While not required for ES cell self-renewal, two other ATP-dependent nucleosome remodeling factors, Lsh and NURF, appear to be required for proper ES cell differentiation. KD of Lsh, a Swi2/Snf2 superfamily ATPase that functions in retrotransposon silencing, resulted in failure to methylate and silence the promoters of pluripotency TFs during differentiation [20
]. NURF is a multisubunit nucleosome remodeling complex involved in gene regulation in metazoans. ES cells lacking NURF subunit Bptf exhibit defects in differentiation of all three germ layers [21
Two bi-functional chromatin regulatory complexes, the Tip60-p400 and NURD complexes, have also been shown to play important roles in ES cell self-renewal and pluripotency [15
]. The NURD complex exhibits two chromatin regulatory activities: ATP-dependent nucleosome remodeling, catalyzed by the Mi-2 Swi2/Snf2 superfamily ATPase, and histone deacetylase activity, catalyzed by Hdac1 and Hdac2. Homozygous deletion of the non-catalytic NURD subunit Mbd3 allows mutant ES cells to self-renew in the absence of leukemia-inhibitory factor (LIF) [23
]. Furthermore, loss of Mbd3 impairs ES cell differentiation in general and alters the spectrum of cell types produced during differentiation [23
]. Knockout or KD of Mbd3 in ES cells causes misregulation of a number of genes [23
], including upregulation of genes expressed in trophectoderm (TE) [25
]. Consistent with these data, in vitro differentiation of Mbd3−/− ES cells in embryoid bodies (EBs) results in induction of markers of TE [23
], a cell type not normally produced during differentiation of ES cells in vitro or in vivo.
In addition, a second form of the NURD complex lacking Mbd3 and Rbbp7, has recently been identified in ES cells [15
]. This complex, called NODE (Nanog and Oct4 associated deacetylase), appears to form a high molecular weight complex with both Nanog and Oct4 that functions to repress expression of developmentally regulated genes in ES cells [15
]. Similarly, one or both NURD-like complexes has been shown to interact with ES cell TF Sall4 [32
]. KD of Mta1, a subunit shared by the NURD and NODE complexes, caused different changes in gene expression than Mbd3 KD or KO, confirming the different functions of these complexes [15
]. Unlike Mbd3 loss, which inhibits ES cell differentiation, Mta1 KD resulted in upregulation of differentiation genes of multiple lineages, as well as ES cell differentiation. It remains to be determined how the levels, assembly and activities of the two NURD-like complexes are regulated in ES cells.