A novel SNF2 ATPase complex inTrypanosoma bruceiwith a role in H2A.Z-mediated chromatin remodelling

Abstract

A cascade of histone acetylation events with subsequent incorporation of a histone H2A variant plays an essential part in transcription regulation in various model organisms. A key player in this cascade is the chromatin remodelling complex SWR1, which replaces the canonical histone H2A with its variant H2A.Z. Transcriptional regulation of polycistronic transcription units in the unicellular parasite Trypanosoma brucei has been shown to be highly dependent on acetylation of H2A.Z, which is mediated by the histone-acetyltransferase HAT2. The chromatin remodelling complex which mediates H2A.Z incorporation is not known and an SWR1 orthologue in trypanosomes has not yet been reported. In this study, we identified and characterised an SWR1-like remodeller complex in T. brucei that is responsible for Pol II-dependent transcriptional regulation. Bioinformatic analysis of potential SNF2 DEAD/Box helicases, the key component of SWR1 complexes, identified a 1211 amino acids-long protein that exhibits key structural characteristics of the SWR1 subfamily. Systematic protein-protein interaction analysis revealed the existence of a novel complex exhibiting key features of an SWR1-like chromatin remodeller. RNAi-mediated depletion of the ATPase subunit of this complex resulted in a significant reduction of H2A.Z incorporation at transcription start sites and a subsequent decrease of steady-state mRNA levels. Furthermore, depletion of SWR1 and RNA-polymerase II (Pol II) caused massive chromatin condensation. The potential function of several proteins associated with the SWR1-like complex and with HAT2, the key factor of H2A.Z incorporation, is discussed.

A systematic analysis of Trypanosoma brucei chromatin factors identifies novel protein interaction networks associated with sites of transcription initiation and termination

“…Counterparts of yeast SWR1 H2A-to-H2A.Z exchange complex and NuA4 HAT complex components were identified, some of which were enriched where H2A.Z is prevalent at TSRs. A recent report indicates that both TbSWR1 and TbNuA4 complexes are indeed involved in the deposition of T. brucei H2A.Z (Vellmer et al 2021).…”

“Reading” a new chapter in protozoan parasite transcriptional regulation

“…Two YEATS domain-containing proteins have been identified in Tryp . brucei , TbYEA1 (also named TbSWRC1 in [ 53 ]) and TbYEA2 that appear to be involved in chromatin remodeling. TbYEA1, revealed to be a Gas41/Yaf9 homolog by structural analysis [ 53 ], is associated with the methyl-lysine reader protein TbZCW1 and the bromodomain protein TbBDF2 [ 34 ].…”

“…brucei , TbYEA1 (also named TbSWRC1 in [ 53 ]) and TbYEA2 that appear to be involved in chromatin remodeling. TbYEA1, revealed to be a Gas41/Yaf9 homolog by structural analysis [ 53 ], is associated with the methyl-lysine reader protein TbZCW1 and the bromodomain protein TbBDF2 [ 34 ]. Further co-immunoprecipitation (co-IP) experiments showed that TbYEA1 interacts with TbRuvB2, a helicase protein that is conserved in the SWR1 chromatin remodeling complex [ 53 ].…”

“…TbYEA1, revealed to be a Gas41/Yaf9 homolog by structural analysis [ 53 ], is associated with the methyl-lysine reader protein TbZCW1 and the bromodomain protein TbBDF2 [ 34 ]. Further co-immunoprecipitation (co-IP) experiments showed that TbYEA1 interacts with TbRuvB2, a helicase protein that is conserved in the SWR1 chromatin remodeling complex [ 53 ]. Depletion of TbYEA1 resulted in decreased chromatin-associated H2A.Z, indicating that TbYEA1 contributes to H2A.Z incorporation and may be a part of the SWR1 complex [ 53 ].…”

“…Further co-immunoprecipitation (co-IP) experiments showed that TbYEA1 interacts with TbRuvB2, a helicase protein that is conserved in the SWR1 chromatin remodeling complex [ 53 ]. Depletion of TbYEA1 resulted in decreased chromatin-associated H2A.Z, indicating that TbYEA1 contributes to H2A.Z incorporation and may be a part of the SWR1 complex [ 53 ]. The second YEATS protein, designated as TbYEA2, is another potential Gas41/Yaf9 homolog that is associated with TbBDF6, TbEAF6, and TbHAT1 [ 34 ].…”