Zeng Lu, Pederson Stephen M, Cao Danfeng, Qu Zhipeng, Hu Zhiqiang, Adelson David L, Wei Chaochun
1 School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , Shanghai, China .
2 School of Biological Sciences, The University of Adelaide , Adelaide, Australia .
J Comput Biol. 2018 Jun;25(6):551-562. doi: 10.1089/cmb.2017.0228. Epub 2018 Apr 30.
Nearly half of the human genome is made up of transposable elements (TEs), and there is evidence that TEs are involved in gene regulation. In this study, 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 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 upregulated gene expression. Furthermore, Alu elements had the highest probability of any TE class contributing to regulatory regions of any type defined by chromatin state. This suggests a general model where clade-specific short interspersed elements (SINEs) may contribute more to gene regulation than ancient/ancestral TEs. 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, that is, clade- or species-specific SINES, have the greatest overall impact on gene regulation.
近一半的人类基因组由转座元件（TEs）组成，并且有证据表明转座元件参与基因调控。在本研究中，我们整合了公开可用的基因组、表观基因组和转录组数据，以全基因组方式对此进行研究。应用了一种自展统计方法，以尽量减少不同重复类型的混杂效应。我们的结果表明，尽管大多数TE类别主要与基因表达降低相关，但Alu元件与基因表达上调相关。此外，在所有TE类别中，Alu元件对由染色质状态定义的任何类型调控区域的贡献概率最高。这表明了一个通用模型，即进化枝特异性短散在元件（SINEs）可能比古老/祖先转座元件对基因调控的贡献更大。我们的详尽分析扩展并更新了我们对转座元件在基因调控方面全球影响的理解，并表明转座元件中最新衍生的类型，即进化枝或物种特异性SINEs，对基因调控的总体影响最大。
