Defining potentially conserved RNA regulons of homologous zinc-finger RNA-binding proteins

Tanja Scherrer,Christian Femmer,André P Gerber,Ruedi Aebersold,Ralph Schiess

doi:10.1186/gb-2011-12-1-r3

Abstract

BackgroundGlucose inhibition of gluconeogenic growth suppressor 2 protein (Gis2p) and zinc-finger protein 9 (ZNF9) are conserved yeast and human zinc-finger proteins. The function of yeast Gis2p is unknown, but human ZNF9 has been reported to bind nucleic acids, and mutations in the ZNF9 gene cause the neuromuscular disease myotonic dystrophy type 2. To explore the impact of these proteins on RNA regulation, we undertook a systematic analysis of the RNA targets and of the global implications for gene expression.ResultsHundreds of mRNAs were associated with Gis2p, mainly coding for RNA processing factors, chromatin modifiers and GTPases. Target mRNAs contained stretches of G(A/U)(A/U) trinucleotide repeats located in coding sequences, which are sufficient for binding to both Gis2p and ZNF9, thus implying strong structural conservation. Predicted ZNF9 targets belong to the same functional categories as seen in yeast, indicating functional conservation, which is further supported by complementation of the large cell-size phenotype of gis2 mutants with ZNF9. We further applied a matched-sample proteome-transcriptome analysis suggesting that Gis2p differentially coordinates expression of RNA regulons, primarily by reducing mRNA and protein levels of genes required for ribosome assembly and by selectively up-regulating protein levels of myosins.ConclusionsThis integrated systematic exploration of RNA targets for homologous RNA-binding proteins indicates an unexpectedly high conservation of the RNA-binding properties and of potential targets, thus predicting conserved RNA regulons. We also predict regulation of muscle-specific genes by ZNF9, adding a potential link to the myotonic dystrophy related phenotypes seen in ZNF9 mouse models.

Highlights

Glucose inhibition of gluconeogenic growth suppressor 2 protein (Gis2p) and zinc-finger protein 9 (ZNF9) are conserved yeast and human zinc-finger proteins
Thereby, RNA isolated from extracts and from the purified samples was competitively analyzed with yeast DNA oligo arrays that contained probes for all annotated yeast open reading frame (ORF) and noncoding RNAs, as well as some intergenic regions
To select RNAs that were consistently enriched with Gis2p and represent likely targets, we compared the association of transcripts from three independent Gis2p affinity purifications with those from five mock control isolates performed with untagged wild-type cells using Significance Analysis of Microarrays (SAM) [35], and determined false discovery rates (FDRs) for each arrayed feature [8,9]

Summary

Introduction

Glucose inhibition of gluconeogenic growth suppressor 2 protein (Gis2p) and zinc-finger protein 9 (ZNF9) are conserved yeast and human zinc-finger proteins. An increasing number of studies in diverse model organisms, applying genomic tools such as DNA microarrays or next-generation sequencing, revealed that RBPs bind to distinct RNA groups that often encode functionally related proteins [7,8,9]. Such organization of RNAs into ‘post-transcriptional operons’ or ‘RNA regulons’ may allow the coherent coordination of mRNA fates [5,10,11]. An extensive bioinformatics study integrating a variety of microarray-based gene expression profile data suggested that Gis is co-regulated with factors contributing to cytoplasmic ribosome function - some of them crucial for cell size control - predicting roles of Gis2p in ribosome biogenesis [17,18]

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Conclusion