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- Title
The bromodomain-containing protein Ibd1 links multiple chromatin-related protein complexes to highly expressed genes in <italic>Tetrahymena thermophila</italic>.
- Authors
Saettone, Alejandro; Garg, Jyoti; Lambert, Jean-Philippe; Nabeel-Shah, Syed; Ponce, Marcelo; Burtch, Alyson; Thuppu Mudalige, Cristina; Gingras, Anne-Claude; Pearlman, Ronald E.; Fillingham, Jeffrey
- 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 <italic>Tetrahymena thermophila</italic>. 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 <italic>Tetrahymena</italic> 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 <italic>Tetrahymena</italic> where it subsequently might coordinate the recruitment of several chromatin-remodeling complexes to regulate the transcriptional landscape of vegetatively growing <italic>Tetrahymena</italic> cells.
- Subjects
BROMODOMAIN-containing proteins; CHROMATIN; GENE expression; TETRAHYMENA thermophila; TRANSCRIPTION factors; MASS spectrometry
- Publication
Epigenetics & Chromatin, 2018, Vol 11, p1
- ISSN
1756-8935
- Publication type
Article
- DOI
10.1186/s13072-018-0180-6