H2A.Z-H2B.V nucleosomes form a specialised scaffold for transcription initiation in Trypanosoma brucei
Regions of transcription initiation are often enriched in the histone variant H2A.Z. This is especially true in the divergent eukaryote Trypanosoma brucei, where broad domains of H2A.Z and a kinetoplastid-specific variant H2B.V define a limited number of polycistronic transcription start sites. To explore the chromatin underpinning this unusual transcription, we reconstituted H2A.Z-H2B.V nucleosomes in vitro and found that they are inherently unstable, form open chromatin structures, and serve as a direct interaction scaffold for gene regulators, in line with their role in transcription activation. A single particle cryo-EM structure reveals why H2A.Z-H2B.V form obligate dimers, pack differently within nucleosomes, and exhibit altered binding to DNA. We identified unique features of H2A.Z and H2B.V that result in differential activity of chromatin modifying enzymes, including the H2A.Z C-terminal tail and an atypical acidic patch. An affinity purification mass spectrometry screening approach revealed that H2A.Z-H2B.V nucleosomes have a distinct protein interaction profile, suggesting that interactions with chromatin factors are directly tuned for transcription control. Overall, this work reveals how trypanosome-specific histone features both inherently alter the biomechanical properties of nucleosomes as well as reshape chromatin binding and modification patterns at transcription start sites.