The divergent role of two PRDM1 isoforms during human naïve pluripotency reprogramming [CUT&Tag]

Induced pluripotent stem cells (iPSCs) technology offers great promise for scientific research and clinical applications. iPSCs can be generated from various cell types through different strategies. Two different pluripotent states, naive and primed, can be captured in vitro, corresponding to the pre- and post-implantation stages of in vivo development, respectively, with naive pluripotency being considered to possess better developmental potential. We can obtain naïve iPSCs and primed iPSCs through somatic cell reprogramming. Despite well-characterized transcriptional and epigenetic changes, the dynamic of the chromatin landscape during naïve and primed iPSC reprogramming is poorly understood, especially in humans. In this study, we applied ATAC-seq and RNA-seq to delineate the chromatin landscape in the human secondary reprogramming system towards naive and primed pluripotency. We identified several transcription factors and epigenetic factors which were crucial to reprogramming chromatin remodeling. We found that two isoforms of the same gene PRDM1, PRDM1alpha and PRDM1beta, targeted different genomic loci to function in divergent roles during naive reprogramming. We proposed a cross-regulation model of PRDM1alpha and PRDM1beta function. Together, this research highlights the diversity of the transcription factors in determining the chromatin landscape dynamics and regulating pluripotent cell fates. We examined the genomic binding sites of PRDM1alpha and PRDM1beta proteins on day 10 of reprogramming using CUT&Tag technology.

诱导多能干细胞（induced pluripotent stem cells, iPSCs）技术为科学研究与临床应用带来了巨大前景。iPSCs可通过不同策略从多种细胞类型中诱导生成。体外可捕获两种不同的多能状态：初始态（naive）与始发态（primed），二者分别对应体内发育的植入前和植入后阶段，其中初始态多能性被认为具备更优异的发育潜能。我们可通过体细胞重编程获取初始态iPSCs与始发态iPSCs。尽管目前对二者的转录与表观遗传变化已有较为充分的表征，但初始态与始发态iPSCs重编程过程中染色质调控景观的动态变化机制仍有待阐明，在人类样本中这一问题尤为突出。本研究中，我们利用ATAC-seq与RNA-seq技术，解析了人类次级重编程系统向初始态与始发态多能性转化过程中的染色质调控景观。我们鉴定出了多个对染色质重塑重编程至关重要的转录因子与表观遗传调控因子。研究发现，同一基因PRDM1的两种同工型——PRDM1alpha与PRDM1beta，可通过靶向不同基因组位点，在初始态重编程过程中发挥截然不同的功能。我们提出了PRDM1alpha与PRDM1beta功能的交叉调控模型。综上，本研究凸显了转录因子在调控染色质动态景观与决定多能细胞命运过程中的多样性。我们利用CUT&Tag技术，在重编程第10天时检测了PRDM1alpha与PRDM1beta蛋白的基因组结合位点。