Cosmin's RNA resources ⋰⋱⋰

Publications

Posted on Jan 9, 2023

Selected publications (or preprints)

Poly(A) tail dynamics under wt and deadenylase deficient conditions

Audebert L, Feuerbach F, Decourty L, Namane A, Permal E, Badis G, Saveanu C* (2023) Deadenylation rate is not a major determinant of RNA degradation in yeast. bioRxiv. - preprint link

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Inhibition of deadenylation by rapid degradation (degron-induced) of the two deadenylase components of the CCR4-NOT complex leads to longer poly(A) tails for a reporter mRNA, even if the half-life of the reporter was not affected.

Network of interactions among NMD factors

Gilbert A & Saveanu C* (2022) Unusual SMG suspects recruit degradation enzymes in nonsense-mediated mRNA decay. Bioessays e2100296. - review PMID: 35266563

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Network of interactions among NMD factors, as described by large-scale studies.

BioS/B/Y refers to proximity biotinylation studies and AffH/L/Br refers to large scale co-purification results.

Scatterplot with MS results for yeast Upf1

Namane A & Saveanu C* (2022) Composition and dynamics of protein complexes measured by quantitative mass spectrometry of affinity purified samples. book chapter in Methods in Molecular Biology 2477:225-236, Yeast functional genomics, (Springer), preprint at HAL pasteur-03384570v1 . PMID: 35524120 ISBN: 978-1-0716-2257-5

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Dissection of protein interactions by using truncated protein (horizontal axis) in comparison with full length Upf1 (vertical axis) for purification.

Protein enrichment is on a log2 scale, in comparison with total protein abundance. The interaction of Upf2, Upf3, and decapping complex components depend on the CH region of yeast Upf1

Example of results obtained by large-scale genetic screens, for Puf4 and a physiological mRNA target

Decourty L, Malabat C, Frachon E, Jacquier A & Saveanu C*. Investigation of RNA metabolism through large-scale genetic interaction profiling in yeast. Nucleic Acids Research (2021), Sep 7;49(15):8535-8555. PMID: 34358317

The results can be explored through an interactive web interface at : hub05.hosting.pasteur.fr/GIM_interactions/→

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Example of using quantitative genetic interaction screen results to identify a physiologically relevant substrate for the RNA binding protein Puf4.

Ribosomal protein gene deletion led to growth phenotypes that were either alleviated by the absence of PUF4 or aggravated by it. In the case of RPL9A deletion, the suppression is due to the inhibitory effect of Puf4 on RPL9B expression.

Definition of distinct complexes around the NMD RNA helicase Upf1

Dehecq M, Decourty L, Namane A, Proux C, Kanaan J, Le Hir H, Jacquier A & Saveanu C*. Nonsense-mediated mRNA decay involves two distinct Upf1-bound complexes. EMBO J (2018), Nov 2;37(21):e99278. PMID: 30275269

The protein association results can be explored through an interactive web interface at : hub05.hosting.pasteur.fr/NMD_complexes/→

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Quantitative mass spectrometry defined two distinct NMD complexes.

A little more than 100 purification experiments under various conditions identified proteins that are mutually exclusive in their association with Upf1.

mRNA degradation depends on the size of the coding sequence

Decourty L, Doyen A, Malabat C, Frachon E, Rispal D, Séraphin B, Feuerbach F, Jacquier A & Saveanu C*. Long open reading frame transcripts escape nonsense-mediated mRNA decay in yeast. Cell Rep (2014), Feb 27;;6(4):593-8. PMID: 24529707

A multiplexed assay for over 800 NMD reporters identified coding sequence length as a major determinant of mRNA stability.

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Example of reporter NMD mRNA with different coding sequence length.

Degradation of reporter mRNA was followed over time after specifically blocking their transcription. Longer coding sequences were protective against mRNA degradation through NMD.

Other publications:

PubMed logo PubMed search for C. Saveanu →, for papers as first author→ or last author→ (links open in new tab).