How Coordination Between Transcription and RNA Processing Tunes Gene Expression

  • 8 June 2023
    4:00 PM
  • University Campus Bohunice (pavilion B11/ seminar room 132)

Lecture will be held in English


Hosted by

Dalibor Blažek

About the lecture


Control of gene output by co-transcriptional RNA processing mechanisms

Karla M Neugebauer, Tucker Carrocci, Helia Gagnon, Jackson Gordon, David Phizicky, Leonard Schaerfen, Dagmar Zigackova

Our lab has been investigating the coordination of splicing with other RNA processing events and with transcription. We have developed methods that detect temporal and spatial coupling between transcription and splicing, in which splicing chemistry often occurs prior to the synthesis of the complete nascent RNA chain. For yeast and mammalian genes, spliced exon-exon junctions can be observed when RNA polymerase II (Pol II) is just downstream of the 3’ splice site. We have used PRO-seq to evaluate transcription behavior and do not observe pausing at 5' or 3' splice sites, indicating that splicing occurs rapidly and on the timescale of transcription elongation. Here I will discuss two recent discoveries: First, we discovered “all-or-none” RNA processing by sequencing individual nascent transcripts from S. pombe, S. cerevisiae, mouse, and human cells. “All” transcripts are efficiently spliced and cleaved at the polyA site, while “none” transcripts have all introns retained and fail to cleave at the 3’ end. Second, we have found that productive splicing takes place when Pol II is elongating through a limited gene region downstream of introns, which we call the “splicing zone”. This limitation in space and time creates a gene-specific amount of “none” transcripts, since inefficient intron sequences reduce the number of transcripts that are spliced while Pol II is in the splicing zone. If splicing were to continue indefinitely, the efficiency of intron splicing might have no impact on gene expression. Accordingly, we have created a new reporter system in budding yeast that clearly establishes the importance of splicing efficiency for mRNA and protein production on a gene-specific and sequence-specific basis. One implication of these findings could be that the intron or its splice sites become inaccessible to the spliceosome after a certain amount of nascent RNA is transcribed. Interestingly, some genes like human and mouse b-globin are highly susceptible to all-or-none RNA processing behavior, and we are currently investigating the molecular mechanisms that contribute to all-or-none behavior as well as the fate of intron-retained RNAs in the cell nucleus. I will discuss our evidence that “none” transcripts can persist in the nucleus until their degradation, explaining why intron half-life is not a good proxy for splicing kinetics. Although some individual introns can be specifically and temporarily retained in certain developmental pathways, “none” transcripts can significantly reduce gene output akin to the activity of a transcriptional repressor. We are interested in understanding the potential function of the resulting unprocessed transcripts, which could in some cases serve an important off-pathway function and/or undergo maturation later.


Registration for lunch with the speaker /for Ph.D. students/

The sponsored lunch usually takes place in the Campus River restaurant. Please meet the speaker and other students at 12:45 at the reception desk at the main entrance (building B22, see the map below).

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