Human stem cell and mouse transchromosomic (hsa11) embryonic stem cell (with and without ectopic ZNF91 expression) ChIP-seq

We compared the binding patterns in embryonic stem cells of KAP1 and KRAB Zinc Finger (KZNF) proteins as well as H3K4me3 DNA under several conditions. Native human stem cells. Mouse stem cells containing a transchromosomic copy of human chromosome 11, with and without the introduction of plasmids containing KRAB Zinc Finger sequences. We show that certain KZNFs are responsible for the repression of certain retrotransposons in embryonic stem cells, preventing their spread across the genome. ChIP-seq of HESCs and mouse TC11 ESCs with ZNF91 plasmids and with empty vector plasmids. ChIP of KAP1, ZNF486, H3K4me3. At least 2 replicates of each condition.本研究对比了多种实验条件下，胚胎干细胞（embryonic stem cells）中KAP1、KRAB锌指（KRAB Zinc Finger, KZNF）蛋白以及H3K4me3 DNA的结合模式。实验样本涵盖天然人类干细胞，以及携带人类11号染色体转染色体拷贝的小鼠干细胞，后者分别设置导入含KRAB锌指序列质粒与未导入质粒的两组。本研究证实，部分KZNF可介导胚胎干细胞内特定逆转录转座子的基因沉默，阻止其在基因组内扩散。实验方法包括：对转染ZNF91质粒与空载体质粒的人类胚胎干细胞（Human Embryonic Stem Cells, HESCs）及转染色体11小鼠胚胎干细胞（mouse TC11 ESCs）开展染色质免疫共沉淀测序（Chromatin Immunoprecipitation sequencing, ChIP-seq）；对KAP1、ZNF486、H3K4me3进行染色质免疫共沉淀（Chromatin Immunoprecipitation, ChIP）；所有实验条件均至少设置2次生物学重复。