TET activity propagates transcriptional memory through embryonic dormancy [CUT&TAG]

Dormancy is an essential biological process for the propagation of many life forms through generations and stressful conditions. Early embryos of many mammals are preservable for weeks to months within the uterus under dormancy, which can be induced in vitro through mTOR inhibition. Dormancy features silencing of the genome and abundant heterochromatin formation, which conflicts with the permissive and uncommitted genomic profile of pluripotent cells. Cellular strategies to maintain pluripotency in the fate of this conflict are not known. Here we probed chromatin regulation during embryonic stem cells’ (ESC) entry into dormancy to identify mechanisms that ensure nsure faithful propagation of cellular identity through dormancy. We show a global increase in DNA methylation and loss of chromatin accessibility in dormant ESCs and find that TET DNA demethylases are essential to counteract this trend at key pluripotency regulatory elements. Perturbation of TET activity compromises transcriptional programs and embryo survival through dormancy; whereas its enhancement improves survival rates. We propose that key regulatory elements are bookmarked coordinately by TETs and transcription factors in dormancy for maintenance of cellular identity. Our results reveal the first essential chromatin regulator in establishing mammalian dormancy and paves the way to building its temporal regulatory code in embryonic and adult tissues. Either wild-type or TET1/2 double-knock out embryonic stem were cultured with or without mTOR inhibition using Ink128

休眠（dormancy）是诸多生命实现跨代繁衍并耐受胁迫环境的核心生物学过程。诸多哺乳动物的早期胚胎可在休眠状态下于子宫内存活数周至数月，该休眠状态可通过体外抑制雷帕霉素靶蛋白（mTOR）诱导产生。休眠状态以基因组沉默与大量异染色质形成为特征，这与多能干细胞（pluripotent cells）开放且未定型的基因组特征相悖。目前学界尚未明确细胞在该冲突背景下维持多能性的具体策略。本研究通过探究胚胎干细胞（embryonic stem cells, ESC）进入休眠状态过程中的染色质调控机制，旨在明确可确保细胞身份在休眠过程中得以忠实传递的分子通路。我们发现，休眠状态下的ESC整体DNA甲基化水平升高，染色质开放度降低；同时发现TET DNA去甲基化酶（TET DNA demethylases）可在关键多能性调控元件处抵消这一变化，发挥核心调控作用。干扰TET活性会破坏转录程序，降低胚胎通过休眠状态存活的概率；而增强TET活性则可提升胚胎存活率。我们提出，休眠状态下关键调控元件可由TET家族与转录因子协同标记，从而维持细胞身份的稳定性。本研究首次明确了调控哺乳动物休眠建立的核心染色质调控因子，同时为解析胚胎与成体组织中休眠的时序调控密码奠定了基础。本研究使用Ink128试剂，对野生型及TET1/2双敲除胚胎干细胞分别开展有无mTOR抑制的培养实验。