The structure of messenger RNA is important for post-transcriptional regulation, mainly because it affects binding of trans-acting factors. However, little is known about the in vivo structure of ...full-length mRNAs. Here we present hiCLIP, a biochemical technique for transcriptome-wide identification of RNA secondary structures interacting with RNA-binding proteins (RBPs). Using this technique to investigate RNA structures bound by Staufen 1 (STAU1) in human cells, we uncover a dominance of intra-molecular RNA duplexes, a depletion of duplexes from coding regions of highly translated mRNAs, an unexpected prevalence of long-range duplexes in 3' untranslated regions (UTRs), and a decreased incidence of single nucleotide polymorphisms in duplex-forming regions. We also discover a duplex spanning 858 nucleotides in the 3' UTR of the X-box binding protein 1 (XBP1) mRNA that regulates its cytoplasmic splicing and stability. Our study reveals the fundamental role of mRNA secondary structures in gene expression and introduces hiCLIP as a widely applicable method for discovering new, especially long-range, RNA duplexes.
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DOBA, IJS, IZUM, KILJ, KISLJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Cold shock domain (CSD)-containing proteins have been found in all three domains of life and function in a variety of processes that are related, for the most part, to post-transcriptional gene ...regulation. The CSD is an ancient β-barrel fold that serves to bind nucleic acids. The CSD is structurally and functionally similar to the S1 domain, a fold with otherwise unrelated primary sequence. The flexibility of the CSD/S1 domain for RNA recognition confers an enormous functional versatility to the proteins that contain them. This review summarizes the current knowledge on eukaryotic CSD/S1 domain-containing proteins with a special emphasis on UNR (upstream of N-ras), a member of this family with multiple copies of the CSD.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
Genetic equality between males and females is established by chromosome-wide dosage-compensation mechanisms. In the fruitfly Drosophila melanogaster, the dosage-compensation complex promotes twofold ...hypertranscription of the single male X-chromosome and is silenced in females by inhibition of the translation of msl2, which codes for the limiting component of the dosage-compensation complex. The female-specific protein Sex-lethal (Sxl) recruits Upstream-of-N-ras (Unr) to the 3' untranslated region of msl2 messenger RNA, preventing the engagement of the small ribosomal subunit. Here we report the 2.8 Å crystal structure, NMR and small-angle X-ray and neutron scattering data of the ternary Sxl-Unr-msl2 ribonucleoprotein complex featuring unprecedented intertwined interactions of two Sxl RNA recognition motifs, a Unr cold-shock domain and RNA. Cooperative complex formation is associated with a 1,000-fold increase of RNA binding affinity for the Unr cold-shock domain and involves novel ternary interactions, as well as non-canonical RNA contacts by the α1 helix of Sxl RNA recognition motif 1. Our results suggest that repression of dosage compensation, necessary for female viability, is triggered by specific, cooperative molecular interactions that lock a ribonucleoprotein switch to regulate translation. The structure serves as a paradigm for how a combination of general and widespread RNA binding domains expands the code for specific single-stranded RNA recognition in the regulation of gene expression.
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DOBA, IJS, IZUM, KILJ, KISLJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Dosage compensation is a regulatory process that balances the expression of X-chromosomal genes between males (XY) and females (XX). In Drosophila, this requires non-coding RNAs and RNA-binding ...proteins (RBPs) whose specific functions remain elusive. Here we show that the Drosophila RBP UNR promotes the targeting of the activating male-specific-lethal complex to the X-chromosome by facilitating the interaction of two crucial subunits: the RNA helicase MLE and the long non-coding RNA roX2.
RNA regulation plays a major role in the generation of diversity at the molecular and cellular levels, and furnishes the cell with flexibility potential to adapt to changing environments. Often, the ...regulation by/of RNA dictates when, where, and how the information encoded in the nucleus is revealed. One example is the regulation of X‐chromosome dosage compensation. In Drosophila, differences in X‐linked gene dosage between males and females are compensated by the transcriptional upregulation of the single male X chromosome. Mechanisms of alternative splicing and translational control, among others, enforce dosage compensation in males while inhibiting this process in females. In this review, we discuss the posttranscriptional RNA regulatory mechanisms that ensure appropriate dosage compensation in Drosophila, drawing parallels with the mammalian system when appropriate. WIREs RNA 2011 2 534–545 DOI: 10.1002/wrna.75
This article is categorized under:
RNA Interactions with Proteins and Other Molecules > RNA–Protein Complexes
Translation > Translation Regulation
RNA Processing > Splicing Regulation/Alternative Splicing
RNA in Disease and Development > RNA in Development
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FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
Upstream of N-ras (UNR) is a conserved RNA-binding protein that regulates mRNA translation and stability by binding to sites generally located in untranslated regions (UTRs). In Drosophila, ...sex-specific binding of UNR to msl2 mRNA and the noncoding RNA roX is believed to play key roles in the control of X-chromosome dosage compensation in both sexes. To investigate broader sex-specific functions of UNR, we have identified its RNA targets in adult male and female flies by high-throughput RNA binding and transcriptome analysis. Here we show that UNR binds to a large set of protein-coding transcripts and to a smaller set of noncoding RNAs in a sex-specific fashion. The analyses also reveal a strong correlation between sex-specific binding of UNR and sex-specific differential expression of UTRs in target genes. Validation experiments indicate that UNR indeed recognizes sex-specifically processed transcripts. These results suggest that UNR exploits the transcript diversity generated by alternative processing and alternative promoter usage to bind and regulate target genes in a sex-specific manner.
In yeast, many environmental stimuli are sensed and signaled by the MAP kinases pathways. In a previous work, we showed that cesium chloride activates the HOG pathway and modulates the transcription ...of several genes, especially those involved in cell wall biosynthesis and organization. The response to cesium was largely overlapping with the response to salt and osmotic stress. However, when low cesium chloride concentrations were used, a specific response was eventually elicited. The cesium-specific response involved the Yaf9 protein and its activity of chromatin remodeling and transcription regulation. In this paper we show that the osmotic activity of cesium salt is detected and signaled by the two branches downstream of the Sln1 and Sho1 sensors of the HOG pathway, that seem to possess different but exchangeables functions in cesium signaling. However, the cesium-specific response mediated by Yaf9, that counteracts the efficiency of the HOG pathway, is not routed by these sensors. In addition, the cesium response also involves the cell wall integrity (CWI) pathway, which is activated by low concentration of cesium chloride. Mutations blocking the CWI pathway show sensitivity to this salt.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
En Drosophila, el desequilibrio en cuanto al contenido de genes ligados al cromosoma X entre hembras (XX) y machos (XY) es corregido mediante la duplicación de la transcripción del único cromosoma X ...del macho. Este proceso, llamado compensación de dosis, es mediado por un ensamblaje molecular compuesto por al menos cinco proteínas (MSL1, MSL2, MSL3, MLE y MOF) y dos RNAs largos no codificantes (roX1 y roX2), llamado complejo de compensación de dosis (DCC). La compensación de dosis requiere dos condiciones fundamentales: el reconocimiento específico del cromosoma X por el DCC, y la restricción del proceso a moscas macho.
La proteína de unión a RNA Upstream-of-N-Ras (UNR) está implicada en la consecución de ambas condiciones, y aquí hemos estudiado los mecanismos moleculares por los que UNR actúa. Hemos encontrado que, en machos, UNR promueve la compensación de dosis facilitando la asociación de roX2 a MLE, necesaria para una correcta formación del DCC y para su unión al cromosoma X. En hembras, UNR inhibe la compensación de dosis, al menos en parte, promoviendo la unión de SXL al extremo 3’ UTR del mRNA que codifica para msl2, lo que resulta en represión de la traducción de msl2 e inhibición de la formación del DCC.
In Drosophila, the imbalance in X-linked gene content between females (XX) and males (XY) is restored through the 2-fold hypertranscription of the single male X-chromosome. This process, which is called dosage compensation, is mediated by the action of the dosage compensation complex (DCC), a ribonucleoprotein assembly composed of at least five proteins (MSL1, MSL2, MSL3, MLE and MOF) and two long non-coding RNAs (roX1 and roX2). Two features are essential for correct dosage compensation: the specific recognition of the X-chromosome by the DCC and the confinement of the DCC function to the male organism.
The RNA binding protein Upstream of N-ras (UNR) is involved in the regulation of these two processes and we have dissected the molecular mechanisms by which this regulation occurs. We have found that, in male flies, UNR promotes dosage compensation by facilitating the association of roX2 with MLE, which is required for correct DCC formation and X-chromosome targeting. In female flies, UNR represses dosage compensation in part by enhancing the binding of SXL to the 3’UTR of msl2 mRNA, thus ensuring tight msl2 translational repression and subsequent inhibition of DCC formation.
Dosage compensation is a regulatory process that balances the expression of X-chromosomal genes between males (XY) and females (XX). In Drosophila, this requires non-coding RNAs and RNA-binding ...proteins (RBPs) whose specific functions remain elusive. Here we show that the Drosophila RBP UNR promotes the targeting of the activating male-specific-lethal complex to the X-chromosome by facilitating the interaction of two crucial subunits: the RNA helicase MLE and the long non-coding RNA roX2.
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