The histone chaperone CAF-1 safeguards somatic cell identity

Abstract

Cellular differentiation involves profound remodeling of chromatic landscapes, yet the mechanisms by which somatic cell identity is subsequently maintained remain incompletely understood. To further elucidate regulatory pathways that safeguard the somatic state, we performed two comprehensive RNAi screens targeting chromatin factors during transcription factor-mediated reprogramming of mouse fibroblasts to induced pluripotent stem cells (iPSCs). Remarkably, subunits of the chromatin assembly factor-1 (CAF-1) complex emerged as the most prominent hits from both screens, followed by modulators of lysine sumoylation and heterochromatin maintenance. Optimal modulation of both CAF-1 and transcription factor levels increased reprogramming efficiency by several orders of magnitude and facilitated iPSC formation in as little as 4 days. Mechanistically, CAF-1 suppression led to a more accessible chromatin structure at enhancer elements early during reprogramming. These changes were accompanied by a decrease in somatic heterochromatin domains, increased binding of Sox2 to pluripotency-specific targets and activation of associated genes. Notably, suppression of CAF-1 also enhanced the direct conversion of B cells into macrophages and fibroblasts into neurons. Together, our findings reveal the histone chaperone CAF-1 as a novel regulator of somatic cell identity during transcription factor-induced cell fate transitions and provide a potential strategy to modulate cellular plasticity in a regenerative setting.

Histone chaperone APLF regulates induction of pluripotency in murine fibroblasts

“…However, the role of histone chaperones in the context of the induction of pluripotency is poorly understood. Recently, histone chaperone Asf1a has been shown to be necessary for the reprogramming of human dermal fibroblasts into iPSCs (Gonzalez-Muñoz et al, 2014), whereas the function of Caf1 has been shown to retain the identity of somatic cells, thereby acting as an obstacle in reprogramming (Cheloufi et al, 2015). In this study, we observed that the expression of the newly found histone chaperone APLF was lower in embryonic stem cells (ESCs) than in mouse embryonic fibroblasts (MEFs).…”

Heterochromatin and the molecular mechanisms of ‘parent-of-origin’ effects in animals

“…Recent RNAi screens have identified CAF-1, the SUMO-conjugating enzyme UBE2i, SUMO2, SETDB1, ATRX and DAXX as factors whose inhibition significantly enhances IPS reprogramming efficiency (Cheloufi et al 2015;Borkent et al 2016). All of these proteins are involved in regulation of heterochromatin (Cheloufi et al 2015;Borkent et al 2016) and heterochromatin-like domains (Figures 3 and 5; Table 1). RNAi ' knock-down' of CAF-1 also reduces levels of H3K9me3 at the RRRs (Cheloufi et al 2015) that are regions resistant to reprogramming at the 2-cell stage after SCNT (Matoba et al 2014).…”

Direct neuronal reprogramming: learning from and for development

“…To this end, direct reprogramming contributes essential new information about the mechanisms that stabilize cell fate, which also represent hurdles in reprogramming. For example, the histone chaperone LIN-53 limits the reprogramming of non-neuronal cells in larvae or adult worms (Caenorhabditis elegans) into neurons (Tursun et al, 2011) and the mammalian orthologue Rbbp4 is part of the histone chaperone complex CAF-1 that has recently been shown to limit reprogramming towards several cell types, including neurons (Cheloufi et al, 2015).…”