APRICOT: an integrated computational pipeline for the sequence-based identification and characterization of RNA-binding proteins

M Sharan, KU Förstner, A Eulalio… - Nucleic acids …, 2017 - academic.oup.com
RNA-binding proteins (RBPs) have been established as core components of several post-
transcriptional gene regulation mechanisms. Experimental techniques such as cross-linking …

Quantitative proteomic analysis reveals concurrent RNA–protein interactions and identifies new RNA-binding proteins in Saccharomyces cerevisiae

DM Klass, M Scheibe, F Butter, GJ Hogan… - Genome …, 2013 - genome.cshlp.org
A growing body of evidence supports the existence of an extensive network of RNA-binding
proteins (RBPs) whose combinatorial binding affects the post-transcriptional fate of every …

Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast

AP Gerber, D Herschlag, PO Brown - PLoS biology, 2004 - journals.plos.org
Genes encoding RNA-binding proteins are diverse and abundant in eukaryotic genomes.
Although some have been shown to have roles in post-transcriptional regulation of the …

Multifunctional RNA-binding proteins influence mRNA abundance and translational efficiency of distinct sets of target genes

V Schneider-Lunitz, J Ruiz-Orera… - PLoS Computational …, 2021 - journals.plos.org
RNA-binding proteins (RBPs) can regulate more than a single aspect of RNA metabolism.
We searched for such previously undiscovered multifunctionality within a set of 143 RBPs …

Systems perspectives on mRNA processing

AE McKee, PA Silver - Cell research, 2007 - nature.com
The application of genomic technologies to the study of mRNA processing is increasingly
conducted in metazoan organisms in order to understand the complex events that occur …

A catalog of stability-associated sequence elements in 3'UTRs of yeast mRNAs

R Shalgi, M Lapidot, R Shamir, Y Pilpel - Genome biology, 2005 - Springer
Background In recent years, intensive computational efforts have been directed towards the
discovery of promoter motifs that correlate with mRNA expression profiles. Nevertheless, it is …

Global analysis of yeast mRNPs

SF Mitchell, S Jain, M She, R Parker - Nature structural & molecular …, 2013 - nature.com
Proteins regulate gene expression by controlling mRNA biogenesis, localization, translation
and decay. Identifying the composition, diversity and function of mRNA–protein complexes …

Profiling condition-specific, genome-wide regulation of mRNA stability in yeast

BC Foat, SS Houshmandi, WM Olivas… - Proceedings of the …, 2005 - National Acad Sciences
The steady-state abundance of an mRNA is determined by the balance between
transcription and decay. Although regulation of transcription has been well studied both …

RNA regulons: coordination of post-transcriptional events

JD Keene - Nature Reviews Genetics, 2007 - nature.com
Recent findings demonstrate that multiple mRNAs are co-regulated by one or more
sequence-specific RNA-binding proteins that orchestrate their splicing, export, stability …

Conserved mRNA-binding proteomes in eukaryotic organisms

AM Matia-González, EE Laing, AP Gerber - Nature structural & …, 2015 - nature.com
RNA-binding proteins (RBPs) are essential for post-transcriptional regulation of gene
expression. Recent high-throughput screens have dramatically increased the number of …