Abstract

In-depth analysis of the transcriptomes of several model organisms has revealed that genomes are pervasively transcribed, giving rise to an abundance of non-canonical and mainly antisense RNA -polymerase II-derived transcripts that are produced from almost any genomic context. These RNAs are degraded by surveillance mechanisms, but the repertoire of cellular factors that control the fate of these non-productive transcripts is still incomplete. Trypanosomes are single-celled eukaryotes that show constitutive RNA polymerase II transcription and have a very unusual genome architecture. In these organisms, the initiation and termination of transcription occur at a limited number of sites per chromosome, and the regulation of gene expression is exerted mainly at the post-transcriptional level. It is not known whether pervasive transcription exists in organisms with unregulated RNA polymerase II activity, and which factors could be involved in the process. In this work, we show that depletion of RBP33 , an RNA -binding protein apparently unique in trypanosomatids, results in the overexpression of up to 40% of all annotated genes in the genome, with a marked accumulation of sense and antisense transcripts derived from silenced regions. RBP33 loss does not result in a significant increase in chromatin accessibility, as judged by ATAC -seq analysis. Finally, we have found that transcripts that increase in abundance upon RBP33 knockdown are significantly more stable in RBP33 -depleted trypanosomes, and that the exosome complex is responsible for their degradation. Our results provide strong evidence that RBP33 dampens non-productive transcription in trypanosomes.

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