A systematic analysis of Trypanosoma brucei chromatin factors identifies novel protein interaction networks associated with sites of transcription initiation and termination
- Desislava P. Staneva1,2,4,
- Roberta Carloni1,2,4,
- Tatsiana Auchynnikava1,
- Pin Tong5,
- Juri Rappsilber1,3,
- A. Arockia Jeyaprakash1,
- Keith R. Matthews2 and
- Robin C. Allshire1
- 1Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom;
- 2Institute of Immunology and Infection Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom;
- 3Institute of Biotechnology, Technische Universität, 13355 Berlin, Germany
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↵4 These authors contributed equally to this work.
Abstract
Nucleosomes composed of histones are the fundamental units around which DNA is wrapped to form chromatin. Transcriptionally active euchromatin or repressive heterochromatin is regulated in part by the addition or removal of histone post-translational modifications (PTMs) by “writer” and “eraser” enzymes, respectively. Nucleosomal PTMs are recognized by a variety of “reader” proteins that alter gene expression accordingly. The histone tails of the evolutionarily divergent eukaryotic parasite Trypanosoma brucei have atypical sequences and PTMs distinct from those often considered universally conserved. Here we identify 65 predicted readers, writers, and erasers of histone acetylation and methylation encoded in the T. brucei genome and, by epitope tagging, systemically localize 60 of them in the parasite's bloodstream form. ChIP-seq shows that 15 candidate proteins associate with regions of RNAPII transcription initiation. Eight other proteins show a distinct distribution with specific peaks at a subset of RNAPII transcription termination regions marked by RNAPIII-transcribed tRNA and snRNA genes. Proteomic analyses identify distinct protein interaction networks comprising known chromatin regulators and novel trypanosome-specific components. Notably, several SET- and Bromo-domain protein networks suggest parallels to RNAPII promoter–associated complexes in conventional eukaryotes. Further, we identify likely components of TbSWR1 and TbNuA4 complexes whose enrichment coincides with the SWR1-C exchange substrate H2A.Z at RNAPII transcription start regions. The systematic approach used provides details of the composition and organization of the chromatin regulatory machinery in T. brucei and establishes a route to explore divergence from eukaryotic norms in an evolutionarily ancient but experimentally accessible eukaryote.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at https://www.genome.org/cgi/doi/10.1101/gr.275368.121.
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Freely available online through the Genome Research Open Access option.
- Received February 9, 2021.
- Accepted August 9, 2021.
This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.
