Intrachromosomal Looping Is Required for Activation of Endogenous Pluripotency Genes during Reprogramming

Abstract

Generation of induced pluripotent stem cells (iPSCs) by defined factors is an extremely inefficient process, because there is a strong epigenetic block preventing cells from achieving pluripotency. Here we report that virally expressed factors bound to the promoters of their target genes to the same extent in both iPSCs and unreprogrammed cells (URCs). However, expression of endogenous pluripotentcy genes was observed only in iPSCs. Comparison of local chromatin structure of the OCT4 locus revealed that there was a cohesin-complex-mediated intrachromosomal loop that juxtaposes a downstream enhancer to the gene's promoter, enabling activation of endogenous stemness genes. None of these long-range interactions were observed in URCs. Knockdown of the cohesin-complex gene SMC1 by RNAi abolished the intrachromosomal interaction and affected pluripotency. These findings highlight the importance of the SMC1-orchestrated intrachromosomal loop as a critical epigenetic barrier to the induction of pluripotency.

Initiation and maintenance of pluripotency gene expression in the absence of cohesin

“…As the activation of stress responses interferes with the expression of pluripotency genes (Lin et al 2005;Maimets et al 2008), the impact of cohesin on ES cell selfrenewal may well be indirect. Similar considerations apply to reports that cohesin facilitates the reprogramming of somatic cells toward induced pluripotent stem (iPS) cells Apostolou et al 2013;Wei et al 2013;Zhang et al 2013) because iPS cell reprogramming requires Ó 2015 Lavagnolli et al This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genesdev.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http:// creativecommons.org/licenses/by-nc/4.0/.…”

“…In addition, cohesin has a role in DNA replication (Terret et al 2009;Guillou et al 2010;Tittel-Elmer et al 2012;Tedeschi et al 2013) and contributes to the regulation of gene expression (Dorsett and Merkenschlager 2013) at least in part by forming long-range chromatin interactions (Hadjur et al 2009;Mishiro et al 2009;Nativio et al 2009;Hou et al 2010;Kagey et al 2010;Seitan et al 2011;Apostolou et al 2013;Merkenschlager and Odom 2013;Wei et al 2013;Zhang et al 2013) that contribute to the establishment and maintenance of cell type-specific gene expression patterns (Bickmore and van Steensel 2013;Merkenschlager and Odom 2013).…”

C/EBPα poises B cells for rapid reprogramming into induced pluripotent stem cells

“…In agreement, the presence of macroH2A potently inhibits transcription-factor-induced reprogramming of somatic cells to pluripotency by maintaining pluripotency loci in a repressed state (Barrero et al, 2013;GasparMaia et al, 2013;Pasque et al, 2012). In addition to local chromatin structure, (Wei et al, 2013;Zhang et al, 2013).…”

“…Importantly, these interactions took place specifically in those rare cells that were poised to form iPSCs, and they preceded transcriptional activation, suggesting a causal effect for 3D chromatin structure on transcription (Wei et al, 2013;Zhang et al, 2013).…”

Epigenetic Regulation of Open Chromatin in Pluripotent Stem Cells

“…Later, a cohesin-dependent enhancer-promoter interaction was also reported at the OCT4 locus in human ESCs. 87 Extending these studies of local chromosomal interactions, a genome-wide study unraveled numerous chromosomal interactions in PSCs, some of which are specific to pluripotency as shown by the loss of the interactions after differentiation of the cells. [88][89][90][91][92][93] These interactions are generally dependent on the presence of mediator, cohesin, and the CCCTC-binding factor (CTCF), which serves as an insulator dividing 2 chromosomal domains.…”