A CRISPR Knockout Screen Identifies Retroelement Silencing Factors in Embryonic Stem Cells

In mouse embryonic stem cells (mESCs), expression of provirus and endogenous retroelements is epigenetically repressed. Although many cellular factors involved in the silencing processes have been identified, the complete molecular mechanism remains elusive. In this study, we performed a genome-wide CRISPR screen to advance our understanding of retroelement silencing in mESCs. We identified more than 80 genes involved in retroelement silencing. In particular, the BAF and HUSH complex components are linked with the repression of most of the Setdb1 targets. We characterized two factors, namely Morc2a and Dres1, which have not hitherto been implicated in retroelement silencing. Although both factors are recruited to repress provirus, their roles in repression are different. Morc2a seems to function downstream repressive epigenetic modifications. Dres1 regulates repressive epigenetic modifications associated with Setdb1. Our genome-wide CRISPR screen cataloged genes of factors, which function at different levels in retroelement silencing and provides a useful resource for further molecular studies.在小鼠胚胎干细胞（mouse embryonic stem cells, mESCs）中，前病毒与内源性反转录元件的表达受到表观遗传沉默调控。尽管目前已鉴定出诸多参与该沉默过程的细胞因子，但其完整的分子机制仍未阐明。本研究通过全基因组CRISPR筛选，加深了我们对mESCs中反转录元件沉默过程的理解。我们鉴定出80余个参与反转录元件沉默的基因，其中BAF复合物与HUSH复合物的组分与大多数Setdb1靶位点的沉默调控密切相关。我们对两个此前未被报道参与反转录元件沉默的因子——Morc2a与Dres1进行了功能表征：二者虽均被招募至前病毒位点以发挥沉默功能，但各自的作用模式存在差异。Morc2a似乎在抑制性表观遗传修饰的下游发挥功能，而Dres1则调控与Setdb1相关的抑制性表观遗传修饰。本研究的全基因组CRISPR筛选编目了在反转录元件沉默过程中发挥不同层级功能的因子编码基因，为后续的分子机制研究提供了宝贵的资源。