Constitutive heterochromatin reorganization during somatic cell reprogramming

Abstract

Induced pluripotent stem (iPS) cell reprogramming is a gradual epigenetic process that reactivates the pluripotent transcriptional network by erasing and establishing repressive epigenetic marks. In contrast to loci-specific epigenetic changes, heterochromatin domains undergo epigenetic resetting during the reprogramming process, but the effect on the heterochromatin ultrastructure is not known. Here, we characterize the physical structure of heterochromatin domains in full and partial mouse iPS cells by correlative electron spectroscopic imaging. In somatic and partial iPS cells, constitutive heterochromatin marked by H3K9me3 is highly compartmentalized into chromocentre structures of densely packed chromatin fibres. In contrast, chromocentre boundaries are poorly defined in pluripotent embryonic stem and full iPS cells, and are characterized by unusually dispersed 10 nm heterochromatin fibres in high Nanog-expressing cells, including pluripotent cells of the mouse blastocyst before differentiation. This heterochromatin reorganization accompanies retroviral silencing during conversion of partial iPS cells by MEK/GSK3 2i inhibitor treatment. Thus, constitutive heterochromatin is compacted in partial iPS cells but reorganizes into dispersed 10 nm chromatin fibres as the fully reprogrammed iPS cell state is acquired.

Embryonic stem cell and induced pluripotent stem cell: an epigenetic perspective

“…Rearrangement of the heterochromatin, characterized by the presence of histone H3 lysine 9 trimethylation (H3K9me3) and HP1, precedes the activation of Nanog, while enrichment of euchromatin marks occurs concurrently with Nanog activation [14]. Consistently, heterochromatin is rearranged and becomes dispersed when partially reprogrammed cells are converted to iPSCs by dual inhibition of MEK and GSK3 [13]. Thus, chromatin reorganization from the somatic state to an ESC-like one seems to be required for the activation of pluripotency circuitry.…”

“…The epigenetic barrier restricting the pluripotency establishment in this step is likely reflected in the global non-permissive chromatin configuration and/or the inherent non-permissive chromatin context at the pioneer pluripotency genes. The molecular natures of the epigenetic barriers probably include H3K9me3/2 [13,14,71], H3K27me3 [110], insufficient histone acetylation [25,49,51,52], hypermethylation and hypo-hydroxylmethylation on DNA [7,147], and the lack of proper chromatin remodeling activities [34,42]. At this point, many questions remain unresolved.…”

“…The permissive chromatin state may lead to the activation of the pluripotency network with the help of the introduced reprogramming factors. In fact, expression of the other pluripotency gene, Nanog, has been shown to take place upon radical chromatin reorganization, and after this the pluripotency is established [13,14].…”

“…During iPSC generation, the somatic cell chromatin needs to be reorganized to an ESC-like state with loosely organized heterochromatin and abundant euchromatin modifications [13,14]. It appears that the chromatin reorganization events take place in a coordinated and sequential manner.…”

“…iPSCs have been shown to be highly similar to ESCs, in terms of transcription program, chromatin modification profiles [5][6][7][8][9][10][11][12] and global chromatin configuration [6,13,14]. Functionally, at least some of the iPSCs have the developmental potential equivalent to ESCs, as entirely iPSC-derived animals ("all-iPSC" mice) can be generated through tetraploid complementation [15][16][17].…”