RT Journal Article
SR Electronic
T1 A Cell type-specific Class of Chromatin Loops Anchored at Large DNA Methylation Nadirs
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 212928
DO 10.1101/212928
A1 Mira Jeong
A1 Xingfan Huang
A1 Xiaotian Zhang
A1 Jianzhong Su
A1 Muhammad S. Shamim
A1 Ivan D. Bochkov
A1 Jaime Reyes
A1 Haiyoung Jung
A1 Emily Heikamp
A1 Aviva Presser Aiden
A1 Wei Li
A1 Erez Lieberman Aiden
A1 Margaret A. Goodell
YR 2017
UL http://biorxiv.org/content/early/2017/11/09/212928.1.abstract
AB Higher order chromatin structure and DNA methylation are implicated in multiple developmental processes, but their relationship to cell state is unknown. Here, we found that large (~10kb) DNA methylation nadirs can form long loops connecting anchor loci that may be dozens of megabases apart, as well as interchromosomal links. The interacting loci comprise ~3.5Mb of the human genome. The data are more consistent with the formation of these loops by phase separation of the interacting loci to form a genomic subcompartment, rather than with CTCF-mediated extrusion. Interestingly, unlike previously characterized genomic subcompartments, this subcompartment is only present in particular cell types, such as stem and progenitor cells. Further, we identify one particular loop anchor that is functionally associated with maintenance of the hematopoietic stem cell state. Our work reveals that H3K27me3-marked large DNA methylation nadirs represent a novel set of very long-range loops and links associated with cellular identity.Summary Hi-C and DNA methylation analyses reveal novel chromatin loops between distant sites implicated in stem and progenitor cell function.