Histone H3 trimethylated at lysine 4 is enriched at probable transcription start sites in Trypanosoma brucei

Abstract

Recent studies have identified histone modifications and suggested a role for epigenetic gene regulation in Trypanosoma brucei. The histone modification H4K10ac and histone variants H2AZ and H2BV localize to probable sites of transcription initiation. Although all T. brucei histones have very evolutionarily divergent N-terminal tails, histone H3 shows conservation with other eukaryotic organisms in 6 of 8 amino acids encompassing lysine 4. Tri-methylation of H3K4 is generally associated with transcription. We therefore generated a specific antibody to T. brucei H3K4me3 and performed chromosome immunoprecipitation and high-throughput sequencing. We show that H3K4me3 is enriched at the start of polycistronic transcription units at divergent strand-switch regions and at other sites of RNA Polymerase II transcription reinitiation. H3K4me3 largely co-localizes with H4K10ac, but with a skew towards the upstream side of the H4K10ac peak, suggesting that it is a component of specific nucleosomes that play a role in Pol II transcription initiation.

Cell Biology of the Trypanosome Genome

“…The idea that transcription initiation and termination were occurring at the SSRs was strengthened by the finding that acetylated histones are concentrated at divergent SSRs (putative sites of transcription initiation) but are absent from convergent SSRs (putative sites of transcription termination) in T. cruzi (154). Moreover, recent data from genome-wide chromatin immunoprecipitation (ChIP-seq and ChIP-chip) studies of T. brucei and Leishmania show that certain histone modifications and transcription factors are specifically enriched at genome regions predicted to be associated with either transcription initiation or termination (162,174,191). In T. brucei, two histone modifications associated with open chromatin (H4K10ac and H3K4me3) and two histone variants (H2AZ and H2BV) are enriched in divergent SSRs and other putative pol II transcription start sites, whereas variants of H3 and H4 are found near the ends of DGCs (162,191).…”

“…Moreover, recent data from genome-wide chromatin immunoprecipitation (ChIP-seq and ChIP-chip) studies of T. brucei and Leishmania show that certain histone modifications and transcription factors are specifically enriched at genome regions predicted to be associated with either transcription initiation or termination (162,174,191). In T. brucei, two histone modifications associated with open chromatin (H4K10ac and H3K4me3) and two histone variants (H2AZ and H2BV) are enriched in divergent SSRs and other putative pol II transcription start sites, whereas variants of H3 and H4 are found near the ends of DGCs (162,191). Interestingly, the putative transcription start sites are also predicted from deep sequencing of mRNA, where they have a signature of increased levels of partially processed mRNA (92), which might be a by-product of proximal transcription initiation.…”

“…They have been implicated in trypanosome transcription initiation and termination (154,162,174,191), cell cycle progression (70,85), and telomeric silencing (90). Acetylated histone H4 is distributed in a punctate pattern in the T. brucei and T. cruzi nucleoplasm (133,162,165).…”

TbISWI Regulates Multiple Polymerase I (Pol I)-Transcribed Loci and Is Present at Pol II Transcription Boundaries in Trypanosoma brucei

“…Recent data have identified enrichment of various modified histones and histone variants in regions between polycistronic Pol II transcription units in T. brucei (50,63). Since ISWI complexes are involved in Pol II transcription initiation and termination in other organisms (30), this led us to hypothesize that TbISWI may play a role in establishing the epigenetic marks found at strand switch regions (SSR).…”

“…It has recently become clear that epigenetic marks are also present at the strand switch regions (SSRs) located between the polycistronic T. brucei Pol II transcription units (50,63). The divergent SSRs, which contain putative transcription start sites (TSS), are enriched in the histone variants H2AZ and H2BV, as well as the histones H3K4me3 and H4K10ac.…”