The RNA fold interactome of evolutionary conserved RNA structures in S. cerevisiae

N Casas-Vila, S Sayols, L Pérez-Martínez… - Nature …, 2020 - nature.com
RNA-binding proteins play key roles in regulation of gene expression via recognition of
structural features in RNA molecules. Here we apply a quantitative RNA pull-down approach …

Nuclear mRNA Quality Control and Cytoplasmic NMD Are Linked by the Guard Proteins Gbp2 and Hrb1

YY Lu, H Krebber - International Journal of Molecular Sciences, 2021 - mdpi.com
Pre-mRNA splicing is critical for cells, as defects in this process can lead to altered open
reading frames and defective proteins, potentially causing neurodegenerative diseases and …

PAR-CLIP for discovering target sites of RNA-binding proteins

A Garzia, P Morozov, M Sajek, C Meyer… - mRNA Decay: Methods …, 2018 - Springer
RNA-binding proteins (RBPs) establish posttranscriptional gene regulation (PTGR) by
coordinating the maturation, editing, transport, stability, and translation of cellular RNAs. A …

RNA recognition by Npl3p reveals U2 snRNA-binding compatible with a chaperone role during splicing

A Moursy, A Cléry, S Gerhardy, KM Betz, S Rao… - Nature …, 2023 - nature.com
The conserved SR-like protein Npl3 promotes splicing of diverse pre-mRNAs. However, the
RNA sequence (s) recognized by the RNA Recognition Motifs (RRM1 & RRM2) of Npl3 …

Genetic and pharmacological evidence for kinetic competition between alternative poly (A) sites in yeast

RE Turner, PF Harrison, A Swaminathan… - Elife, 2021 - elifesciences.org
Most eukaryotic mRNAs accommodate alternative sites of poly (A) addition in the
3'untranslated region in order to regulate mRNA function. Here, we present a systematic …

Ipa1 is an RNA polymerase II elongation factor that facilitates termination by maintaining levels of the poly (A) site endonuclease Ysh1

EL Pearson, JH Graber, SD Lee, KS Naggert… - Cell reports, 2019 - cell.com
The yeast protein Ipa1 was recently discovered to interact with the Ysh1 endonuclease of
the pre-mRNA cleavage and polyadenylation (C/P) machinery, and Ipa1 mutation impairs …

Emerging properties of nuclear RNP biogenesis and export

M Oeffinger, B Montpetit - Current Opinion in Cell Biology, 2015 - Elsevier
RNA biology has recently seen an explosion of data due to advances in RNA sequencing,
proteomic, and RNA imaging technologies. In this review, we highlight progress that has …

Modeling the ribosomal small subunit dynamic in Saccharomyces cerevisiae based on TCP-seq data

T Neumann, T Tuller - Nucleic Acids Research, 2022 - academic.oup.com
Abstract Translation Complex Profile Sequencing (TCP-seq), a protocol that was developed
and implemented on Saccharomyces cerevisiae, provides the footprints of the small subunit …

Loss of PABPC1 is compensated by elevated PABPC4 and correlates with transcriptome changes

J Xie, X Wei, Y Chen, K Gehring - BioRxiv, 2021 - biorxiv.org
Cytoplasmic poly (A) binding protein (PABP) is an essential translation factor that binds to
the 3'tail of mRNAs to promote translation and regulate mRNA stability. PABPC1 is the most …

A guard protein mediated quality control mechanism monitors 5'-capping of pre-mRNAs

S Klama, AG Hirsch, UM Schneider… - Nucleic acids …, 2022 - academic.oup.com
Efficient gene expression requires properly matured mRNAs for functional transcript
translation. Several factors including the guard proteins monitor maturation and act as …