The RNA-binding protein RBP33 dampens non-productive transcription in trypanosomes.

Area of Science:

• Molecular Biology
• Genetics
• Eukaryotic Gene Regulation

Background:

• Genomes are pervasively transcribed, producing abundant non-canonical and antisense RNA polymerase II transcripts.
• RNA surveillance mechanisms degrade these non-productive transcripts, but the involved proteins are not fully identified.
• Trypanosomes exhibit constitutive RNA polymerase II transcription with limited initiation/termination sites.

Purpose of the Study:

• To investigate pervasive transcription in trypanosomes, organisms with unregulated RNA polymerase II activity.
• To identify factors involved in regulating pervasive transcription in trypanosomes.
• To determine the role of RBP33 in controlling non-productive transcription.

Main Methods:

• Depletion of RBP33 protein in trypanosomes using knockdown techniques.
• Transcriptome analysis to identify changes in gene expression and RNA abundance.
• Assessment of chromatin accessibility.
• RNA stability assays and investigation of the exosome complex's role.

Main Results:

• RBP33 depletion caused overexpression of approximately 40% of annotated genes.
• Accumulation of sense and antisense transcripts from silenced regions was observed upon RBP33 loss.
• Chromatin accessibility did not significantly increase after RBP33 depletion.
• Transcripts accumulating upon RBP33 knockdown were more stable, and the exosome complex mediated their degradation.

Conclusions:

• RBP33 plays a crucial role in dampening non-productive transcription in trypanosomes.
• The exosome complex is essential for degrading pervasive transcripts that accumulate when RBP33 is depleted.
• These findings reveal a novel regulatory mechanism for pervasive transcription in eukaryotes.