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2013 ; 12
(6
): 699-712
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Genome-wide chromatin interactions of the Nanog locus in pluripotency,
differentiation, and reprogramming
#MMPMID23665121
Apostolou E
; Ferrari F
; Walsh RM
; Bar-Nur O
; Stadtfeld M
; Cheloufi S
; Stuart HT
; Polo JM
; Ohsumi TK
; Borowsky ML
; Kharchenko PV
; Park PJ
; Hochedlinger K
Cell Stem Cell
2013[Jun]; 12
(6
): 699-712
PMID23665121
show ga
The chromatin state of pluripotency genes has been studied extensively in
embryonic stem cells (ESCs) and differentiated cells, but their potential
interactions with other parts of the genome remain largely unexplored. Here, we
identified a genome-wide, pluripotency-specific interaction network around the
Nanog promoter by adapting circular chromosome conformation capture sequencing.
This network was rearranged during differentiation and restored in induced
pluripotent stem cells. A large fraction of Nanog-interacting loci were bound by
Mediator or cohesin in pluripotent cells. Depletion of these proteins from ESCs
resulted in a disruption of contacts and the acquisition of a
differentiation-specific interaction pattern prior to obvious transcriptional and
phenotypic changes. Similarly, the establishment of Nanog interactions during
reprogramming often preceded transcriptional upregulation of associated genes,
suggesting a causative link. Our results document a complex,
pluripotency-specific chromatin "interactome" for Nanog and suggest a functional
role for long-range genomic interactions in the maintenance and induction of
pluripotency.