Abstract
In embryonic stem cells (ESCs), the Tip60 histone acetyltransferase activates genes required for proliferation and silences genes that promote differentiation. Here we show that the class II histone deacetylase Hdac6 co-purifies with Tip60-p400 complex from ESCs. Hdac6 is necessary for regulation of most Tip60-p400 target genes, particularly those repressed by the complex. Unlike differentiated cells, where Hdac6 is mainly cytoplasmic, Hdac6 is largely nuclear in ESCs, neural stem cells (NSCs), and some cancer cell lines, and interacts with Tip60-p400 in each. Hdac6 localizes to promoters bound by Tip60-p400 in ESCs, binding downstream of transcription start sites. Surprisingly, Hdac6 does not appear to deacetylate histones, but rather is required for Tip60-p400 binding to many of its target genes. Finally, we find that, like canonical subunits of Tip60-p400, Hdac6 is necessary for robust ESC differentiation. These data suggest that Hdac6 plays a major role in the modulation of Tip60-p400 function in stem cells. DOI: http://dx.doi.org/10.7554/eLife.01557.001.
Highlights
embryonic stem cells (ESCs) self-renewal and differentiation are controlled by multiple pathways: exogenous factors that act through well-defined signaling pathways that are employed in adult cells, and a network of nuclear factors that regulate the ESC transcriptome (Hanna et al, 2010)
We observed several bands within Tip60 purifications from ESCs that were not observed in purifications from Tip60-H3F mouse embryo fibroblasts (MEFs) or untagged cells (Figure 1A), consistent with the possibility that ESCs express a distinct form of Tip60-p400 complex
Consistent with our finding that Hdac6 does not interact with Tip60-p400 in differentiated cells, we found that Hdac6-dependent Tip60-target genes in ESCs were not bound by Tip60 in MEFs (Figure 4—figure supplement 3)
Summary
ESC self-renewal and differentiation are controlled by multiple pathways: exogenous factors that act through well-defined signaling pathways that are employed in adult cells, and a network of nuclear factors that regulate the ESC transcriptome (Hanna et al, 2010). Regulators of gene expression can be further sub-divided into (i) sequence-specific transcription factors, including ESC-specific master regulators, (ii) non-coding RNAs that act both in cis and in trans to regulate specific subsets of genes, and (iii) chromatin regulatory complexes, most of which are expressed in multiple cell and tissue types, and often act very broadly in the genome to covalently modify histones, remodel nucleosomes, or modify higher-order chromatin folding (Hanna et al, 2010; Young, 2011). For most chromatin regulatory complexes, several key questions remain, including how they find their genomic targets, how their catalytic activities lead to alteration of gene expression, and how the activities of these factors are altered to facilitate differentiation. The mammalian SWI/SNF-family complex BAF (Brg1/Brahma Associated Factor) consists of several related
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