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Recent Publications

Total: displaying 10 out of 57 results

  • Structure and Dynamics of the CCCH-Type Tandem Zinc Finger Domain of POS-1 and Implications for RNA Binding Specificity

    Wednesday, September 25, 2024
    Author(s): Asli Ertekin,Brittany R Morgan,Sean P Ryder,Francesca Massi
    Source: Biochemistry
    CCCH-type tandem zinc finger (TZF) motifs are found in many RNA-binding proteins involved in regulating mRNA stability, translation, and splicing. In Caenorhabditis elegans, several RNA-binding protei...

  • The mex-3 3' untranslated region is essential for reproduction during temperature stress

    Monday, May 27, 2024
    Author(s): Hannah E Brown,Haik V Varderesian,Sara A Keane,Sean P Ryder
    Source: bioRxiv : the preprint server for biology
    Organisms must sense temperature and modify their physiology to ensure survival during environmental stress. Elevated temperature leads to reduced fertility in most sexually reproducing organisms. Mat...

  • A nematode model to evaluate microdeletion phenotype expression

    Monday, November 13, 2023
    Author(s): Katianna R Antkowiak,Peren Coskun,Sharon T Noronha,Davide Tavella,Francesca Massi,Sean P Ryder
    Source: G3 (Bethesda, Md.)
    Microdeletion syndromes are genetic diseases caused by multilocus chromosomal deletions too small to be detected by karyotyping. They are typified by complex pleiotropic developmental phenotypes that ...

  • The role of RNA-binding proteins in orchestrating germline development in Caenorhabditis elegans

    Monday, January 23, 2023
    Author(s): Mennatallah M Y Albarqi,Sean P Ryder
    Source: Frontiers in cell and developmental biology
    RNA passed from parents to progeny controls several aspects of early development. The germline of the free-living nematode Caenorhabditis elegans contains many families of evolutionarily conserved RNA...

  • The endogenous mex-3 3´UTR is required for germline repression and contributes to optimal fecundity in C. elegans

    Monday, August 23, 2021
    Author(s): Mennatallah M Y Albarqi,Sean P Ryder
    Source: PLoS genetics
    RNA regulation is essential to successful reproduction. Messenger RNAs delivered from parent to progeny govern early embryonic development. RNA-binding proteins (RBPs) are the key effectors of this pr...

  • Analysis of Emerging Variants in Structured Regions of the SARS-CoV-2 Genome

    Friday, May 21, 2021
    Author(s): Sean P Ryder,Brittany R Morgan,Peren Coskun,Katianna Antkowiak,Francesca Massi
    Source: Evolutionary bioinformatics online
    The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has motivated a widespread effort to understand its epidemiology and pathogenic mechanisms. Modern high-throughput sequencing ...

  • Analysis of Rapidly Emerging Variants in Structured Regions of the SARS-CoV-2 Genome

    Thursday, June 25, 2020
    Author(s): Sean P Ryder,Brittany R Morgan,Francesca Massi
    Source: bioRxiv : the preprint server for biology
    The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has motivated a widespread effort to understand its epidemiology and pathogenic mechanisms. Modern high-throughput sequencing ...

  • A Disorder-to-Order Transition Mediates RNA Binding of the Caenorhabditis elegans Protein MEX-5

    Thursday, April 16, 2020
    Author(s): Davide Tavella,Asli Ertekin,Hila Schaal,Sean P Ryder,Francesca Massi
    Source: Biophysical journal
    CCCH-type tandem zinc finger (TZF) domains are found in many RNA-binding proteins (RBPs) that regulate the essential processes of post-transcriptional gene expression and splicing through direct prote...

  • #CRISPRbabies: Notes on a Scandal

    Tuesday, January 29, 2019
    Author(s): Sean P Ryder
    Source: The CRISPR journal
    No abstract

  • Multi-modal regulation of C. elegans hermaphrodite spermatogenesis by the GLD-1-FOG-2 complex

    Wednesday, January 02, 2019
    Author(s): Shuang Hu,Lauren E Skelly,Ebru Kaymak,Lindsay Freeberg,Te-Wen Lo,Scott Kuersten,Sean P Ryder,Eric S Haag
    Source: Developmental biology
    Proper germ cell sex determination in Caenorhabditis nematodes requires a network of RNA-binding proteins (RBPs) and their target mRNAs. In some species, changes in this network enabled limited XX spe...

  • Polo-like Kinase Couples Cytoplasmic Protein Gradients in the C. elegans Zygote

    Tuesday, December 26, 2017
    Author(s): Bingjie Han,Katianna R Antkowiak,Xintao Fan,Mallory Rutigliano,Sean P Ryder,Erik E Griffin
    Source: Current biology : CB
    Intracellular protein gradients underlie essential cellular and developmental processes, but the mechanisms by which they are established are incompletely understood. During the asymmetric division of...

  • Protein-mRNA interactome capture: cartography of the mRNP landscape

    Saturday, November 04, 2017
    Author(s): Sean P Ryder
    Source: F1000Research
    RNA-binding proteins play a variety of roles in cellular physiology. Some regulate mRNA processing, mRNA abundance, and translation efficiency. Some fight off invader RNA through small RNA-driven sile...

  • Horizontal Gel Electrophoresis for Enhanced Detection of Protein-RNA Complexes

    Wednesday, August 09, 2017
    Author(s): Megan E Dowdle,Susanne Blaser Imboden,Sookhee Park,Sean P Ryder,Michael D Sheets
    Source: Journal of visualized experiments : JoVE
    Native polyacrylamide gel electrophoresis is a fundamental tool of molecular biology that has been used extensively for the biochemical analysis of RNA-protein interactions. These interactions have be...

  • PRIMA: a gene-centered, RNA-to-protein method for mapping RNA-protein interactions

    Friday, July 14, 2017
    Author(s): Alex M Tamburino,Ebru Kaymak,Shaleen Shrestha,Amy D Holdorf,Sean P Ryder,Albertha J M Walhout
    Source: Translation (Austin, Tex.)
    Interactions between RNA binding proteins (RBPs) and mRNAs are critical to post-transcriptional gene regulation. Eukaryotic genomes encode thousands of mRNAs and hundreds of RBPs. However, in contrast...

  • Efficient generation of transgenic reporter strains and analysis of expression patterns in Caenorhabditis elegans using library MosSCI

    Tuesday, June 14, 2016
    Author(s): Ebru Kaymak,Brian M Farley,Samantha A Hay,Chihua Li,Samantha Ho,Daniel J Hartman,Sean P Ryder
    Source: Developmental dynamics : an official publication of the American Association of Anatomists
    CONCLUSIONS: The results provide a generalizable and efficient strategy to assess the functional relevance of protein-RNA interactions in vivo, and reveal new regulatory connections between key RNA-bi...

  • POS-1 Promotes Endo-mesoderm Development by Inhibiting the Cytoplasmic Polyadenylation of neg-1 mRNA

    Tuesday, June 23, 2015
    Author(s): Ahmed Elewa,Masaki Shirayama,Ebru Kaymak,Paul F Harrison,David R Powell,Zhuo Du,Christopher D Chute,Hannah Woolf,Dongni Yi,Takao Ishidate,Jagan Srinivasan,Zhirong Bao,Traude H Beilharz,Sean P Ryder,Cr...
    Source: Developmental cell
    The regulation of mRNA translation is of fundamental importance in biological mechanisms ranging from embryonic axis specification to the formation of long-term memory. POS-1 is one of several CCCH zi...

  • The ssDNA Mutator APOBEC3A Is Regulated by Cooperative Dimerization

    Tuesday, April 28, 2015
    Author(s): Markus-Frederik Bohn,Shivender M D Shandilya,Tania V Silvas,Ellen A Nalivaika,Takahide Kouno,Brian A Kelch,Sean P Ryder,Nese Kurt-Yilmaz,Mohan Somasundaran,Celia A Schiffer
    Source: Structure (London, England : 1993)
    Deaminase activity mediated by the human APOBEC3 family of proteins contributes to genomic instability and cancer. APOBEC3A is by far the most active in this family and can cause rapid cell death when...

  • Personal reflection (RNA journal 20th anniversary)

    Wednesday, March 18, 2015
    Author(s): Sean P Ryder
    Source: RNA (New York, N.Y.)
    No abstract

  • A conserved three-nucleotide core motif defines Musashi RNA binding specificity

    Wednesday, November 05, 2014
    Author(s): N Ruth Zearfoss,Laura M Deveau,Carina C Clingman,Eric Schmidt,Emily S Johnson,Francesca Massi,Sean P Ryder
    Source: The Journal of biological chemistry
    Musashi (MSI) family proteins control cell proliferation and differentiation in many biological systems. They are overexpressed in tumors of several origins, and their expression level correlates with...

  • Allosteric inhibition of a stem cell RNA-binding protein by an intermediary metabolite

    Wednesday, June 18, 2014
    Author(s): Carina C Clingman,Laura M Deveau,Samantha A Hay,Ryan M Genga,Shivender M D Shandilya,Francesca Massi,Sean P Ryder
    Source: eLife
    Gene expression and metabolism are coupled at numerous levels. Cells must sense and respond to nutrients in their environment, and specialized cells must synthesize metabolic products required for the...

  • RNA recognition by the Caenorhabditis elegans oocyte maturation determinant OMA-1

    Tuesday, September 10, 2013
    Author(s): Ebru Kaymak,Sean P Ryder
    Source: The Journal of biological chemistry
    Maternally supplied mRNAs encode proteins that pattern early embryos in many species. In the nematode Caenorhabditis elegans, a suite of RNA-binding proteins regulates expression of maternal mRNAs dur...

  • hnRNP A1 and secondary structure coordinate alternative splicing of Mag

    Saturday, May 25, 2013
    Author(s): N Ruth Zearfoss,Emily S Johnson,Sean P Ryder
    Source: RNA (New York, N.Y.)
    Myelin-associated glycoprotein (MAG) is a major component of myelin in the vertebrate central nervous system. MAG is present in the periaxonal region of the myelin structure, where it interacts with n...

  • Metabolite sensing in eukaryotic mRNA biology

    Thursday, May 09, 2013
    Author(s): Carina C Clingman,Sean P Ryder
    Source: Wiley interdisciplinary reviews. RNA
    All living creatures change their gene expression program in response to nutrient availability and metabolic demands. Nutrients and metabolites can directly control transcription and activate second-m...

  • A compendium of Caenorhabditis elegans RNA binding proteins predicts extensive regulation at multiple levels

    Friday, February 08, 2013
    Author(s): Alex M Tamburino,Sean P Ryder,Albertha J M Walhout
    Source: G3 (Bethesda, Md.)
    Gene expression is regulated at multiple levels, including transcription and translation, as well as mRNA and protein stability. Although systems-level functions of transcription factors and microRNAs...

  • End-labeling oligonucleotides with chemical tags after synthesis

    Tuesday, October 16, 2012
    Author(s): N Ruth Zearfoss,Sean P Ryder
    Source: Methods in molecular biology (Clifton, N.J.)
    Many experimental strategies for determining nucleic acid function require labeling the nucleic acid with radioisotopes or a chemical tag. Labels enable nucleic acid detection, yield information about...

  • POS-1 and GLD-1 repress glp-1 translation through a conserved binding-site cluster

    Friday, October 05, 2012
    Author(s): Brian M Farley,Sean P Ryder
    Source: Molecular biology of the cell
    RNA-binding proteins (RBPs) coordinate cell fate specification and differentiation in a variety of systems. RNA regulation is critical during oocyte development and early embryogenesis, in which RBPs ...

  • Argonaute protein identity and pairing geometry determine cooperativity in mammalian RNA silencing

    Thursday, September 01, 2011
    Author(s): Jennifer A Broderick,William E Salomon,Sean P Ryder,Neil Aronin,Phillip D Zamore
    Source: RNA (New York, N.Y.)
    Small RNAs loaded into Argonaute proteins direct silencing of complementary target mRNAs. It has been proposed that multiple, imperfectly complementary small interfering RNAs or microRNAs, when bound ...

  • FBF represses the Cip/Kip cell-cycle inhibitor CKI-2 to promote self-renewal of germline stem cells in C. elegans

    Tuesday, August 09, 2011
    Author(s): Irene Kalchhauser,Brian M Farley,Sandra Pauli,Sean P Ryder,Rafal Ciosk
    Source: The EMBO journal
    Although the decision between stem cell self-renewal and differentiation has been linked to cell-cycle modifications, our understanding of cell-cycle regulation in stem cells is very limited. Here, we...

  • Pumilio RNA recognition: the consequence of promiscuity

    Tuesday, March 15, 2011
    Author(s): Sean P Ryder
    Source: Structure (London, England : 1993)
    In this issue, Lu and Hall (2011) reveal the structural basis for degenerate RNA recognition by human Pumilio proteins. The structures suggest an appealing model where nucleotides that do not contribu...

  • Quaking regulates Hnrnpa1 expression through its 3' UTR in oligodendrocyte precursor cells

    Saturday, January 22, 2011
    Author(s): N Ruth Zearfoss,Carina C Clingman,Brian M Farley,Lisa M McCoig,Sean P Ryder
    Source: PLoS genetics
    In mice, Quaking (Qk) is required for myelin formation; in humans, it has been associated with psychiatric disease. QK regulates the stability, subcellular localization, and alternative splicing of se...

  • Insights into the structural basis of RNA recognition by STAR domain proteins

    Friday, December 31, 2010
    Author(s): Sean P Ryder,Francesca Massi
    Source: Advances in experimental medicine and biology
    STAR proteins regulate diverse cellular processes and control numerous developmental events. They function at the post-transcriptional level by regulating the stability, sub-cellular distribution, alt...

  • A quantitative RNA code for mRNA target selection by the germline fate determinant GLD-1

    Tuesday, December 21, 2010
    Author(s): Jane E Wright,Dimos Gaidatzis,Mathias Senften,Brian M Farley,Eric Westhof,Sean P Ryder,Rafal Ciosk
    Source: The EMBO journal
    RNA-binding proteins (RBPs) are critical regulators of gene expression. To understand and predict the outcome of RBP-mediated regulation a comprehensive analysis of their interaction with RNA is neces...

  • Quantitative approaches to monitor protein-nucleic acid interactions using fluorescent probes

    Thursday, November 25, 2010
    Author(s): John M Pagano,Carina C Clingman,Sean P Ryder
    Source: RNA (New York, N.Y.)
    Sequence-specific recognition of nucleic acids by proteins is required for nearly every aspect of gene expression. Quantitative binding experiments are a useful tool to measure the ability of a protei...

  • Hidden ribozymes in eukaryotic genome sequence

    Saturday, October 16, 2010
    Author(s): Sean P Ryder
    Source: F1000 biology reports
    The small self-cleaving ribozymes fold into complex tertiary structures to promote autocatalytic cleavage or ligation at a precise position within their sequence. Until recently, relatively few exampl...

  • An economic framework to prioritize confirmatory tests after a high-throughput screen

    Wednesday, June 16, 2010
    Author(s): S Joshua Swamidass,Joshua A Bittker,Nicole E Bodycombe,Sean P Ryder,Paul A Clemons
    Source: Journal of biomolecular screening
    How many hits from a high-throughput screen should be sent for confirmatory experiments? Analytical answers to this question are derived from statistics alone and aim to fix, for example, the false di...

  • Structure and function of nematode RNA-binding proteins

    Tuesday, April 27, 2010
    Author(s): Ebru Kaymak,L M Wee,Sean P Ryder
    Source: Current opinion in structural biology
    RNA-binding proteins are critical effectors of gene expression. They guide mRNA localization, translation, and stability, and potentially play a role in regulating mRNA synthesis. The structural basis...

  • RNA recognition by the embryonic cell fate determinant and germline totipotency factor MEX-3

    Tuesday, November 17, 2009
    Author(s): John M Pagano,Brian M Farley,Kingsley I Essien,Sean P Ryder
    Source: Proceedings of the National Academy of Sciences of the United States of America
    Totipotent stem cells have the potential to differentiate into every cell type. Renewal of totipotent stem cells in the germline and cellular differentiation during early embryogenesis rely upon postt...

  • The N-terminal peptide of the syntaxin Tlg2p modulates binding of its closed conformation to Vps45p

    Wednesday, August 12, 2009
    Author(s): Melonnie L M Furgason,Chris MacDonald,Scott G Shanks,Sean P Ryder,Nia J Bryant,Mary Munson
    Source: Proceedings of the National Academy of Sciences of the United States of America
    The Sec1/Munc18 (SM) protein family regulates intracellular trafficking through interactions with individual SNARE proteins and assembled SNARE complexes. Revealing a common mechanism of this regulati...

  • Monitoring assembly of ribonucleoprotein complexes by isothermal titration calorimetry

    Wednesday, November 05, 2008
    Author(s): Michael I Recht,Sean P Ryder,James R Williamson
    Source: Methods in molecular biology (Clifton, N.J.)
    Isothermal titration calorimetry (ITC) is a useful technique to study RNA-protein interactions as it provides the only method by which the thermodynamic parameters of free energy, enthalpy, and entrop...

  • Quantitative analysis of protein-RNA interactions by gel mobility shift

    Wednesday, November 05, 2008
    Author(s): Sean P Ryder,Michael I Recht,James R Williamson
    Source: Methods in molecular biology (Clifton, N.J.)
    The gel mobility shift assay is routinely used to visualize protein-RNA interactions. Its power resides in the ability to resolve free from bound RNA with high resolution in a gel matrix. We review th...

  • RNA target specificity of the embryonic cell fate determinant POS-1

    Tuesday, October 28, 2008
    Author(s): Brian M Farley,John M Pagano,Sean P Ryder
    Source: RNA (New York, N.Y.)
    Specification of Caenorhabditis elegans body axes and cell fates occurs prior to the activation of zygotic transcription. Several CCCH-type tandem zinc finger (TZF) proteins coordinate local activatio...

  • Post-transcriptional regulation of myelin formation

    Wednesday, July 02, 2008
    Author(s): N Ruth Zearfoss,Brian M Farley,Sean P Ryder
    Source: Biochimica et biophysica acta
    Myelin is a specialized structure of the nervous system that both enhances electrical conductance and protects neurons from degeneration. In the central nervous system, extensively polarized oligodend...

  • Regulation of maternal mRNAs in early development

    Friday, March 28, 2008
    Author(s): Brian M Farley,Sean P Ryder
    Source: Critical reviews in biochemistry and molecular biology
    Most sexually reproducing metazoans are anisogamous, meaning that the two gametes that combine during fertilization differ greatly in size. By convention, the larger gametes are considered female and ...

  • Molecular basis of RNA recognition by the embryonic polarity determinant MEX-5

    Thursday, February 01, 2007
    Author(s): John M Pagano,Brian M Farley,Lisa M McCoig,Sean P Ryder
    Source: The Journal of biological chemistry
    Embryonic development requires maternal proteins and RNA. In Caenorhabditis elegans, a gradient of CCCH tandem zinc finger (TZF) proteins coordinates axis polarization and germline differentiation. Th...

  • Oskar gains weight

    Tuesday, May 23, 2006
    Author(s): Sean P Ryder
    Source: Nature structural & molecular biology
    No abstract

  • Specificity of the STAR/GSG domain protein Qk1: implications for the regulation of myelination

    Tuesday, July 27, 2004
    Author(s): Sean P Ryder,James R Williamson
    Source: RNA (New York, N.Y.)
    Inadequate formation and maintenance of myelin is the basis for several neurodegenerative disorders, including leukodystrophy and multiple sclerosis. In mice, oligodendrocyte differentiation and subse...

  • RNA target specificity of the STAR/GSG domain post-transcriptional regulatory protein GLD-1

    Wednesday, January 14, 2004
    Author(s): Sean P Ryder,Leah A Frater,Dana L Abramovitz,Elizabeth B Goodwin,James R Williamson
    Source: Nature structural & molecular biology
    The post-transcriptional regulation of gene expression underlies several critical developmental phenomena. In metazoa, gene products that are expressed, silenced and packaged during oogenesis govern e...

  • Biochemical detection of adenosine and cytidine ionization within RNA by interference analysis

    Saturday, September 27, 2003
    Author(s): Scott A Strobel,Fatima D Jones,Adegboyega K Oyelere,Sean P Ryder
    Source: Nucleic acids research. Supplement (2001)
    Perturbation of active site functional group pKas is an important strategy employed by protein enzymes to achieve catalysis. There is increasing evidence to indicate that RNAs also utilize functional ...

  • Comparative analysis of hairpin ribozyme structures and interference data

    Saturday, March 09, 2002
    Author(s): Sean P Ryder,Scott A Strobel
    Source: Nucleic acids research
    Great strides in understanding the molecular underpinnings of RNA catalysis have been achieved with advances in RNA structure determination by NMR spectroscopy and X-ray crystallography. Despite these...

  • An efficient ligation reaction promoted by a Varkud Satellite ribozyme with extended 5'- and 3'-termini

    Tuesday, January 29, 2002
    Author(s): F D Jones,S P Ryder,S A Strobel
    Source: Nucleic acids research
    The Neurospora Varkud Satellite (VS) RNA is capable of promoting a reversible self-cleavage reaction important for its replication pathway. In vivo the VS RNA performs a cis-cleavage reaction to gener...

  • Investigation of adenosine base ionization in the hairpin ribozyme by nucleotide analog interference mapping

    Tuesday, October 30, 2001
    Author(s): S P Ryder,A K Oyelere,J L Padilla,D Klostermeier,D P Millar,S A Strobel
    Source: RNA (New York, N.Y.)
    Tertiary structure in globular RNA folds can create local environments that lead to pKa perturbation of specific nucleotide functional groups. To assess the prevalence of functionally relevant adenosi...

  • Biological catalysis. The hairpin's turn

    Thursday, April 12, 2001
    Author(s): S A Strobel,S P Ryder
    Source: Nature
    No abstract

  • Chemical probing of RNA by nucleotide analog interference mapping

    Thursday, June 01, 2000
    Author(s): S P Ryder,L Ortoleva-Donnelly,A B Kosek,S A Strobel
    Source: Methods in enzymology
    No abstract

  • Nucleotide analog interference mapping of the hairpin ribozyme: implications for secondary and tertiary structure formation

    Tuesday, August 10, 1999
    Author(s): S P Ryder,S A Strobel
    Source: Journal of molecular biology
    The hairpin ribozyme is a small, naturally occurring RNA capable of folding into a distinct three-dimensional structure and catalyzing a specific phosphodiester transfer reaction. We have adapted a hi...

  • Nucleotide analog interference mapping

    Tuesday, April 20, 1999
    Author(s): S P Ryder,S A Strobel
    Source: Methods (San Diego, Calif.)
    Single-atom substitution experiments provide atomic resolution biochemical information concerning RNA structure and function. Traditionally, these experiments are performed using chimeric RNAs generat...

  • A minor groove RNA triple helix within the catalytic core of a group I intron

    Thursday, December 10, 1998
    Author(s): A A Szewczak,L Ortoleva-Donnelly,S P Ryder,E Moncoeur,S A Strobel
    Source: Nature structural biology
    Close packing of several double helical and single stranded RNA elements is required for the Tetrahymena group I ribozyme to achieve catalysis. The chemical basis of these packing interactions is larg...

  • Complementary sets of noncanonical base pairs mediate RNA helix packing in the group I intron active site

    Friday, January 23, 1998
    Author(s): S A Strobel,L Ortoleva-Donnelly,S P Ryder,J H Cate,E Moncoeur
    Source: Nature structural biology
    Helix packing is critical for RNA tertiary structure formation, although the rules for helix-helix association within structured RNAs are largely unknown. Docking of the substrate helix into the activ...

 

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