Title: The bromodomain-containing protein Ibd1 links multiple chromatin related protein complexes to highly expressed genes in Tetrahymena thermophila,
Abstract: Background: 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/Brg1.
Results: Using 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 (MAC) 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.
Conclusions: Our 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.