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Epigenetics Chromatin. 2018 Mar 9;11(1):10. doi: 10.1186/s13072-018-0180-6.

The bromodomain-containing protein Ibd1 links multiple chromatin-related protein complexes to highly expressed genes in Tetrahymena thermophila.

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Department of Chemistry and Biology, Ryerson University, 350 Victoria St., Toronto, M5B 2K3, Canada.
Department of Biology, York University, 4700 Keele St., Toronto, M3J 1P3, Canada.
Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Toronto, M5G 1X5, Canada.
Department of Molecular Medicine, Université Laval, Quebec, Canada.
Centre Hospitalier Universitaire de Québec Research Center, CHUL, 2705 Boulevard Laurier, Quebec, G1V 4G2, Canada.
Department of Molecular Genetics, University of Toronto, Toronto, M5S 1A8, Canada.
SciNet HPC Consortium, University of Toronto, 661 University Ave, Suite 1140, Toronto, M5G 1M1, Canada.
Department of Chemistry and Biology, Ryerson University, 350 Victoria St., Toronto, M5B 2K3, Canada.



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.


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 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.


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.


Bromodomain; Chromatin-remodeling complexes; Tetrahymena

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