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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.

Author information

1
Department of Chemistry and Biology, Ryerson University, 350 Victoria St., Toronto, M5B 2K3, Canada.
2
Department of Biology, York University, 4700 Keele St., Toronto, M3J 1P3, Canada.
3
Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Toronto, M5G 1X5, Canada.
4
Department of Molecular Medicine, Université Laval, Quebec, Canada.
5
Centre Hospitalier Universitaire de Québec Research Center, CHUL, 2705 Boulevard Laurier, Quebec, G1V 4G2, Canada.
6
Department of Molecular Genetics, University of Toronto, Toronto, M5S 1A8, Canada.
7
SciNet HPC Consortium, University of Toronto, 661 University Ave, Suite 1140, Toronto, M5G 1M1, Canada.
8
Department of Chemistry and Biology, Ryerson University, 350 Victoria St., Toronto, M5B 2K3, Canada. Jeffrey.fillingham@ryerson.ca.

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 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.

KEYWORDS:

Bromodomain; Chromatin-remodeling complexes; Tetrahymena

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