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Proteomics analysis of the bromodomain protein IBD2 reveals mechanistic insights into H2A.Z (Hv1) dynamics in Tetrahymena

ABSTRACT: INO80 and SWR1 are evolutionarily related ATP-dependent chromatin remodeling complexes that regulate the chromatin occupancy of the histone variant H2A.Z, playing critical roles in transcriptional regulation, genome replication, and DNA repair. While INO80 and SWR1’s H2A.Z-related functions are well characterized in budding yeast and metazoans, much less is known about their composition and conserved roles outside the Opisthokonts. Here, we report that in the ciliate protozoan Tetrahymena thermophila, a distinct bromodomain-containing protein, IBD2, functions as a component of a putative INO80 complex. Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) demonstrates that IBD2 is enriched near transcription start sites and promoter regions. Notably, the IBD2 genomic binding profile strongly correlates with that of H2A.Z (Hv1), supporting its association with the INO80 complex.

ORGANISM(S): Tetrahymena thermophila

PROVIDER: GSE297756 | GEO | 2025/07/27

REPOSITORIES: GEO

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RNA-seq analysis of Tetrahymena thermophila

Project description:We present a comprehensive transcriptome of ciliate T. thermophila using the Illumina RNA-seq platform. The data was generated from the six mRNA samples of growth, starvation and conjugation of Tetrahymena. Despite an AT rich genome, there are about 124.6 million reads mapped to T. thermophila genome. Using these mapped reads, we have significantly improved the previous genome annotation and investigated the gene expression. Besides, our result also provided a comprehensive understanding of the alternative splicing in T. thermophila, and suggested the existence of the regulated unproductive splicing and translation (RUST) in the single-celled eukaryote. RNA-seq for six samples of Tetrahymena growth, starvation and conjugation.

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Multilevel interrogation of H3.3 dynamics reveals a primordial role in transcription regulation in Tetrahymena [ChIP-seq]

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The histone variant H2A.Z in yeast is almost exclusively incorporated into the +1 nucleosome in the direction of transcription

Project description:To investigate the incorporation dynamics of histone variant H2A.Z, we determined its genomic localization at single nucleosome resolution, as well as the localization of its chromatin remodelers Swr1 and Ino80. We find that Swr1 binding alone is a poor predictor of H2A.Z occupancy levels, and that normal Swr1 and Ino80 localization are actually dependent on H2A.Z. Additionally, we find that H2A.Z’s bimodal incorporation on either side of the NDR is not a general feature of TSS, but is specifically a marker for bidirectional transcription, such that the upstream flanking -1 H2A.Z-containing nucleosome is more appropriately considered as a +1 H2A.Z nucleosome for antisense transcription.

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Tetrahymena thermophila

Project description:Tetrahymena thermophila

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Nucleosome mapping of Tetrahymena thermophila chromatin in vivo and in vitro

2015-07-30 | GSE64061 | GEO

Nucleosome mapping of Tetrahymena thermophila chromatin in vivo and in vitro

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2015-07-30 | E-GEOD-64061 | biostudies-arrayexpress

Transcriptional response of Tetrahymena thermophila to exogenous cholesterol

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