Abstract
In eukaryotic cells, aberrant mRNPs with processing and packaging defects are targeted co-transcriptionally by a surveillance system that triggers their nuclear retention and ultimately the degradation of their mRNA component by the 3′–5′ activity of the exosome-associated exonuclease Rrp6. This mRNP quality control process is stimulated by the NNS complex (Nrd1-Nab3-Sen1), which otherwise mediates termination, processing, and decay of ncRNAs. The process involves also the exosome co-activator TRAMP complex (Trf4-Air2-Mtr4). Here, we describe a genome-wide approach to visualize the dynamic movement and coordination of these quality control components over the yeast chromosomes upon perturbation of mRNP biogenesis. The method provides valuable information on how the surveillance system is precisely coordinated both physically and functionally with the transcription machinery to detect the faulty events during perturbation of mRNP biogenesis. The overview shows also that the gathering of the quality control components over affected mRNA genes takes place at the expense of their commitment to be recruited at ncRNA genomic features, provoking termination and processing defects of ncRNAs.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Bentley DL (2014) Coupling mRNA processing with transcription in time and space. Nat Rev Genet 15:163–175
Luna R, Gaillard H, Gonzalez-Aguilera C et al (2008) Biogenesis of mRNPs: integrating different processes in the eukaryotic nucleus. Chromosoma 117:319–331
Doma MK, Parker R (2007) RNA quality control in eukaryotes. Cell 131:660–668
Fasken MB, Corbett AH (2005) Process or perish: quality control in mRNA biogenesis. Nat Struct Mol Biol 12:482–488
Schmid M, Jensen TH (2013) Transcription-associated quality control of mRNP. Biochim Biophys Acta 1829:158–168
Rougemaille M, Gudipati RK, Olesen JR et al (2007) Dissecting mechanisms of nuclear mRNA surveillance in THO/sub2 complex mutants. EMBO J 26:2317–2326
Villa T, Rougemaille M, Libri D (2008) Nuclear quality control of RNA polymerase II ribonucleoproteins in yeast: tilting the balance to shape the transcriptome. Biochim Biophys Acta 1779:524–531
Mosrin-Huaman C, Honorine R, Rahmouni AR (2009) Expression of bacterial Rho factor in yeast identifies new factors involved in the functional interplay between transcription and mRNP biogenesis. Mol Cell Biol 29:4033–4044
Mosrin-Huaman C, Hervouet-Coste N, Le Dantec A, Stuparevic I, Rahmouni AR (2014) Bacterial Rho helicase: a new tool to dissect mRNP biogenesis and quality control in yeast. Trends Cell Mol Biol 9:79–93
Vasiljeva L, Kim M, Mutschler H et al (2008) The Nrd1-Nab3-Sen1 termination complex interacts with the Ser5-phosphorylated RNA polymerase II C-terminal domain. Nat Struct Mol Biol 15:795–804
Honorine R, Mosrin-Huaman C, Hervouet-Coste N et al (2011) Nuclear mRNA quality control in yeast is mediated by Nrd1 co-transcriptional recruitment, as revealed by the targeting of Rho-induced aberrant transcripts. Nucleic Acids Res 39:2809–2820
Stuparevic I, Mosrin-Huaman C, Hervouet-Coste N et al (2013) Cotranscriptional recruitment of RNA exosome cofactors Rrp47p and Mpp6p and two distinct Trf-Air-Mtr4 polyadenylation (TRAMP) complexes assists the exonuclease Rrp6p in the targeting and degradation of an aberrant messenger ribonucleoprotein particle (mRNP) in yeast. J Biol Chem 288:31816–31829
Moreau K, Le Dantec A, Mosrin-Huaman C et al (2019) Perturbation of mRNP biogenesis reveals a dynamic landscape of the Rrp6-dependent surveillance machinery trafficking along the yeast genome. RNA Biol 16:879–889
Baudin-Baillieu A, Guillemet E, Cullin C et al (1997) Construction of a yeast strain deleted for the TRP1 promoter and coding region that enhances the efficiency of the polymerase chain reaction-disruption method. Yeast 13:353–356
Schmitt ME, Brown TA, Trumpower BL (1990) A rapid and simple method for preparation of RNA from Saccharomyces cerevisiae. Nucleic Acids Res 18:3091–3092
Xu Z, Wei W, Gagneur J et al (2009) Bidirectional promoters generate pervasive transcription in yeast. Nature 457:1033–1037
Neil H, Malabat C, d’Aubenton-Carafa Y et al (2009) Widespread bidirectional promoters are the major source of cryptic transcripts in yeast. Nature 457:1038
Janke C, Magiera MM, Rathfelder N et al (2004) A versatile toolbox for PCR-based tagging of yeast genes: new fluorescent proteins, more markers and promoter substitution cassettes. Yeast 21:947–962
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2021 Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Moreau, K., Le Dantec, A., Rahmouni, A.R. (2021). Deciphering the Dynamic Landscape of Transcription-Associated mRNP Quality Control Components Over the Whole Yeast Genome. In: Boudvillain, M. (eds) RNA Remodeling Proteins. Methods in Molecular Biology, vol 2209. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0935-4_16
Download citation
DOI: https://doi.org/10.1007/978-1-0716-0935-4_16
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-0716-0934-7
Online ISBN: 978-1-0716-0935-4
eBook Packages: Springer Protocols