Site Menu
Search Close Search
Search Close Search
Page Menu

Publications

Recent Publications:

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

Albarqi, M.M.Y. and Ryder, S.P.
Front. Cell. Dev. Biol., (2023) 10:1094295.doi:10.3389/fcell.2022.1094295

A nematode model to evaluate microdeletion phenotype expression.

Antkowiak, K., Coskun, P., Noronha, S., Tavelle, D., Massi, F., and Ryder, S.P.
bioRxiv 2022.11.09.515676.

Preprint: https://doi.org/10.1101/2022.11.09.515676

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

Albarqi, M.M.Y. and Ryder S.P.
PLOS Genet. (2021) Aug 23;17(8):e1009775. doi: 10.1371/journal.pgen.1009775.

Analysis of emerging variants in structured regions of the SARS-CoV-2 genome.

Ryder, S.P., Morgan B., Coskun, P., Antkowiak, K.A., and Massi F. (2021)
Evol. Bioinform. May 5;17:11769343211014167. doi: 10.1177/11769343211014167. eCollection 2021.

A disorder-to-order transition mediates RNA-binding of the Caenorhabditis elegans protein MEX-5.

Tavella, D., Ertekin, A, Schaal, H, Ryder, S.P., and Massi, F. 
Biophys J. (2020) 118, 2001-2014.

All Ryder Lab Publications on PubMed

Total: 55 results

  • 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 depend both on the extent of the deletion and variations in genetic background. Microdeletion alleles cause a wide array of consequences involving multiple pathways. How simultaneous haploinsufficiency of numerous adjacent genes leads to complex and variable pleiotropic phenotypes is not well...

  • 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-binding proteins (RBPs) that target the untranslated regions of mRNA transcripts to regulate their translation and stability. In this review, we summarize what is known about the binding specificity of C. elegans germline RNA-binding proteins and the mechanisms of mRNA regulation that contribute to...

  • 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 process, regulating the translation and stability of parental transcripts to control cell fate specification events prior to zygotic gene activation. The KH-domain RBP MEX-3 is conserved from nematode to human. It was first discovered in Caenorhabditis elegans, where it is essential for anterior cell...

  • 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 technology has led to the deposition of vast numbers of SARS-CoV-2 genome sequences in curated repositories, which have been useful in mapping the spread of the virus around the globe. They also provide a unique opportunity to observe virus evolution in real time. Here, we evaluate two sets of...

  • 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 technology has led to the deposition of vast numbers of SARS-CoV-2 genome sequences in curated repositories, which have been useful in mapping the spread of the virus around the globe. They also provide a unique opportunity to observe virus evolution in real time. Here, we evaluate two cohorts of...

  • 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 protein-RNA interactions. In Caenorhabditis elegans, RBPs control the translation, stability, or localization of maternal messenger RNAs required for patterning decisions before zygotic gene activation. MEX-5 (Muscle EXcess) is a C. elegans protein that leads a cascade of RBP localization events that is...

  • #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 spermatogenesis, and thus self-fertility. In C. elegans, one of these selfing species, the global sex-determining gene tra-2 is regulated in germ cells by a conserved RBP, GLD-1, via the 3' untranslated region (3'UTR) of its transcript. A C. elegans-specific GLD-1 cofactor, FOG-2, is also required for...

  • 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 the C. elegans zygote, the RNA-binding protein MEX-5 forms an anterior-rich cytoplasmic gradient that causes the RNA-binding protein POS-1 to form an opposing, posterior-rich gradient. We demonstrate that the polo-like kinase PLK-1 mediates the repulsive coupling between MEX-5 and POS-1 by...

  • 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 silencing pathways. Others sense foreign sequences in the form of double-stranded RNA and activate the innate immune response. Yet others, for example cytoplasmic aconitase, act as bi-functional proteins, processing metabolites in one conformation and regulating metabolic gene expression in another. Not...

  • 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 been traditionally analyzed with polyacrylamide gels generated between two glass plates and samples electrophoresed vertically. However, polyacrylamide gels cast in trays and electrophoresed horizontally offers several advantages. For example, horizontal gels used to analyze complexes between...

  • 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 to interactions between transcription factors (TFs) and DNA, the interactome between RBPs and RNA has been explored for only a small number of proteins and RNAs. This is largely because the focus has been on using 'protein-centered' (RBP-to-RNA) interaction mapping methods that identify the RNAs...

  • 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-binding proteins and their maternal mRNA targets. Developmental Dynamics 245:925-936, 2016. © 2016 Wiley Periodicals, Inc.

  • 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,Craig C Mello
    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 zinc-finger RNA-binding proteins that regulate cell fate specification during C. elegans embryogenesis. Paradoxically, pos-1 mutants exhibit striking defects in endo-mesoderm development but have wild-type distributions of SKN-1, a key determinant of endo-mesoderm fates. RNAi screens for pos-1...

  • 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 overexpressed, but in general how the activity of APOBEC3s is regulated on a molecular level is unclear. In this study, the biochemical and structural basis of APOBEC3A substrate binding and specificity is elucidated. We find that specific binding of single-stranded DNA is regulated by the...

  • 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 poor prognosis. MSI proteins control gene expression by binding RNA and regulating its translation. They contain two RNA recognition motif (RRM) domains, which recognize a defined sequence element. The relative contribution of each nucleotide to the binding affinity and specificity is unknown. We...

  • 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 their function. Pluripotent stem cells have the ability to differentiate into a wide variety of specialized cells. How metabolic state contributes to stem cell differentiation is not understood. In this study, we show that RNA-binding by the stem cell translation regulator Musashi-1 (MSI1) is...

  • 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 during oogenesis, the oocyte to embryo transition, and early embryogenesis. To understand how these RNA-binding proteins contribute to development, it is necessary to determine how they select specific mRNA targets for regulation. OMA-1 and OMA-2 are redundant proteins required for oocyte...

  • 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 neuronal proteins to inhibit axon outgrowth and protect neurons from degeneration. Two alternatively spliced isoforms of Mag mRNA have been identified. The mRNA encoding the shorter isoform, known as S-MAG, contains a termination codon in exon 12, while the mRNA encoding the longer isoform, known as...

  • 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-messenger systems. More recent studies reveal that metabolites also affect post-transcriptional regulatory mechanisms. Here, we review the increasing number of connections between metabolism and post-transcriptional regulation in eukaryotic organisms. First, we present evidence that riboswitches, a...

  • 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 are rapidly being characterized, few studies have focused on the posttranscriptional gene regulation by RNA binding proteins (RBPs). RBPs are important to many aspects of gene regulation. Thus, it is essential to know which genes encode RBPs, which RBPs regulate which gene(s), and how RBP genes are...

  • 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 its state, and can serve as a handle by which the nucleic acid and associated factors can be purified from a mixture. Radioactive phosphate is commonly added to the 5' or 3' end of an oligonucleotide post synthesis using enzyme-catalyzed reactions. In contrast, chemical tags are usually added...

  • 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 control expression from maternal mRNAs encoding key cell fate determinants. The Caenorhabditis elegans Notch homologue glp-1 coordinates germline progenitor cell proliferation and anterior fate specification in embryos. A network of sequence-specific RBPs is required to pattern GLP-1 translation....

  • 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 to the 3' untranslated region of a target mRNA, function cooperatively to silence target expression. We report that, in cultured human HeLa cells and mouse embryonic fibroblasts, Argonaute1 (Ago1), Ago3, and Ago4 act cooperatively to silence both perfectly and partially complementary target RNAs...

  • 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 report that FBF/Pumilio, a conserved RNA-binding protein, promotes self-renewal of germline stem cells by repressing CKI-2(Cip/Kip), a Cyclin E/Cdk2 inhibitor. We have previously shown that repression of CYE-1 (Cyclin E) by another RNA-binding protein, GLD-1/Quaking, promotes germ cell...

  • 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 contribute to binding affinity define Pumilio regulatory activity by adopting distinctive conformations with differential ability to recruit regulatory cofactors.

  • 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 several myelin-related transcripts, yet little is known about how QK governs these activities. Here, we show that QK enhances Hnrnpa1 mRNA stability by binding a conserved 3' UTR sequence with high affinity and specificity. A single nucleotide mutation in the binding site eliminates QK-dependent...

  • 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, alternative splicing, or translational efficiency of specific mRNA targets. Significant effort has been expended to define the determinants of RNA recognition by STAR proteins, in hopes of identifying new mRNA targets that contribute their role in cellular metabolism and development. This work has lead...

  • 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 necessary. The signal transduction and activation of RNA (STAR) family of RBPs includes developmental regulators and tumour suppressors such as Caenorhabditis elegans GLD-1, which is a key regulator of germ cell development. To obtain a comprehensive picture of GLD-1 interactions with the transcriptome,...

  • 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 protein to distinguish between multiple sequences. Here, we describe the use of fluorophore-labeled oligonucleotide probes to quantitatively monitor protein/nucleic acid interactions. We review two complementary experimental methods, fluorescence polarization and fluorescence electrophoretic mobility...

  • 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 examples had been identified. Two papers now reveal that self-cleaving ribozymes are prevalent in eukaryotic genomes and, in some cases, might play a role in regulating gene expression.

  • 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 discovery rate at a predetermined tolerance. These methods, however, neglect local economic context and consequently lead to irrational experimental strategies. In contrast, the authors argue that this question is essentially economic, not statistical, and is amenable to an economic analysis that...

  • 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 for RNA recognition by RNA-binding proteins is the key to understand how they target specific transcripts for regulation. Compared to other metazoans, nematode genomes contain a significant expansion in several RNA-binding protein families, including Pumilio-FBF (PUF), TTP-like zinc finger (TZF),...

  • 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 posttranscriptional regulatory mechanisms. The Caenorhabditis elegans RNA binding protein, MEX-3, plays a key role in both processes. MEX-3 is a maternally-supplied factor that controls the RNA metabolism of transcripts encoding critical cell fate determinants. However, the nucleotide sequence...

  • 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 regulation has been challenging, largely because of the multiple modes of interaction observed between SM proteins and their cognate syntaxin-type SNAREs. These modes include binding of the SM to a closed conformation of syntaxin, binding to the N-terminal peptide of syntaxin, binding to assembled SNARE...

  • 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 entropy can be directly determined. This chapter presents a general procedure for studying RNA-protein interactions using ITC and gives specific examples for monitoring the binding of Caenorhabditis elegans GLD-1 STAR domain to TGE RNA and the binding of Aquifex aeolicus S6:S18 ribosomal protein...

  • 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 the quantitative application of this approach to elucidate thermodynamic properties of protein-RNA complexes. Assay designs for titration, competition, and stoichiometry experiments are presented for two unrelated model complexes.

  • 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 activation of quiescent maternal mRNAs after fertilization, leading to asymmetric expression of factors required for patterning. The primary determinant of posterior fate is the TZF protein POS-1. Mutants of pos-1 are maternal effect lethal with a terminal phenotype that includes excess pharyngeal tissue and...

  • 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 oligodendrocytes form myelin by wrapping cellular processes in a spiral pattern around neuronal axons. Myelin formation requires the oligodendrocyte to regulate gene expression in response to changes in its extracellular environment. Because these changes occur at a distance from the cell body,...

  • 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 are called ova, while the smaller gametes are male and are called sperm. In most cases, both gametes contribute similarly to the chromosomal content of the new organism. In contrast, the maternal gamete contributes nearly all of the cytoplasm. This cytoplasmic contribution is crucial to patterning...

  • 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. These proteins govern expression from maternal mRNAs by an unknown mechanism. Here we show that the TZF protein MEX-5, a primary anterior determinant, is an RNA-binding protein that recognizes linear RNA sequences with high affinity but low specificity. The minimal binding site is a tract of six or...

  • 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 subsequent formation of myelin requires the Quaking gene. Mutation of this gene leads to embryonic lethality or to a trembling phenotype characteristic of dysmyelination. Quaking encodes Qk1, a member of the highly conserved STAR/GSG family of RNA-binding proteins that function as master developmental...

  • 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 early developmental processes prior to nascent transcription activation. Furthermore, tissue-specific alternative splicing of several transcription factors controls pattern formation and organ development. A highly conserved family of proteins containing a STAR/GSG RNA-binding domain is essential to...

  • 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 group pKa perturbation for folding and reactivity. The two best candidates for a functionally relevant pKa perturbation are the N3 of C (pKa 4.2) and the N1 of A (pKa 3.5), either of which could be sufficiently raised to allow protonation near physiological pH. Here we report the synthesis and use...

  • 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 successes the functional relevance of a given structure can only be assessed upon comparison with biochemical studies performed on functioning RNA molecules. The hairpin ribozyme presents an excellent case study for such a comparison. The active site is comprised of two stems each with an internal...

  • 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 generate monomeric length transcripts that are subsequently ligated to produce circular VS RNA. The predominant form of VS RNA observed in vivo is the closed circular form, though minimal VS ribozyme self-cleavage constructs lack detectable ligation activity. MFOLD analysis of the entire VS RNA sequence...

  • 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 adenosine-specific pKa perturbation in RNA structure, we have altered the nucleotide analog interference mapping (NAIM) approach to include a series of a phosphorothioate-tagged adenosine analogs with shifted N1 pKa values. We have used these analogs to analyze the hairpin ribozyme, a small...

  • 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 high throughput screening procedure entitled nucleotide analog interference mapping (NAIM) to identify functional groups important for proper folding and catalysis of this ribozyme. A total of 18 phosphorothioate-tagged nucleotide analogs were used to determine the contribution made by individual...

  • 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 generated by reassembly of full-length RNA from a synthetic substituted oligonucleotide and a truncated RNA transcript. Unfortunately, this technique is limited by the technical difficulty of assembling and measuring the effect of each singly substituted molecule in a given RNA. Here we review an alternate...

  • 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 largely unknown. Using nucleotide analog interference suppression (NAIS), we demonstrate that the P1 substrate helix and J8/7 single stranded segment form an extended minor groove triple helix within the catalytic core of the ribozyme. Because each triple in the complex is mediated by at least one 2'-OH...

  • 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 active site of the Tetrahymena group I ribozyme provides a model system to study this question. Using a novel chemogenetic method to analyze RNA structure in atomic detail, we report that complementary sets of noncanonical base pairs (a G.U wobble pair and two consecutively stacked sheared A.A pairs)...

Contact:

Sean Ryder, Ph.D. (he/him)
Professor and Vice Chair for Outreach

Biochemistry and Molecular Biotechnology
UMass Chan Medical School
364 Plantation Street LRB-906
Worcester, MA, 01605

Office (LRB-906)
508-856-1372
Lab (LRB-970W,X)
508-856-3568