally, non-coding regions were found to have a high probability of TE content within regulatory sequences, most notably in repressors. Our exhaustive analysis has extended and updated our understanding of TEs in terms of their global impact on gene regulation, and suggests that the most recently derived types of TEs, i.e. clade or species specific SINES, have the greatest overall impact on gene regulation.

scholarly journals Genome-wide analysis of enhancer RNA in gene regulation across 12 mouse tissues

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Jen-Hao Cheng ◽  
David Zhi-Chao Pan ◽  
Zing Tsung-Yeh Tsai ◽  
Huai-Kuang Tsai
Keyword(s):  
Gene Regulation ◽  
Genome Wide Analysis ◽  
Enhancer Rna ◽  
Genome Wide ◽  
Mouse Tissues

scholarly journals Genome-wide analysis of transposable elements and tandem repeats in the compact placozoan genome

2010 ◽  
Vol 5 (1) ◽  
pp. 18 ◽  
Author(s):  
Shi Wang ◽  
Lingling Zhang ◽  
Eli Meyer ◽  
Zhenmin Bao
Keyword(s):  
Transposable Elements ◽  
Tandem Repeats ◽  
Genome Wide Analysis ◽  
Genome Wide

Genome-Wide Analysis of MuDR-Related Transposable Elements Insertion Population in Maize

2011 ◽  
Vol 37 (5) ◽  
pp. 772-777
Author(s):  
Jing FENG ◽  
Xue-Qian FU ◽  
Ting-Ting WANG ◽  
Yong-Sheng TAO ◽  
You-Jun GAO ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Genome Wide Analysis ◽  
Genome Wide
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