Genome Wide Chromatin Interaction Analysis with Hi-C in Mouse Embryonic Stem Cells

We select three identified Sox2 associated enhancers (E1, E2 and E3), representing different distal interaction categories, to further explore their biological effects and how this diversity influence gene transcription. Enhancer-deletion is constructed via CRISPR/Cas9 system in mouse embryonic stem cells (mESCs). Results indicate that these associations show quantitative regulation without causing dramatic changes in gene expression and phenotype faultiness. E1 potentially speeds up cell cycle and restrains nerve differentiation and involves in cardiac development, which has been validated in vivo. In contrast, the E2 has potential effect on nervous system function and lipid metabolism. E3 functions in ion transport and metabolism which might play essential role in the pluripotent maintenance. Further, integrated with the Hi-C analysis, enhancer-deletion associated genes show dynamic promoter-enhancer interactions also. Two expreimental repeats represent wild type and E1-E3 enhancer knock out cells were used to generate ten Hi-C library.