Project description:The study investigates CTCF/cohesin binding and chromatin looping by ChIP-seq and Micro-C. By ChIP-seq, we determined the genome-wide binding profiles of CTCF and Smc1a cohesin subunit in a knock-in mouse ES cell line (wt-CTCF; clone C59) with endogenously tagged wild type CTCF (FLAG-Halo-mCTCF) and Rad21 (mRad21-SNAPf-V5), and compared them to the same ES line expressing a mutant CTCF (ΔRBR-CTCF; clone C59D2), where we replaced a previously described RNA binding region with a short linker (GDGAGLINS) followed by a 3xHA tag (N576_D611del::3xHA). By Micro-C, we compared nucleosome-resolution chromosome folding maps of the same ES cell lines C59 and C59D2 described above, to determine the effect of deleting CTCF RNA binding region on chromatin looping.
Project description:Genome-wide maps of SMARCAD1 binding and histone modification H3R26Cit in mouse ES cells, histone modification H3K9me3, H3K4me3, H3K27Ac in Smarcad1 KD mouse ES cells, and histone modification H3K9me3 in mouse ES cells after PADI inhibition. Together with RNA-seq data for mouse ICM, blastocyst, embryonic stem cells and Smarcad1 KD cells.
