Four histone variants mark the boundaries of polycistronic transcription units in Trypanosoma brucei

Abstract

Unusually for a eukaryote, genes transcribed by RNA polymerase II (pol II) in Trypanosoma brucei are arranged in polycistronic transcription units. With one exception, no pol II promoter motifs have been identified, and how transcription is initiated remains an enigma. T. brucei has four histone variants: H2AZ, H2BV, H3V, and H4V. Using chromatin immunoprecipitation (ChIP) and sequencing (ChIP-seq) to examine the genome-wide distribution of chromatin components, we show that histones H4K10ac, H2AZ, H2BV, and the bromodomain factor BDF3 are enriched up to 300-fold at probable pol II transcription start sites (TSSs). We also show that nucleosomes containing H2AZ and H2BV are less stable than canonical nucleosomes. Our analysis also identifies >60 unexpected TSS candidates and reveals the presence of long guanine runs at probable TSSs. Apparently unique to trypanosomes, additional histone variants H3V and H4V are enriched at probable pol II transcription termination sites. Our findings suggest that histone modifications and histone variants play crucial roles in transcription initiation and termination in trypanosomes and that destabilization of nucleosomes by histone variants is an evolutionarily ancient and general mechanism of transcription initiation, demonstrated in an organism in which general pol II transcription factors have been elusive. The protozoan parasite Trypanosoma brucei branched early in eukaryotic evolution and is probably the most divergent well-studied eukaryote. Many discoveries of general interest have been made in T. brucei, emphasizing its value for understanding the evolution of core molecular processes.Transcription of protein-coding genes by RNA polymerase II (pol II) in T. brucei differs in two important aspects from most other eukaryotes. First, transcription is polycistronic: Arrays of sometimes >100 genes are transcribed in polycistronic transcription units (PTUs). This organization is reminiscent of operons in prokaryotes except that there is no evidence to suggest clustering of functionally related genes in T. brucei. Second, mRNAs are separated post-transcriptionally by coupled splicing and polyadenylation reactions that add a 39-nucleotide (nt) ''spliced-leader'' to every mRNA (for review, see Liang et al. 2003). Within a PTU, genes are transcribed from the same strand, but transcription of two neighboring PTUs can either be convergent or divergent. The regions between PTUs are referred to as strand switch regions (SSRs). Strand-specific nuclear run-on assays performed in Leishmania (Martinez-Calvillo et al. 2003), a genus related to T. brucei, have shown that pol II transcription starts at SSRs between two transcriptionally divergent PTUs (divergent SSRs) and ends at SSRs between two transcriptionally convergent PTUs (convergent SSRs). Because 75% of all Leishmania major genes can be found in the same genomic context in T. brucei (El-Sayed et al. 2005), indicating a high degree of synteny, it is reasonable to hypothesize that divergent SSRs in T. brucei are transcription start s...

Innovation in gene regulation: The case of chromatin computation

“…Hv1 and Hv2 are H2A and H3 variants exclusively used in the macronucleus of Tetrahymena thermophila. Trypanosomes use specific combinations of numerous histone variants to ensure demarcation of polycistronic transcription units [156]. In addition, ChAPs can deviate from non-specific DNA binding, and binding preferences of each variant can diverge.…”

“…Only trypanosomatids rely largely on chromatin, and in particular, on variations in nucleosome compositions, [162,156] to regulate gene epxression. In nearly all organisms, the local chromatin composition sets the stage for further, more specific mechanisms of regulation, such as sequence-specific transcription factors [97].…”

Trypanosoma brucei TIF2 suppresses VSG switching by maintaining subtelomere integrity

“…ChIP was performed according to [64]. ChIP products were hybridized with a TTAGGG or a 50-bp repeat probes in slot blot analysis.…”

Structure of the C-terminal domain of transcription factor IIB from Trypanosoma brucei

“…The lack of an extensive basic surface on trypanosome TFIIB may reflect a relaxed specificity of tRNAP-II orientation at promoters in trypanosomes. Most trypanosome protein-encoding genes are transcribed in large arrays that appear to initiate bidirectionally from strand switch regions (35)(36)(37). Weak specificity of preinitiation complex orientation could cause bidirectional transcription from strand switch regions.…”