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TOM COOPER

TitleProfessor
InstitutionBaylor College of Medicine
DepartmentDepartment of Pathology & Immunology
AddressOne Baylor Plaza
Email
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    Other Positions
    TitleProfessor
    InstitutionBaylor College of Medicine
    DepartmentDepartment of Integrative Physiology
    DivisionMolecular Physiology & Biophysics

    TitleProfessor
    InstitutionBaylor College of Medicine
    DepartmentDepartment of Molecular & Cellular Biology
    DivisionMolecular & Cellular Biology


    Collapse Affiliation 
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    Collapse Biography 
    Collapse awards and honors
    1981 - 1982NIH Medical Research Trainee predoctoral award, University of California, San Francisco
    1982 - 1985NIH NRSA Postdoctoral Fellowship, University of California, San Francisco
    1985 - 1986Bank of America Giannini Foundation Postdoctoral Award, University of California, San Francisco
    1991 - 1994March of Dimes Basil O'Connor Starter Scholar Research Award, Baylor College of Medicine
    1992 - 1997Established Investigator Award, American Heart Association, Baylor College of Medicine
    1998Michael E. DeBakey, M.D. Excellence in Research Award, Baylor College of Medicine
    2003S. Donald Greenberg Endowed Chair, Baylor College of Medicine
    2014Michael E. DeBakey, M.D. Excellence in Research Award, Baylor College of Medicine
    2015R. Clarence and Irene H. Fulbright Endowed Chair, Baylor College of Medicine

    Collapse Overview 
    Collapse overview
    See our lab webpage: https://www.bcm.edu/research/labs/tom-cooper/?PMID=14453
    The realization that most human genes generate multiple mRNAs encoding different protein isoforms and variable untranslated regions via alternative splicing and alternative polyadenylation has revealed an extensive degree of regulation that remains to be explored.

    The Cooper Lab is interested in understanding the mechanisms of this regulation, from how RNA binding proteins regulate splicing of individual pre-mRNAs to the signaling events that coordinate RNA processing networks during development.

    A second major interest in the lab is the pathogenic mechanism of myotonic dystrophy in which disruption of developmentally regulated RNA processing causes primary features of the disease. Mechanistic understanding of myotonic dystrophy has led to development of therapeutic approaches being testing using mouse models established in the lab.

    Collapse Research 
    Collapse research activities and funding
    R01AR082852     (COOPER, THOMAS A)Sep 6, 2023 - Aug 31, 2028
    NIH
    Mechanisms of Skeletal Muscle Pathogenesis in Myotonic Dystrophy Type 1
    Role: Principal Investigator
    R21AR081472     (COOPER, THOMAS A)Apr 1, 2023 - Mar 31, 2025
    NIH
    Identification of components and mechanisms regulating expanded CUG-repeat RNP complexes in Myotonic Dystrophy Type 1 muscle cells
    Role: Principal Investigator
    R01HL147020     (COOPER, THOMAS A)Apr 15, 2019 - Mar 31, 2024
    NIH
    Pathogenic mechanisms and therapeutics for the cardiac manifestations of myotonic dystrophy type 1
    Role: Principal Investigator
    R01AR060733     (COOPER, THOMAS A)Apr 1, 2011 - Jan 31, 2025
    NIH
    Transcriptome processing networks in skeletal muscle: mechanisms and functions
    Role: Principal Investigator
    RC2HG005624     (BURGE, CHRISTOPHER B)Sep 30, 2009 - Aug 31, 2012
    NIH
    Deep Sequencing Analysis of mRNA Isoform Expression Changes in Myotonic Dystrophy
    Role: Co-Principal Investigator
    R01GM076493     (COOPER, THOMAS A)Feb 1, 2006 - Jul 31, 2011
    NIH
    Mechanisms of Developmentally Regulated Splicing
    Role: Principal Investigator
    R01AR045653     (COOPER, THOMAS A)Feb 8, 1999 - Aug 31, 2021
    NIH
    Molecular Pathogenesis of Myotonic Dystrophy
    Role: Principal Investigator
    R01HL045565     (COOPER, THOMAS A)Jul 1, 1991 - Nov 30, 2019
    NIH
    Troponin T Alternative Splicing in Embryonic Heart
    Role: Principal Investigator
    R29HL045565     (COOPER, THOMAS ALEXANDER)Jan 1, 1991 - Jul 16, 1996
    NIH
    TROPONIN T ALTERNATIVE SPLICING IN EMBRYONIC HEART
    Role: Principal Investigator
    T32GM008231     (NELSON, DAVID LOREN)Jul 1, 1990 - Jun 30, 2020
    NIH
    Training Program in Cell and Molecular Biology
    Role: Co-Principal Investigator

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Penna MS, Hu RC, Rodney GG, Cooper TA. The role of Limch1 alternative splicing in skeletal muscle function. Life Sci Alliance. 2023 06; 6(6). PMID: 36977593; PMCID: PMC10052820.
      Citations:    Fields:    Translation:AnimalsCells
    2. Payer LM, Steranka JP, Ardeljan D, Fitzgerald KC, Calabresi PA, Cooper TA, Burns KH, Walker J. Alu insertion variants alter mRNA splicing. Nucleic Acids Res. 2019 01 10; 47(1):421-431. PMID: 30418605; PMCID: PMC6326789.
      Citations: 27     Fields:    Translation:HumansCells
    3. Blue RE, Koushik A, Engels NM, Wiedner HJ, Cooper TA, Giudice J. Modulation of alternative splicing of trafficking genes by genome editing reveals functional consequences in muscle biology. Int J Biochem Cell Biol. 2018 12; 105:134-143. PMID: 30316870; PMCID: PMC6289647.
      Citations: 3     Fields:    Translation:AnimalsCells
    4. Morriss GR, Rajapakshe K, Huang S, Coarfa C, Cooper TA. Mechanisms of skeletal muscle wasting in a mouse model for myotonic dystrophy type 1. Hum Mol Genet. 2018 08 15; 27(16):2789-2804. PMID: 29771332; PMCID: PMC6077786.
      Citations: 12     Fields:    Translation:HumansAnimalsCells
    5. Singh RK, Kolonin AM, Fiorotto ML, Cooper TA. Rbfox-Splicing Factors Maintain Skeletal Muscle Mass by Regulating Calpain3 and Proteostasis. Cell Rep. 2018 07 03; 24(1):197-208. PMID: 29972780; PMCID: PMC6070147.
      Citations: 21     Fields:    Translation:AnimalsCells
    6. Rao AN, Cooper TA. A Therapeutic Double Whammy: Transcriptional or Post-transcriptional Suppression of Microsatellite Repeat Toxicity by Cas9. Mol Cell. 2017 11 02; 68(3):473-475. PMID: 29100050.
      Citations:    Fields:    Translation:AnimalsCells
    7. Brinegar AE, Xia Z, Loehr JA, Li W, Rodney GG, Cooper TA. Extensive alternative splicing transitions during postnatal skeletal muscle development are required for calcium handling functions. Elife. 2017 08 11; 6. PMID: 28826478; PMCID: PMC5577920.
      Citations: 28     Fields:    Translation:AnimalsCells
    8. Sharpe JJ, Cooper TA. Unexpected consequences: exon skipping caused by CRISPR-generated mutations. Genome Biol. 2017 06 14; 18(1):109. PMID: 28615035; PMCID: PMC5470267.
      Citations: 31     Fields:    
    9. Morriss GR, Cooper TA. Protein sequestration as a normal function of long noncoding RNAs and a pathogenic mechanism of RNAs containing nucleotide repeat expansions. Hum Genet. 2017 09; 136(9):1247-1263. PMID: 28484853; PMCID: PMC5677592.
      Citations: 13     Fields:    Translation:HumansCells
    10. Giudice J, Loehr JA, Rodney GG, Cooper TA. Alternative Splicing of Four Trafficking Genes Regulates Myofiber Structure and Skeletal Muscle Physiology. Cell Rep. 2016 11 15; 17(8):1923-1933. PMID: 27851958; PMCID: PMC5140099.
      Citations: 17     Fields:    Translation:AnimalsCells
    11. Giudice J, Xia Z, Li W, Cooper TA. Neonatal cardiac dysfunction and transcriptome changes caused by the absence of Celf1. Sci Rep. 2016 10 19; 6:35550. PMID: 27759042; PMCID: PMC5069560.
      Citations: 9     Fields:    Translation:HumansAnimalsCells
    12. Cox DC, Cooper TA. Non-canonical RAN Translation of CGG Repeats Has Canonical Requirements. Mol Cell. 2016 04 21; 62(2):155-156. PMID: 27105111.
      Citations: 1     Fields:    Translation:Humans
    13. Brinegar AE, Cooper TA. Roles for RNA-binding proteins in development and disease. Brain Res. 2016 09 15; 1647:1-8. PMID: 26972534; PMCID: PMC5003702.
      Citations: 63     Fields:    Translation:HumansAnimalsCells
    14. Hsu TY, Simon LM, Neill NJ, Marcotte R, Sayad A, Bland CS, Echeverria GV, Sun T, Kurley SJ, Tyagi S, Karlin KL, Hartman JD, Renwick A, Scorsone K, Bernardi RJ, Skinner SO, Jain A, Orellana M, Lagisetti C, Golding I, Jung SY, Neilson JR, Zhang XH, Cooper TA, Webb TR, Neel BG, Shaw CA, Westbrook TF, Dominguez-Vida?a R. The spliceosome is a therapeutic vulnerability in MYC-driven cancer. Nature. 2015 Sep 17; 525(7569):384-8. PMID: 26331541; PMCID: PMC4831063.
      Citations: 211     Fields:    Translation:HumansAnimalsCells
    15. Wang ET, Ward AJ, Cherone JM, Giudice J, Wang TT, Treacy DJ, Lambert NJ, Freese P, Saxena T, COOPER TA, Burge CB. \Antagonistic regulation of mRNA expression and splicing by CELF and MBNL proteins. Genome Res. 2015; 25(6):858-71.
    16. Wang ET, Ward AJ, Cherone JM, Giudice J, Wang TT, Treacy DJ, Lambert NJ, Freese P, Saxena T, Cooper TA, Burge CB. Antagonistic regulation of mRNA expression and splicing by CELF and MBNL proteins. Genome Res. 2015 Jun; 25(6):858-71. PMID: 25883322; PMCID: PMC4448682.
      Citations: 95     Fields:    Translation:HumansAnimalsCells
    17. Pedrotti S, Giudice J, Dagnino-Acosta A, Knoblauch M, Singh RK, Hanna A, Mo Q, Hicks J, Hamilton S, Cooper TA. The RNA-binding protein Rbfox1 regulates splicing required for skeletal muscle structure and function. Hum Mol Genet. 2015 Apr 15; 24(8):2360-74. PMID: 25575511; PMCID: PMC4380076.
      Citations: 34     Fields:    Translation:HumansAnimalsCells
    18. Xia Z, Donehower LA, Cooper TA, Neilson JR, Wheeler DA, Wagner EJ, Li W. Dynamic analyses of alternative polyadenylation from RNA-seq reveal a 3'-UTR landscape across seven tumour types. Nat Commun. 2014 Nov 20; 5:5274. PMID: 25409906; PMCID: PMC4467577.
      Citations: 208     Fields:    Translation:HumansCells
    19. Singh RK, Xia Z, Bland CS, Kalsotra A, Scavuzzo MA, Curk T, Ule J, Li W, Cooper TA. Rbfox2-coordinated alternative splicing of Mef2d and Rock2 controls myoblast fusion during myogenesis. Mol Cell. 2014 Aug 21; 55(4):592-603. PMID: 25087874; PMCID: PMC4142074.
      Citations: 63     Fields:    Translation:HumansAnimalsCells
    20. Giudice J, Xia Z, Wang ET, Scavuzzo MA, Ward AJ, Kalsotra A, Wang W, Wehrens XH, Burge CB, Li W, Cooper TA. Alternative splicing regulates vesicular trafficking genes in cardiomyocytes during postnatal heart development. Nat Commun. 2014 Apr 22; 5:3603. PMID: 24752171; PMCID: PMC4018662.
      Citations: 76     Fields:    Translation:AnimalsCells
    21. Kalsotra A, Singh RK, Gurha P, Ward AJ, Creighton CJ, Cooper TA. The Mef2 transcription network is disrupted in myotonic dystrophy heart tissue, dramatically altering miRNA and mRNA expression. Cell Rep. 2014 Jan 30; 6(2):336-45. PMID: 24412363; PMCID: PMC3927417.
      Citations: 52     Fields:    Translation:HumansAnimals
    22. Echeverria GV, COOPER TA. Muscleblind-like 1 activates insulin receptor exon 11 inclusion by enhancing U2AF65 binding and splicing of the upstream intron. Nucleic Acids Res. 2014; 42(3):1893-903.
    23. Cooper TA. Implications of widespread covalent modification of mRNA. Circ Res. 2012 Dec 07; 111(12):1491-3. PMID: 23223930.
      Citations: 2     Fields:    
    24. Cooper TA. Molecular biology. Neutralizing toxic RNA. Science. 2009 Jul 17; 325(5938):272-3. PMID: 19608901.
      Citations: 8     Fields:    Translation:HumansAnimalsCells
    25. Dhaenens CM, Schraen-Maschke S, Tran H, Vingtdeux V, Ghanem D, Leroy O, Delplanque J, Vanbrussel E, Delacourte A, Vermersch P, Maurage CA, Gruffat H, Sergeant A, Mahadevan MS, Ishiura S, Cooper TA, Caillet-Boudin ML, Charlet-Berguerand N, Sergeant N, Bu?e L, Sablonni?re B. Overexpression of MBNL1 fetal isoforms and modified splicing of Tau in the DM1 brain: two individual consequences of CUG trinucleotide repeats. Exp Neurol. 2008 Apr; 210(2):467-78. PMID: 18177861.
      Citations: 30     Fields:    Translation:HumansAnimalsCells
    26. Greenhill L, Kollins S, Abikoff H, McCracken J, Riddle M, Swanson J, McGough J, Wigal S, Wigal T, Vitiello B, Skrobala A, Posner K, Ghuman J, Cunningham C, Davies M, Chuang S, Cooper T. Efficacy and safety of immediate-release methylphenidate treatment for preschoolers with ADHD. J Am Acad Child Adolesc Psychiatry. 2006 Nov; 45(11):1284-1293. PMID: 17023867.
      Citations: 102     Fields:    Translation:Humans
    27. Cooper TA. Use of minigene systems to dissect alternative splicing elements. Methods. 2005 Dec; 37(4):331-40. PMID: 16314262.
      Citations: 100     Fields:    Translation:HumansAnimalsCells
    28. Savkur RS, Philips AV, Cooper TA, Dalton JC, Moseley ML, Ranum LP, Day JW. Insulin receptor splicing alteration in myotonic dystrophy type 2. Am J Hum Genet. 2004 Jun; 74(6):1309-13. PMID: 15114529; PMCID: PMC1182097.
      Citations: 70     Fields:    Translation:HumansCells
    29. Stickeler E, Fraser SD, Honig A, Chen AL, Berget SM, Cooper TA. The RNA binding protein YB-1 binds A/C-rich exon enhancers and stimulates splicing of the CD44 alternative exon v4. EMBO J. 2001 Jul 16; 20(14):3821-30. PMID: 11447123; PMCID: PMC125550.
      Citations: 85     Fields:    Translation:Cells
    30. Stark JM, Cooper TA, Roth MB. The relative strengths of SR protein-mediated associations of alternative and constitutive exons can influence alternative splicing. J Biol Chem. 1999 Oct 15; 274(42):29838-42. PMID: 10514463.
      Citations: 4     Fields:    Translation:Cells
    31. Stoss O, Schwaiger FW, Cooper TA, Stamm S. Alternative splicing determines the intracellular localization of the novel nuclear protein Nop30 and its interaction with the splicing factor SRp30c. J Biol Chem. 1999 Apr 16; 274(16):10951-62. PMID: 10196175.
      Citations: 16     Fields:    Translation:HumansCells
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