Dataset Information

RNA-dependent interactome allows network-based assignment of RNA-binding protein function

ABSTRACT: RNA-binding proteins (RBPs) form highly diverse and dynamic ribonucleoprotein complexes, whose functions determine the molecular fate of the bound RNA. In the model organism S. cerevisiae, the number of proteins identified as RBPs has largely increased over the last decade. However, the cellular function for most of these novel RBPs still remains largely unexplored. We use mass spectrometry-based quantitative proteomics to systematically identify protein-protein interactions (PPIs), and RNA-dependent interactions (RDIs) to create a novel data set for 40 RBPs associated with the mRNA life cycle. Domain, functional, and pathway enrichment analysis revealed an overrepresentation of RNA functionalities among the enriched interactors. With the creation of extensive PPI and RDI networks, we revealed putative new members within RNA-associated pathways, as well as highlighted potential new roles of several RBPs, such as metabolism. Our RBP interactome resource is available through an online interactive platform as a community tool to guide further in-depth functional studies and RBP network analysis.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Saccharomyces Cerevisiae (baker's Yeast)

SUBMITTER: F Butter

LAB HEAD: Falk Butter

PROVIDER: PXD035979 | Pride | 2023-07-20

REPOSITORIES: Pride

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Publications

RNA-dependent interactome allows network-based assignment of RNA-binding protein function.

Fradera-Sola Albert A Nischwitz Emily E Bayer Marie Elisabeth ME Luck Katja K Butter Falk F

Nucleic acids research 20230601 10

RNA-binding proteins (RBPs) form highly diverse and dynamic ribonucleoprotein complexes, whose functions determine the molecular fate of the bound RNA. In the model organism Sacchromyces cerevisiae, the number of proteins identified as RBPs has greatly increased over the last decade. However, the cellular function of most of these novel RBPs remains largely unexplored. We used mass spectrometry-based quantitative proteomics to systematically identify protein-protein interactions (PPIs) and RNA-d ...[more]

PMID: 37070168

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Project description:RNA-binding proteins (RBPs) are critical regulators of gene expression and elucidating the interactions of RBPs with their RNA targets is necessary to understand how combinations of RBPs control transcriptome expression. The Quaking-related (QR) sub-family of STAR domain RBPs includes developmental regulators and tumor suppressors such as C. elegans GLD-1, which functions as a master regulator of germ line development. To understand how GLD-1 interacts with the transcriptome, we identified GLD-1 associated mRNAs by a ribonomic approach. The scale of GLD-1 mRNA interactions allowed us to determine rules governing GLD-1 target selection and to derive a predictive model where GLD-1 association with mRNA is based on the number and strength of 7-mer GLD-1 binding elements (GBEs) within UTRs. GLD-1/mRNA interactions were quantified, and predictions were verified both in vitro and in live animals, including by M-bM-^@M-^XtransplantationM-bM-^@M-^Y experiments where M-bM-^@M-^XweakM-bM-^@M-^Y and M-bM-^@M-^XstrongM-bM-^@M-^Y GBEs imposed translational repression of increasing strength on a non-target mRNA.Importantly, this study provides a unique quantitative picture of how an RBP interacts with its mRNA targets. As combinatorial regulation by multiple RBPs is thought to regulate gene expression, quantification of RBP/mRNA interactions should be a way to predict and potentially modify biological outcomes of complex posttranscriptional regulatory networks, and our analysis suggests that such an approach is possible. Wild-type (N2) or gld-1(q485); ozIs2 [gld-1::gfp::flag] worms were synchronized and harvested as young adults. To identify GLD-1 associated transcripts, two independent IP strategies were performed: 1. Comparison of anti-FLAG IP to anti-MYC IP on the gld-1(q485); ozIs2 [gld-1::gfp::flag] worm extract, 2. Comparison of anti-FLAG IP on the gld-1(q485); ozIs2 [gld-1::gfp::flag] worm extract to anti-FLAG IP on wild type extract. All IPs were performed in triplicate (12 IPs).

Dataset Information

RNA-dependent interactome allows network-based assignment of RNA-binding protein function

Publications

RNA-dependent interactome allows network-based assignment of RNA-binding protein function.

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