讲座 - Transposable elements, non-coding RNAs and epigenetic control in embryonic stem cells

Dr. Andrew Paul Hutchins
Department of Biology
Southern University of Science and Technology, Shenzhen, China

Every cell contains all of the DNA to encode the plethora of cell types that make up the cells and tissues of the organism. Yet, the vast majority of this DNA is devoted not to genes, but to transposable elements (TEs) and other repetitive sequences. It is increasingly clear that TEs are involved in a wide range of biological processes, from gene regulation, enhancer formation, splicing and the evolution of novel gene regulation networks. In this presentation Dr. Hutchins will describe their efforts to understand the epigenetic control of TEs. Dr. Hutchins’ group find that TEs harbor complex patterns of both activatory and inhibitory epigenetic marks, and much of the epigenetic regulation system is involved in managing TEs. Additionally, Dr. Hutchins will also describe the contribution of TEs to non-coding RNAs. They find that nearly 80% of coding transcripts have a non-coding variant transcript, and that these non-coding variants are loaded with TEs. They have preliminary data that these non-coding variants are critical regulators of the coding transcripts. These observations have important consequences for understanding genomic regulation and non-coding control.

“聪明绝顶”的科研男，现在在南方科技大学当PI，是Dr，那应该还没拿到profess，Google一下便查到其Google scholar。

这次讲座他主要讲了2015年的一篇review，Transposable elements at the center of the crossroads between embryogenesis, embryonic stem cells, reprogramming, and long non-coding RNAs

TE其实是一个生信领域的红人，实验方向的人似乎对它没有太大兴趣。然后这篇review主要阐述了TE在胚胎发育、重编程和非编码RNA（还有epigenetic，也就是转录因子调节）方面发挥了重要作用。

顺便科普一下TE - transposable element

wiki一下，中文翻译为转座因子，顾名思义就是在基因组上可以自由移动的DNA序列，在植物基因组研究得很火，对遗传变异和基因组大小影响很大。

转座因子的发现居然是一个诺贝尔奖，Barbara McClintock's discovery of them earned her a Nobel Prize in 1983. （玉米maize中发现的）

在严建兵的最新的玉米NG中，第一部分注释就是研究TE， We identified ~90% of the genome as transposable-element sequences。

Genome assembly of a tropical maize inbred line provides insights into structural variation and crop improvement

看最开始的那篇综述，里面的科普看着不错。

we can estimate that the human genome consists of approximately 51 % unannotated DNA, 4 % protein-coding genes and other regulatory RNAs, and nearly 40 % of the genome consists of TEs

TEs can be classified into four major categories:
DNA transposons and three classes of retrotransposon:

• long terminal repeat (LTR) containing endogenous retroviruses,
• long interspersed nuclear elements (LINEs)
• short interspersed nuclear elements (SINEs)

最终结论就是：The expanding links between TEs, lncRNAs, epigenetics, and embryogenesis

想了解更多可以Google：human Transposable elements