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

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


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Epigenesis, Genetic
  • Gene Expression Regulation
  • Gene Expression Regulation, Developmental
  • Histones / metabolism
  • Mass Spectrometry
  • Nuclear Proteins / metabolism*
  • Proteomics / methods*
  • Protozoan Proteins / metabolism
  • Tetrahymena thermophila / genetics
  • Tetrahymena thermophila / growth & development*
  • Tetrahymena thermophila / metabolism
  • Transcription, Genetic


  • Histones
  • Nuclear Proteins
  • Protozoan Proteins