Well-positioned nucleosomes punctuate polycistronic pol II transcription units and flank silent VSG gene arrays in Trypanosoma brucei

Abstract

BackgroundThe compaction of DNA in chromatin in eukaryotes allowed the expansion of genome size and coincided with significant evolutionary diversification. However, chromatin generally represses DNA function, and mechanisms coevolved to regulate chromatin structure and its impact on DNA. This included the selection of specific nucleosome positions to modulate accessibility to the DNA molecule. Trypanosoma brucei, a member of the Excavates supergroup, falls in an ancient evolutionary branch of eukaryotes and provides valuable insight into the organization of chromatin in early genomes.ResultsWe have mapped nucleosome positions in T. brucei and identified important differences compared to other eukaryotes: The RNA polymerase II initiation regions in T. brucei do not exhibit pronounced nucleosome depletion, and show little evidence for defined −1 and +1 nucleosomes. In contrast, a well-positioned nucleosome is present directly on the splice acceptor sites within the polycistronic transcription units. The RNA polyadenylation sites were depleted of nucleosomes, with a single well-positioned nucleosome present immediately downstream of the predicted sites. The regions flanking the silent variant surface glycoprotein (VSG) gene cassettes showed extensive arrays of well-positioned nucleosomes, which may repress cryptic transcription initiation. The silent VSG genes themselves exhibited a less regular nucleosomal pattern in both bloodstream and procyclic form trypanosomes. The DNA replication origins, when present within silent VSG gene cassettes, displayed a defined nucleosomal organization compared with replication origins in other chromosomal core regions.ConclusionsOur results indicate that some organizational features of chromatin are evolutionarily ancient, and may already have been present in the last eukaryotic common ancestor.Electronic supplementary materialThe online version of this article (doi:10.1186/s13072-017-0121-9) contains supplementary material, which is available to authorized users.

SUMO polymeric chains are involved in nuclear foci formation and chromatin organization in Trypanosoma brucei procyclic forms

“…Micrococcal assay was adapted from [ 51 ] and [ 52 ]. Parasites (5x10 7 ) were washed in a buffer containing 1 mM L-glutamate, 250 mM sucrose, 2.5 mM CaCl 2 and 1 mM PMSF, and then lysed with the same buffer but also containing 1% Triton X-100.…”

How to create coats for all seasons: elucidating antigenic variation in African trypanosomes

“…The position of individual nucleosomes across all of the core chromosomes has now been determined in both bloodstream-and procyclic-form T. brucei [23,24]. This has allowed us to determine the chromatin state at different types of transcription units.…”

“…Instead, Pol II promoters appear to be predominantly functionally defined by discrete chromatin structure around the strand switch regions where Pol II transcription initiates [24]. In addition, chromatin structure appears to play a role in the repression of the silent VSG genes, and positioned nucleosomes are found flanking the silent VSG gene arrays [23]. The chromatin structure in the border regions of these VSG arrays could represent barrier regions which repress cryptic transcription initiation or readthrough into the VSG arrays, keeping these VSGs silent.…”

The Trypanosoma brucei RNA‐Binding Protein TbRRM1 is Involved in the Transcription of a Subset of RNA Pol II‐Dependent Genes

“…Collectively, these reports indicate that transcriptionally active genes could be found depleted of nucleosomes allowing a more permissive chromatin structure, while silenced or nontranscribed genes are most enriched of nucleosomes leading to a more compacted chromatin. This epigenetic transcription regulation has been involved in the expression of genes with well-defined promoters, while little is known about how chromatin accessibility can regulate Pol II polycistronic transcription initiation since no evidence of obvious nucleosome depletion has been found in transcription start sites (TSSs) (Maree et al 2017;Wedel et al 2017).…”

“…This epigenetic transcription regulation has been involved in the expression of genes with well‐defined promoters, while little is known about how chromatin accessibility can regulate Pol II polycistronic transcription initiation since no evidence of obvious nucleosome depletion has been found in transcription start sites (TSSs) (Maree et al. ; Wedel et al. ).…”