The Functional Roles And Molecular Mechanisms Of Klf5 Adjacent Super Enhancer In Mouse Embryonic Stem Cells

Embryonic Stem Cells(ESCs)are separated from the inner cell mass cells in the blastocyst stage and cultured in vitro under appropriate conditions.ESCs has unlimited self-renewal ability and the potential to differentiate into three embryonic germ layers,and is widely used in the research of embryonic development,cell therapy,tissue repair and regeneration.Recent studies have shown that Super Enhancer(SE),as a cell typespecific large cis-regulatory element,plays a key role in regulating the pluripotency and self-renewal of ESCs,and it suggests that we can use SE as a new entry point for studying the molecular regulation mechanism of ESCs.In this study,through the analysis of mouse embryonic stem cell(m ESCs)H3K27ac chromatin immunoprecipitation sequencing(CHIP-seq)data,334 SEs were identified,and the number one SE was selected for research.In the same topologically associated domain(TAD)as SE,there is a gene that plays an important role in ESCs-Klf5.Therefore,we named this SE Klf5 adjacent super enhancer(K5aSE).First,we used CRISPR-Cas9 technology to knock out K5 a SE and found that compared with WT(Wild type)cells,the loss of K5 a SE significantly affected the proliferation and differentiation potential of m ESCs,and Klf5 gene expression was almost abolished.Klf5 knockout also affects the proliferation and differentiation of m ESCs,and overexpression of Klf5 in K5 a SE knockout cell lines can rescue part of the phenotype and gene expression,indicating that Klf5 is an important downstream target gene for its adjacent SE to play a functional role.At the same time,although the two knockouts produced similar phenotypes,their regulatory effects on the differentiation of the three germ layers of m ESCs were inconsistent: K5 a SE knockout inhibits the differentiation of endoderm and promotes the differentiation of mesoderm,while Klf5 gene knockout mainly inhibits the differentiation of neuroectoderm;Moreover,K5 a SE knocked out most of the down-regulated genes in the cell line,and overexpression of Klf5 could not restore the expression.These results suggest that K5 a SE may have other target genes.Therefore,in order to discover other target genes of K5 a SE,we used chromatin conformation capture(4C-seq)experiments to find target genes that interact with K5 a SE and are down-regulated after its knockout.It shows that besides Klf5,K5 a SE may also regulate other genes and Klf5 gene to play a role together to maintain the proliferation and germ layer differentiation of m ESCs.In summary,we found that K5 a SE,as a new functional SE,is very important for maintaining the proliferation and germ layer differentiation of m ESCs,and verified that its downstream target gene Klf5 plays an important role in the function of K5 a SE.At the same time,it was also found that there may be other target genes in dynamic equilibrium with the regulation of Klf5.Our research provides a new insight into the molecular mechanisms of self-renewal and pluripotency of m ESCs.