Brian Rymond

Research Interests:
Mechanism of pre-mRNA splicing
ribonucleoprotein assembly
yeast and Drosophila Genetics
protein homeostasis and models of human disease
Education

Ph.D. State Univ. of New York at Albany, 1984

Research

Eukaryotic genome complexity is enriched by embedded introns which expand the number of proteins produced by alternative splicing, provide unique environments to embed genes and regulatory elements, and create opportunities for new gene assembly through recombination and intron evolution. Such benefits come at a cost, however, as approximately 15% of human genetic disorders result from splicing errors associated with cis- (splicing substrate) mutations that alter gene-delimited splice patterns or trans- (spliceosome subunit) mutations that may impair general pre-mRNA splicing. A better understanding of spliceosome composition and the molecular basis of splice site selection will facilitate the diagnosis and, ultimately, the treatment or correction of splicing-related disorders. The contribution of spliceosome assembly to the mechanism of pre-mRNA splicing is the focus of our work.

Metazoan genes may contain dozens of intron/exon borders, some of which are used only in response to specific developmental or environmental cues. For many genes it is the stable recruitment of the U2 snRNP to the branchpoint region of the pre-mRNA that modulates splice site choice. Pre-mRNA branchpoint recognition is complex and even in the case unregulated transcripts, progresses through the sequential association of multiple splicing factors (e.g., SF1/BBP – U2AF65/Mud2p) and snRNPs (U1, U2, and U6).

While the basic pathway of spliceosome assembly is well conserved through evolution, Saccharomyces cerevisiae (henceforth yeast) lacks canonical SR splicing factor regulators found in metazoa and relies on more rigidly conserved pre-mRNA consensus elements to direct splice site choice. Yeast gene structure is also simpler, with few genes containing more than a single intron. Accordingly, yeast offers an excellent model to investigate the assembly and function of the basal splicing apparatus in the absence of complications resulting from complex gene organization and splicing. Currently, we using genetic and proteomic approaches to investigate the dynamics of pre-mRNA branchpoint selection in vitro and in living cells.   

Other Publications

Rymond, BC., Going my way?  A tale of enzyme recruitment and activation 2016, Atlas of Science,

Rymond, B.C. The use of Saccharomyces cerevisiae to study the mechanism of pre-mRNA splicing. 2012,  Alternative Pre-mRNA Splicing: Theory and Protocols, Wiley-Blackwell,  (Eds., Stefan Stamm, Chris Smith, Reinhard Luhrmann)

BIO 510

Course Materials

2017 LAB MANUAL, SYLLABUS and HOMEWORK (updated)

2016 Final Exam

2016 Final Exam Answer Key

 

 

FINAL EXAM ANSWER KEY 2015

 

Scientific Resources, Maps, Tools and Course Reading Assignments (reference in manual)

 

Class Data (links active when class data becomes available)

 

 

 

 

 

 

 

BIO 601

CLASS SYLLABUS for BCH/BIO/MI/PLS/PPA 601 Special Topics in Molecular and Cellular Genetics 

 

ORIENTATION OVERVIEW POWERPOINT (when available)

                                

                                      2017 VISITOR INFORMATION

 

 

Dr. Jeffrey Wilusz, Ph.D., Professor, Department of Microboligy, Immunology & Pathology; College of Veterinary Medicine & Biomedical Sciences, Colorado State University, Fort Collins, Colorado http://csu-cvmbs.colostate.edu/academics/mip/Pages/Jeffrey-Wilusz.aspx

Topic: Regulation of mRNA metabolism in mammalian cells & disease

Pre-meeting: March 3, 2017 (Friday), 4:00-5:30 PM 109 TH Morgan Building

Student Lecture: March 6, 2017 (Monday 8:00-8:50 AM, 109 TH Morgan Building

Student Lunch: March 6, 2017 (Monday), 12:30-1:30 PM, 305 TH Morgan Building

Seminar: March 6, 2017 (Monday) 4:00 PM, 116 TH Morgan Building     

            Title: TBA

Host: Brian Rymond, rymond@uky.edu

Reading list for Dr. Wilusz

XRN1 Stalling in the 5’ UTR of Hepatitis C Virus and Bovine Viral Diarrhea Virus Is Associated with Dysregulated Host mRNA Stability (2015) Moon SL, Blackinton JG, Anderson JR, Dozier MK, Dodd BJ, Keene JD, Wilusz CJ, Bradrick SS, Wilusz J. PLOS Pathogens | DOI:10.1371/journal.ppat.1004708

Sindbis Virus Usurps the Cellular HuR Protein to Stabilize Its Transcripts and Promote Productive Infections in Mammalian and Mosquito Cells (2010) Kevin J. Sokoloski, Alexa M. Dickson, Emily L. Chaskey, Nicole L. Garneau, Carol J. Wilusz, and Jeffrey Wilusz,  Cell Host & Microbe, 8: 2, 196–207

Cytoplasmic Viruses: Rage against the (Cellular RNA Decay) Machine (2013, review) Moon SL, Wilusz J. PLoS Pathog. 9(12):e1003762.

Diverse Strategies Used by Picornaviruses to Escape Host RNA Decay Pathways, Ullmer, W, Semler (2016, review) Viruses 8:E335

 

John Dueber, Ph.D., Professor, Department of Bioengineering, University of California, Berkeley, California 94720 http://dueberlab.berkeley.edu/about/     

Topic: Synthetic biology, strategies for introducing designable, modular control in living cells

Pre-meeting: March 24, 2017, 4:00-5:30 PM, Cameron Williams Lecture Hall (Plant Sciences Building)

Student Lecture: March 27, 2017 (Monday), 8:00-8:50 AM, Cameron Williams Lecture Hall (Plant Sciences Building)

Student Lunch: March 27, 2017 (Monday), 12:30-1:30 PM, Room 460 Plant Sciences Building

Seminar: March 27 (Monday) 4:00 PM, Cameron Williams Lecture Hall (Plant Sciences Building)

            Title: TBA

Host: Seth DeBolt, sdebo2@email.uky

Reading list for Dr. Dueber (coming soon)

 

James Patton, Ph.D., Stevenson Professor, Department of Biological Sciences, Vanderbilt University Medical Center, Nashville, TN, https://medschool.vanderbilt.edu/patton-lab/

Topic: The role of miRNAs play in vertebrate development & regeneration; extracellular RNA communication

Pre-meeting: April 7, 2017 (Friday), 4:00-5:30 PM 109 TH Morgan Building

Student Lecture: April 10, 2017 (Monday 8:00-8:50 AM, 109 TH Morgan Building

Student Lunch: April 10, 2017 (Monday), 12:30-1:30 PM, 305 TH Morgan Building

Seminar: April 10, 2017 (Monday) 4:00 PM, 116 TH Morgan Building     

            Title:Regulation of Retina Regeneration by miRNAs, GABA Signaling, and Exosomes

Host: Brian Rymond, rymond@uky.edu

Reading list for Dr. Patton: Posted on Canvas

 

Alejandro Sánchez Alvarado, Ph.D.  Howard Hughes Medical Institute Investigator, Stowers Institute for Medical Research http://www.stowers.org/faculty/s%C3%A1nchez-lab

NOTE: changes in days/times

Topic: The molecular basis for regeneration

Pre-meeting: March 29, 2017 (Wednesday), 4:00-5:30 PM 116 TH Morgan Building (tentative, depending on room availability)

Student Lecture: None

Student Lunch: March 30, 2017 (Thursday), 305 TH Morgan Building times TBA  

Seminar: March 30, 2017 (Thursday) 4:00 PM, 116 TH Morgan Building 

            Title: TBA

Host: Dr. Jeramiah Smith

Reading list for Dr. Alvarado is posted on the 601 Canvas site.

PubMed Publications*: 
  • N Martínez-Matías; N Chorna; S González-Crespo; L Villanueva; I Montes-Rodríguez; LM Melendez-Aponte; A Roche-Lima; K Carrasquillo-Carrión; E Santiago-Cartagena; BC Rymond; M Babu; I Stagljar; Rodriguez -Medina JR"Toward the discovery of biological functions associated with the mechanosensor Mtl1p of Saccharomyces cerevisiae via integrative multi-OMICs analysis."Scientific reports11.1(2021):7411.Details. Full text
  • Vélez -Segarra V; S González-Crespo; E Santiago-Cartagena; LE Vázquez-Quiñones; N Martínez-Matías; Y Otero; JJ Zayas; R Siaca; J Del Rosario; I Mejías; JJ Aponte; NC Collazo; FJ Lasso; J Snider; M Jessulat; H Aoki; BC Rymond; M Babu; I Stagljar; Rodriguez -Medina JR"Protein Interactions of the Mechanosensory Proteins Wsc2 and Wsc3 for Stress Resistance in <i>Saccharomyces cerevisiae</i>."G3 (Bethesda, Md.)10.9(2020):3121-3135.Details.
  • MJ Rivera-Robles; J Medina-Velázquez; GM Asencio-Torres; S González-Crespo; BC Rymond; J Rodríguez-Medina; S Dharmawardhane"Targeting Cdc42 with the anticancer compound MBQ-167 inhibits cell polarity and growth in the budding yeast S. cerevisiae."Small GTPases11.6(2020):430-440.Details. Full text
  • E Santiago-Cartagena; S González-Crespo; Vélez V; N Martínez; J Snider; M Jessulat; H Aoki; Z Minic; P Akamine; I Mejías; LM Pérez; BC Rymond; M Babu; I Stagljar; Rodriguez -Medina JR"Identification and Functional Testing of Novel Interacting Protein Partners for the Stress Sensors Wsc1p and Mid2p of <i>Saccharomyces cerevisiae</i>."G3 (Bethesda, Md.)9.4(2019):1085-1102.Details.
  • E Santiago; P Akamine; J Snider; Wong V; M Jessulat; Deineko V; A Gagarinova; H Aoki; Z Minic; S Phanse; A San Antonio; LA Cubano; BC Rymond; M Babu; I Stagljar; Rodriguez -Medina JR"Novel Interactome of Saccharomyces cerevisiae Myosin Type II Identified by a Modified Integrated Membrane Yeast Two-Hybrid (iMYTH) Screen."G3 (Bethesda, Md.)6.5(2016):1469-74.Details.
  • D Banerjee; PM McDaniel; BC Rymond"Limited portability of G-patch domains in regulators of the Prp43 RNA helicase required for pre-mRNA splicing and ribosomal RNA maturation in Saccharomyces cerevisiae."Genetics200.1(2015):135-47.Details. Full text
  • BC Rymond"The branchpoint binding protein: in and out of the spliceosome cycle."Advances in experimental medicine and biology693.(2010):123-41.Details.
  • S Pandit; S Paul; L Zhang; M Chen; N Durbin; SM Harrison; BC Rymond"Spp382p interacts with multiple yeast splicing factors, including possible regulators of Prp43 DExD/H-Box protein function."Genetics183.1(2009):195-206.Details. Full text
  • Q Wang; L Zhang; B Lynn; BC Rymond"A BBP-Mud2p heterodimer mediates branchpoint recognition and influences splicing substrate abundance in budding yeast."Nucleic acids research36.8(2008):2787-98.Details. Full text
  • B Rymond"Targeting the spliceosome."Nature chemical biology3.9(2007):533-5.Details. Full text
  • S Pandit; B Lynn; BC Rymond"Inhibition of a spliceosome turnover pathway suppresses splicing defects."Proceedings of the National Academy of Sciences of the United States of America103.37(2006):13700-5.Details. Full text
  • Q Wang; J He; B Lynn; BC Rymond"Interactions of the yeast SF3b splicing factor."Molecular and cellular biology25.24(2005):10745-54.Details. Full text
  • N Dembla-Rajpal; R Seipelt; Q Wang; BC Rymond"Proteasome inhibition alters the transcription of multiple yeast genes."Biochimica et biophysica acta1680.1(2004):34-45.Details. Full text
  • Q Wang; K Hobbs; B Lynn; BC Rymond"The Clf1p splicing factor promotes spliceosome assembly through N-terminal tetratricopeptide repeat contacts."The Journal of biological chemistry278.10(2003):7875-83.Details. Full text
  • Q Wang; BC Rymond"Rds3p is required for stable U2 snRNP recruitment to the splicing apparatus."Molecular and cellular biology23.20(2003):7339-49.Details. Full text
  • K Vincent; Q Wang; S Jay; K Hobbs; BC Rymond"Genetic interactions with CLF1 identify additional pre-mRNA splicing factors and a link between activators of yeast vesicular transport and splicing."Genetics164.3(2003):895-907.Details. Full text
  • S Lybarger; K Beickman; Brown V; N Dembla-Rajpal; K Morey; R Seipelt; BC Rymond"Elevated levels of a U4/U6.U5 snRNP-associated protein, Spp381p, rescue a mutant defective in spliceosome maturation."Molecular and cellular biology19.1(1999):577-84.Details. Full text
  • RL Seipelt; B Zheng; A Asuru; BC Rymond"U1 snRNA is cleaved by RNase III and processed through an Sm site-dependent pathway."Nucleic acids research27.2(1999):587-95.Details. Full text
  • S Chung; MR McLean; BC Rymond"Yeast ortholog of the Drosophila crooked neck protein promotes spliceosome assembly through stable U4/U6.U5 snRNP addition."RNA (New York, N.Y.)5.8(1999):1042-54.Details. Full text
  • MR McLean; BC Rymond"Yeast pre-mRNA splicing requires a pair of U1 snRNP-associated tetratricopeptide repeat proteins."Molecular and cellular biology18.1(1998):353-60.Details. Full text
  • J Xie; K Beickman; E Otte; BC Rymond"Progression through the spliceosome cycle requires Prp38p function for U4/U6 snRNA dissociation."The EMBO journal17.10(1998):2938-46.Details. Full text
  • J Roy; B Zheng; BC Rymond; Woolford JL Jr"Structurally related but functionally distinct yeast Sm D core small nuclear ribonucleoprotein particle proteins."Molecular and cellular biology15.1(1995):445-55.Details. Full text
  • Rodriguez -Medina JR; BC Rymond"Prevalence and distribution of introns in non-ribosomal protein genes of yeast."Molecular & general genetics : MGG243.5(1994):532-9.Details.
  • Lockhart SR; BC Rymond"Commitment of yeast pre-mRNA to the splicing pathway requires a novel U1 small nuclear ribonucleoprotein polypeptide, Prp39p."Molecular and cellular biology14.6(1994):3623-33.Details. Full text
  • BC Rymond; LA Rokeach; SO Hoch"Human snRNP polypeptide D1 promotes pre-mRNA splicing in yeast and defines nonessential yeast Smd1p sequences."Nucleic acids research21.15(1993):3501-5.Details. Full text
  • BC Rymond"Convergent transcripts of the yeast PRP38-SMD1 locus encode two essential splicing factors, including the D1 core polypeptide of small nuclear ribonucleoprotein particles."Proceedings of the National Academy of Sciences of the United States of America90.3(1993):848-52.Details. Full text
  • S Blanton; A Srinivasan; BC Rymond"PRP38 encodes a yeast protein required for pre-mRNA splicing and maintenance of stable U6 small nuclear RNA levels."Molecular and cellular biology12.9(1992):3939-47.Details. Full text
  • BC Rymond"Identification of sites of pre-MRNA/spliceosome association."SAAS bulletin, biochemistry and biotechnology4.(1991):76-80.Details.
  • BC Rymond"The branchpoint binding protein: in and out of the spliceosome cycle."Advances in experimental medicine and biology693.(0):123-41.Details.
* Publications are automatically pulled from pubmed.gov based on a user-specific query. Results may include incorrect citations. See: Tutorial on improving PubMed results.