ABSTRACT
Regulation of mRNA stability by RNA-protein interactions contributes significantly to quantitative aspects of gene expression. We have identified potential mRNA targets of the AU-rich element binding protein AUF1. Myc-tagged AUF1 p42 was induced in mouse NIH/3T3 cells and RNA-protein complexes isolated using anti-myc tag antibody beads. Bound mRNAs were analyzed with Affymetrix microarrays. We have identified 508 potential target mRNAs that were at least 3-fold enriched compared to control cells without myc-AUF1. 22.3% of the enriched mRNAs had an AU-rich cluster in the ARED Organism database, against 16.3% of non-enriched control mRNAs. The enrichment towards AU-rich elements was also visible by AREScore with an average value of 5.2 in the enriched mRNAs versus 4.2 in the control group. Yet, numerous mRNAs were enriched without a high ARE score. The enrichment of tetrameric and pentameric sequences suggests a broad AUF1 p42-binding spectrum at short U-rich sequences flanked by A or G. Still, some enriched mRNAs were highly unstable, as those of TNFSF11 (known as RANKL), KLF10, HES1, CCNT2, SMAD6, and BCL6. We have mapped some of the instability determinants. HES1 mRNA appeared to have a coding region determinant. Detailed analysis of the RANKL and BCL6 3'UTR revealed for both that full instability required two elements, which are conserved in evolution. In RANKL mRNA both elements are AU-rich and separated by 30 bases, while in BCL6 mRNA one is AU-rich and 60 bases from a non AU-rich element that potentially forms a stem-loop structure.
Subject(s)
Heterogeneous-Nuclear Ribonucleoprotein D/metabolism , Proto-Oncogene Proteins c-bcl-6/genetics , RANK Ligand/genetics , RNA Stability/genetics , 3' Untranslated Regions/genetics , AU Rich Elements/genetics , Animals , Binding Sites/genetics , HEK293 Cells , Heterogeneous Nuclear Ribonucleoprotein D0 , Heterogeneous-Nuclear Ribonucleoprotein D/genetics , Humans , Mice , NIH 3T3 Cells , Oligonucleotide Array Sequence Analysis , Protein Isoforms/genetics , Protein Isoforms/metabolism , Proto-Oncogene Proteins c-bcl-6/metabolism , RANK Ligand/metabolism , RNA, Messenger/genetics , RNA, Messenger/metabolismABSTRACT
Interleukin-6 mRNA is unstable and degraded with a half-life of 30 min. Instability determinants can entirely be attributed to the 3' untranslated region. By grafting segments of this region to stable green fluorescent protein mRNA and subsequent scanning mutagenesis, we have identified two conserved elements, which together account for most of the instability. The first corresponds to a short noncanonical AU-rich element. The other, 80 nucleotides further 5', comprises a sequence predicted to form a stem-loop structure. Neither element alone was sufficient to confer full instability, suggesting that they might cooperate. Overexpression of myc-tagged AUF1 p37 and p42 isoforms as well as suppression of endogenous AUF1 by RNA interference stabilized interleukin-6 mRNA. Both effects required the AU-rich instability element. Similarly, the proteasome inhibitor MG132 stabilized interleukin-6 mRNA probably through an increase of AUF1 levels. The mRNA coimmunoprecipitated specifically with myc-tagged AUF1 p37 and p42 in cell extracts but only when the AU-rich instability element was present. These results indicate that AUF1 binds to the AU-rich element in vivo and promotes IL-6 mRNA degradation.
Subject(s)
3' Untranslated Regions , Heterogeneous-Nuclear Ribonucleoprotein D/genetics , Interleukin-6/genetics , RNA Processing, Post-Transcriptional , RNA Stability , RNA/metabolism , Animals , Base Sequence , COS Cells , Chlorocebus aethiops , Green Fluorescent Proteins/genetics , Heterogeneous Nuclear Ribonucleoprotein D0 , Heterogeneous-Nuclear Ribonucleoprotein D/metabolism , Interleukin-6/metabolism , Molecular Sequence Data , Mutagenesis , Point Mutation , Proteasome Endopeptidase Complex/genetics , Sequence Homology, Nucleic AcidABSTRACT
Cyclins are the essential regulatory subunits of cyclin-dependent protein kinases. They accumulate and disappear periodically at specific phases of the cell cycle. Here we investigated whether variations in cyclin mRNA levels in exponentially growing cells can be attributed to changes in mRNA stability. Mouse EL4 lymphoma cells and 3T3 fibroblasts were synchronized by elutriation or cell sorting. Steady-state levels and degradation of cyclin mRNAs and some other cell cycle related mRNAs were measured at early G1, late G1, S and G2/M phases. In both cell lines mRNAs of cyclins C, D1 and D3 remained unchanged throughout the cell cycle. In contrast, cyclin A2 and B1 mRNAs accumulated 3.1- and 5.7-fold between early G1 and G2/M phase, whereas cyclin E1 mRNA decreased 1.7-fold. Mouse cyclin A2 and B1 genes, by alternative polyadenylation, gave rise to more than one transcript. In both cases, the longer transcripts were the minor species but accumulated more strongly in G2/M phase. All mRNAs were rather stable with half-lives of 1.5-2 h for cyclin E1 mRNA and 3-4 h for the others. Changes in mRNA stability accounted for the accumulation in G2/M phase of the short cyclin A2 and B1 mRNAs, but contributed only partially to changes in levels of the other mRNAs.
