Project description:ChIP-seq using an anti-GFP antibody to check chromatin binding of Smchd1 in Smchd1-GFPMD43/MD43 and Smchd1-GFP+/+ neural stem cells.
Project description:ChIP-seq using an anti-H3K27me3 antibody to asses histone 3 lysine 27 tri-methylation modification in Smchd1-GFPMD43/MD43 and Smchd1-GFP+/+ neural stem cells.
Project description:Both Smchd1 deletion and its MommeD43 mutant version cause loss of long-range chromatin interactions in NSCs and a strengthening of more local interactions. We assayed CTCF binding in the relevant genotypes to see if this is related to altered CTCF binding. ChIP-seq using an anti-CTCF antibody to check if chromatin binding of CTCF is altered in Smchd1MD43-GFP/MD43-GFP and Smchd1del/del neural stem cells (NSCs) compared to Smchd1GFP/GFP NSCs.
Project description:reduced representation bisulfite sequencing (RRBS) sequencing was performed to analyze methylation profiles regulated by DNMT1 in C3H10T1/2 MSCs with or without OB differentiation.
Project description:We sought to examine whether the non-canonical SMC protein Smchd1 plays a role in chromosome conformation. We used in situ Hi-C to analyse chromosome conformation changes upon deletion of the epigenetic regulator Smchd1 in female neural stem cells. In parallel, we analysed nucleosome accessibility using ATAC-seq, gene expression using RNA-seq, chromatin marks H3K27me3 and H3K27ac and Ctcf binding using ChIP-seq. We additionally analysed Smchd1 binding genome-wide using ChIP-seq. Together, we find that deletion of Smchd1 alters chromosome conformation at Smchd1 target genes including the inactive X chromosome, Hox genes and imprinted loc. Smchd1 deletion results in gain in Ctcf binding and activation of enhancers. We propose Smchd1 functions by limiting Ctcf-mediated chromosome looping.
Project description:To better understand how DNA methylation influences placentation, DNA from first trimester primary trophoblast populations (side-population trophoblasts, cytotrophoblasts and extravillous trophoblasts) isolated using FACS underwent reduced representation bisulfite sequencing and were compared to publicly available data of blastocyst-derived and somatic cell populations.
