DS0405 -

Analysis of the role of non-coding transcription termination in regulation of gene expression (TerReg) – TerReg

Submission summary

Pervasive transcription is a widespread phenomenon both in prokaryotes and in eukaryotes that consists in the massive production of RNAs from unannotated regions of the genome. Pervasive transcription poses a risk that needs to be controlled since it can interfere with normal transcription of canonical genes. In Saccharomyces cerevisiae, a major actor in the control of pervasive transcription is the Nrd1-Nab3-Sen1 (NNS) complex, which elicits early termination of non-coding transcription and promotes degradation of the RNAs produced by the nuclear exosome. The NNS-complex is composed of three essential proteins: the RNA-binding proteins Nrd1 and Nab3 and the conserved RNA and DNA helicase Sen1. Nrd1 and Nab3 provide specificity to the complex by recognizing specific motifs at the target ncRNAs while Sen1 triggers dissociation of the elongation complex in an ATP-dependent manner.
Besides its general role in protecting the genome against pervasive transcription, termination by the NNS-complex can play a role in modulation of gene expression, either directly, by eliciting premature termination of transcription of protein-coding genes, or indirectly, by determining the extent of non-coding transcription events that may impact the expression of an associated gene in a regulated manner. Non-coding RNAs whose transcription potentially or “de facto” affects the expression of an associated gene normally are either transcribed upstream of a tandem gene or antisense to the cognate gene. In both cases, non-coding transcription that progresses through the promoter region of the downstream or antisense gene induces repression by mechanisms that involve the deposition of repressive chromatin modifications at the promoter and/or chromatin remodelling that prevents the association of activator proteins.
Genome-wide studies have revealed more than 1300 ncRNAs that depend on the NNS-complex and that are in one of the two configurations that is suggestive of a possible repressor role. Importantly, in many of these cases depletion of the Nrd1 component of the NNS-complex actually provokes misregulation of the cognate genes, supporting the idea that the efficiency of ncRNA transcription termination is a potentially relevant parameter in regulating gene expression. Thus far, NNS-dependent transcription termination has been considered rather as a “constitutive” process that protects the coding transcriptome from pervasive transcription and keeps the expression of attenuated genes low. In addition, previous works on regulatory non-coding transcription have focused on the regulation of expression of the ncRNA at the level of transcription initiation or RNA stability but to date there is no systematic study considering the step of transcription termination as the target for regulation. The goal of this project is to explore the possibility that regulation of the expression of a subset of genes in response to environmental changes is mediated by modulation of the efficiency of NNS-dependent transcription termination.
Because the helicase Sen1 is the key player in transcription termination by the NNS pathway, the working hypothesis is that most regulatory events act at the level of Sen1 function, either by modulating its recruitment to the elongation complex or by directly affecting its enzymatic activity. This project includes a combination of molecular approaches and genome-wide studies to: i) characterize the mechanisms of control of Sen1 activity by both intra-and inter-molecular interactions as well as by post-translational modifications; ii) understand how these mechanisms can impact the efficiency of transcription termination and therefore gene expression; iii) identify physiological conditions in which non-coding transcription termination is affected in a way that leads to regulation of an associated gene and iv) explore a possible molecular link between this phenomenon and Sen1 activity and identify the actors and mechanisms involved.

Project coordination

Odil PORRUA (Institut Jacques Monod)

The author of this summary is the project coordinator, who is responsible for the content of this summary. The ANR declines any responsibility as for its contents.

Partner

IJM Institut Jacques Monod

Help of the ANR 213,948 euros
Beginning and duration of the scientific project: December 2016 - 42 Months

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