Facilitators and Impediments of the Pluripotency Reprogramming Factors' Initial Engagement with the Genome

Abstract

SUMMARY The ectopic expression of transcription factors can reprogram cell fate, yet it is unknown how the initial binding of factors to the genome relates functionally to the binding seen in the minority of cells that become reprogrammed. We report a map of Oct4, Sox2, Klf4, and c-Myc (O, S, K, and M) on the human genome during the first 48 hours of reprogramming fibroblasts to pluripotency. Three striking aspects of the initial chromatin binding events include: An unexpected role for c-Myc in facilitating OSK chromatin engagement, the primacy of O, S, and K as pioneer factors at enhancers of genes that promote reprogramming, and megabase-scale chromatin domains spanned by H3K9me3, including many genes required for pluripotency, that prevent initial OSKM binding and impede the efficiency of reprogramming. We find diverse aspects of initial factor binding that must be overcome in the minority of cells that become reprogrammed.

Changing POU dimerization preferences converts Oct6 into a pluripotency inducer

“…Possibly, this recruitment process is impaired for the Oct4 21Y,29R protein. Moreover, Oct4 seems to possess an intriguing ability to bind a closed chromatin as a pioneer factor and to initiate chromatin opening 52. Our results strongly suggest that cooperation between Oct4 and Sox2—and not Oct4 alone—is involved in not only maintaining but also establishing pluripotency.…”

Pioneer transcription factors in cell reprogramming

“…How does this set of factors first interact with their target sites to initiate reprogramming? A snapshot of the initial binding events of OSKM in human fibroblasts indicates their preferential occupancy of promoter-distal (i.e., enhancer) target sites (Soufi et al 2012). Many initial binding events occur at genes that elicit reprogramming to pluripotency as well as at genes that promote apoptosis during the early stages of iPSC reprogramming.…”

“…Many initial binding events occur at genes that elicit reprogramming to pluripotency as well as at genes that promote apoptosis during the early stages of iPSC reprogramming. Many more initial binding events are distinct from the definitive binding pattern in embryonic stem (ES) cells or iPSCs that maintains pluripontency (Soufi et al 2012). Thus, the initial binding or scanning of the genome is quite promiscuous during reprogramming of somatic cells to pluripotency, and subsequent reorganization of the factors in the genome must occur to establish the final pluripotent state (Hochedlinger and Plath 2009).…”

“…Of these factors, Oct3/4, Sox2, and Klf4 act as pioneer transcription factors in that they can access closed chromatin whether they bind together or alone ( Fig. 1; Table 1; Soufi et al 2012). ''Closed chromatin'' in this context means to lack DNase hypersensitivity and a lack of a consistent histone modification pattern.…”

“…''Closed chromatin'' in this context means to lack DNase hypersensitivity and a lack of a consistent histone modification pattern. In contrast, c-Myc alone prefers to bind to ''open chromatin'' sites that are DNase-hypersensitive and contain activating histone modifications (Soufi et al 2012). However, c-Myc can bind closed chromatin sites in conjunction with the other factors (Soufi et al 2012).…”