RNA Targets and Specificity of Staufen, a Double-stranded RNA-binding Protein in Caenorhabditis elegans

LeGendre, Jacqueline Baca; Campbell, Zachary T.; Kroll-Conner, Peggy; Anderson, Phil; Kimble, Judith; Wickens, Marvin

doi:10.1074/jbc.m112.397349

Cited by 50 publications

(54 citation statements)

References 72 publications

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“…In some cases structured 3 ′ UTRs in mammals, Drosophila, and C. elegans, act as targeting sequences for the dsRNA-binding protein Staufen (St Johnston et al 1992;Kim et al 2005;LeGendre et al 2013). In mammals, Staufen1 recruits RNA decay factors, triggering mRNA turnover via the Staufen-mediated decay (SMD) pathway (Kim et al 2005(Kim et al , 2007Gong and Maquat 2011).…”

Section: Comparison Of Eer Data Sets With Data Sets Of Related Studiesmentioning

confidence: 99%

“…Double-stranded regions in 3 ′ UTRs of human mRNAs are bound by Staufen1, and subsequently turned over via Staufen-mediated mRNA decay (Gong and Maquat 2011;Gong et al 2013). A Caenorhabditis elegans homolog of Staufen1 binds over 400 mRNAs, raising the possibility that Staufen-mediated decay is an evolutionarily conserved mRNA regulatory mechanism (LeGendre et al 2013). Long 3 ′ -UTR dsRNA formed by inverted Alus, and other repeats, affects the translatability of both human and C. elegans mRNAs (Hundley et al 2008).…”

Section: Introductionmentioning

confidence: 99%

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Genome-wide profiling of the C. elegans dsRNAome

Whipple

Youssef

Aruscavage

et al. 2015

RNA

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Recent studies hint that endogenous dsRNA plays an unexpected role in cellular signaling. However, a complete understanding of endogenous dsRNA signaling is hindered by an incomplete annotation of dsRNA-producing genes. To identify dsRNAs expressed in Caenorhabditis elegans, we developed a bioinformatics pipeline that identifies dsRNA by detecting clustered RNA editing sites, which are strictly limited to long dsRNA substrates of Adenosine Deaminases that act on RNA (ADAR). We compared two alignment algorithms for mapping both unique and repetitive reads and detected as many as 664 editing-enriched regions (EERs) indicative of dsRNA loci. EERs are visually enriched on the distal arms of autosomes and are predicted to possess strong internal secondary structures as well as sequence complementarity with other EERs, indicative of both intramolecular and intermolecular duplexes. Most EERs were associated with protein-coding genes, with ∼1.7% of all C. elegans mRNAs containing an EER, located primarily in very long introns and in annotated, as well as unannotated, 3 ′ UTRs. In addition to numerous EERs associated with coding genes, we identified a population of prospective noncoding EERs that were distant from protein-coding genes and that had little or no coding potential. Finally, subsets of EERs are differentially expressed during development as well as during starvation and infection with bacterial or fungal pathogens. By combining RNA-seq with freely available bioinformatics tools, our workflow provides an easily accessible approach for the identification of dsRNAs, and more importantly, a catalog of the C. elegans dsRNAome.

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Section: Comparison Of Eer Data Sets With Data Sets Of Related Studiesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genome-wide profiling of the C. elegans dsRNAome

Whipple

Youssef

Aruscavage

et al. 2015

RNA

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“…인체 pumilio 단백질의 RNA 결합 관련 구조를 보면 8개의 반복서열의 제 각 각은 목표 RNA 에 있어서 하나의 핵산을 인식하여 결국 8개 의 핵산과 결합하게 된다 (Wang 등, 2002). 이와 같이 특이적이 며 고도의 친화성 결합 때문에 PUF-RNA 관계를 예측하게 하 고 단백질 결합에 유효하게 응용할 수 있게 한다 (Wang 등, 2002;Opperman 등, 2005;Cheong 과 Hall, 2006 Tat, hnRNPA1, YB-1; Arginine rich Glycine/aromatic residue-rich domains ssRNA, dsRNA Chaudhury et al (2010) TFIIIA, Tra-1, WT1; Zinc finger β β α structure dsRNA Carroll (2011) UNR, CspB, YB-1; CSD (cold-shock domain) β-barrel structure ssRNA, ssDNA Brown and Jackson (2004) hnRNP K, FMR 1; KH (K-homology) 3 β-sheet and α-helices ssRNA, ssDNA Bomsztyk et al (2004) PKR, Stufen, RNAseIII Dicer, ADAR1; dsRBD α β β β α fold dsRNA Legendre et al (2013) elF4A, DHH1; RNA helicase Domain 1 and 2 dsRNA Shen et al (2009) (Glisovic 등, 2008).…”

Section: Rna 결합 부위unclassified

RNA Binding Proteins and its Regulation of Gene Expression

Roh

Kang

Kim

et al. 2015

JABC

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The role of RNA-binding proteins (RBPs) to regulate expression of genes seems to be very important. RBPs play important roles in RNA related bioprocess such as transcription, pre-mRNA splicing, polyadenylation, transport, localization, translation, turn over and maintenance of structure. Despite of many researches on RNA binding proteins, detailed mechanisms of these proteins have not been fully understood. It seems that many parts of RBPs remains unknown and should be characterized for the better understanding of gene expression. Recently, genetic, biochemical, and bioinformatic analysis of genomes revealed a vast array of RBPs and many parts are interesting to understand bioprocessing including gene expression. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons. org/licenses/by-nc/3.0/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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“…A similar analysis in C. elegans demonstrated that the worm ortholog, STAU-1, also possesses an ability to bind doublestranded RNA while retaining a specificity for distinct transcripts in vivo. 100 Analyses of human Stau1 and Stau2 by RIP-CHIP showed that there may be few mRNA targets in common between the two human staufen homologs, 101 and a separate study showed a possible role for staufen in neural lineage progression by promoting asymmetric segregation of some target RNAs.…”

Section: Identification Of Trans-factor Binding Sitesmentioning

confidence: 99%

Genomic analysis of RNA localization

2014

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The localization of mRNAs to specific subcellular sites is widespread, allowing cells to spatially restrict and regulate protein production, and playing important roles in development and cellular physiology. This process has been studied in mechanistic detail for several RNAs. However, the generality or specificity of RNA localization systems and mechanisms that impact the many thousands of localized mRNAs has been difficult to assess. In this review, we discuss the current state of the field in determining which RNAs localize, which RNA sequences mediate localization, the protein factors involved, and the biological implications of localization. For each question, we examine prominent systems and techniques that are used to study individual messages, highlight recent genome-wide studies of RNA localization, and discuss the potential for adapting other high-throughput approaches to the study of localization.

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RNA Targets and Specificity of Staufen, a Double-stranded RNA-binding Protein in Caenorhabditis elegans

Cited by 50 publications

References 72 publications

Genome-wide profiling of the C. elegans dsRNAome

Genome-wide profiling of the C. elegans dsRNAome

RNA Binding Proteins and its Regulation of Gene Expression

Genomic analysis of RNA localization

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