Abstract
BackgroundThe chromatin remodelers of the SWI/SNF family are critical transcriptional regulators. Recognition of lysine acetylation through a bromodomain (BRD) component is key to SWI/SNF function; in most eukaryotes, this function is attributed to SNF2/Brg1.ResultsUsing affinity purification coupled to mass spectrometry (AP–MS) we identified members of a SWI/SNF complex (SWI/SNFTt) in Tetrahymena thermophila. SWI/SNFTt is composed of 11 proteins, Snf5Tt, Swi1Tt, Swi3Tt, Snf12Tt, Brg1Tt, two proteins with potential chromatin-interacting domains and four proteins without orthologs to SWI/SNF proteins in yeast or mammals. SWI/SNFTt subunits localize exclusively to the transcriptionally active macronucleus during growth and development, consistent with a role in transcription. While Tetrahymena Brg1 does not contain a BRD, our AP–MS results identified a BRD-containing SWI/SNFTt component, Ibd1 that associates with SWI/SNFTt during growth but not development. AP–MS analysis of epitope-tagged Ibd1 revealed it to be a subunit of several additional protein complexes, including putative SWRTt, and SAGATt complexes as well as a putative H3K4-specific histone methyl transferase complex. Recombinant Ibd1 recognizes acetyl-lysine marks on histones correlated with active transcription. Consistent with our AP–MS and histone array data suggesting a role in regulation of gene expression, ChIP-Seq analysis of Ibd1 indicated that it primarily binds near promoters and within gene bodies of highly expressed genes during growth.ConclusionsOur results suggest that through recognizing specific histones marks, Ibd1 targets active chromatin regions of highly expressed genes in Tetrahymena where it subsequently might coordinate the recruitment of several chromatin-remodeling complexes to regulate the transcriptional landscape of vegetatively growing Tetrahymena cells.
Highlights
The chromatin remodelers of the SWI/SNF family are critical transcriptional regulators
Gene replacement of the WT SNF5Tt and SAF5Tt that occurs by homologous recombination [22] and ‘phenotypic assortment’
We found that 54% (457 open reading frames (ORF)) and 16% (134 ORF) of genes occupied by Ibd1 are highly and moderately expressed, respectively (Fig. 6b, right panel, c; see Additional file 6, localization tab)
Summary
The chromatin remodelers of the SWI/SNF family are critical transcriptional regulators. Recognition of lysine acetylation through a bromodomain (BRD) component is key to SWI/SNF function; in most eukaryotes, this function is attributed to SNF2/Brg. The SAGA histone acetyl transferase complex co-activates transcription by acetylating specific lysine residues in the N-terminus of histone H3 within the nucleosome, which can serve as a platform to recruit the SWI/SNF complex via the bromodomain (BRD) present in SNF2/ Brg1 [1]. When recruited to a genomic region, the SWI/SNF complex co-activates transcription in part by hydrolyzing ATP via the Snf subunit and remodeling nucleosomes to make promoter sequences available to be bound by general transcription factors (TFs) such as TFIID. Additional protein domains that function in transcription complexes by recognizing some of the diverse histone post-translational modifications (PTMs) include the methyl lysine-recognizing PHD and chromodomains [5]. Other ATP-dependent chromatin-remodeling complexes that function in transcription include the SWR complex that exchanges core H2A in the nucleosome for the transcription-friendly histone H2A variant Htz1 [6, 7] and the INO80 complex one function of which is to catalyze the reverse reaction [8]
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