Abstract
Protein-coding genes in trypanosomes occur in polycistronic transcription units (PTUs). How RNA polymerase II (Pol II) initiates transcription of PTUs has not been resolved; the current model favors chromatin modifications inducing transcription rather than sequence-specific promoters. Here, we uncover core promoters by functional characterization of Pol II peaks identified by chromatin immunoprecipitation sequencing (ChIP-seq). Two distinct promoters are located between divergent PTUs, each driving unidirectional transcription. Detailed analysis identifies a 75-bp promoter that is necessary and sufficient to drive full reporter expression and contains functional motifs. Analysis of further promoters suggests transcription initiation is regulated and promoters are either focused or dispersed. In contrast to the previous model of unregulated and promoter-independent transcription initiation, we find that sequence-specific promoters determine the initiation of Pol II transcription of protein-coding genes PTUs. These findings in Trypanosoma brucei suggest that in addition of chromatin modifications, promoter motifs-based regulation of gene expression is deeply conserved among eukaryotes.
Highlights
The eukaryotic core promoter is defined as the shortest DNA sequence recognized by general transcription factors (TFs) that leads to the recruitment of RNA polymerase II (Pol II) to drive transcription
Detailed analysis of one promoter revealed a 75-bp core promoter that was necessary and sufficient to confer full activity in reporter assays. These findings show that trypanosomes have sequence-specific promoters and suggest that mRNA levels are potentially regulated at transcription initiation, in addition to the extensive post-transcriptional mechanisms
Specificity of RPB1 antibodies and subnuclear localization of Pol II To facilitate chromatin immunoprecipitation (ChIP) analysis of Pol II accumulation, we developed a rabbit antiserum against residues 1 to 220 of RPB1 (Tb927.4.5020), the large subunit of RNA polymerase II (Pol II)
Summary
The eukaryotic core promoter is defined as the shortest DNA sequence recognized by general transcription factors (TFs) that leads to the recruitment of RNA polymerase II (Pol II) to drive transcription. Core promoters normally contain short-sequence elements, known as motifs or boxes, such as the TATA box, initiator (INR), or downstream position element (Kadonaga, 2012). One example is the polycistronic transcription of most protein-coding genes, which are arranged in tandem arrays transcribed from occasional Pol II transcription initiation sites (Kolev et al, 2010; Siegel et al, 2009; Wedel et al, 2017). There are around 190 of these polycistronic transcription units (PTUs) in the African trypanosome genome (Berriman et al, 2005; Kolev et al, 2010). Co-transcriptional maturation to monocistronic mRNAs occurs by transsplicing the Pol II-transcribed 140-nt capped spliced leader (SL)
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
