SRA

During mammalian embryogenesis, both the 5-cytosine DNA methylation (5meC) landscape and three dimensional (3D) chromatin architecture are profoundly remodeled during a process known as “epigenetic reprogramming.” An understudied aspect of epigenetic reprogramming is how the 5meC flux, per se, affects the 3D genome. This is pertinent given the 5meC-sensitivity of a key regulator of chromosome folding: CTCF. We profiled the CTCF binding landscape using a mouse embryonic stem cell (ESC) differentiation protocol that models the exit of naive pluripotency, wherein global DNA methylation levels start low and increase to somatic levels within four days. We took advantage of the fact that mouse ESCs lacking DNA methylation machinery exhibit globally similar differentiation dynamics, thus allowing for dissection of more nuanced effects of CTCF misregulation on gene expression. We carried this out by performing CTCF HiChIP in both wild-type and mutant conditions to assess aberrant CTCF-CTCF looping events in the absence of 5meC. We went on to assess the impact misregulated CTCF binding has on cis-regulatory contacts by performing H3K27ac HiChIP, given that H3K27ac is enriched on active promoters and enhancers. Using DNA methylation epigenome editing, we were able to directly demonstrate that the DNA methyl-mark is able to impact CTCF binding. Finally, a detailed dissection of the imprinted Zdbf2 gene showed how 5meC-antagonism of CTCF allows for proper gene regulation during differentiation. This work provides the most global picture to date of how DNA methylation impacts the 3D genome as the embryo prepares for gastrulation and lineage commitment. Overall design: HiChIP, CUT&RUN and 4C was performed on mouse embryonic stem cells and epiblast-like cells for CTCF. H3K27ac HiChIP was also performed on the same cells. 4C-seq was conducted on TET-1 epigenome-edited epiblast-like cells.