Education: B.S. in Industrial Biotechnology, University of Puerto Rico-Mayagüez (UPRM). 2007

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1 Juan B. Rodríguez Molina, Ph.D. University of Wisconsin-Madison Department of Biochemistry 433 Babcock Dr. Madison, WI Education: B.S. in Industrial Biotechnology, University of Puerto Rico-Mayagüez (UPRM) Ph.D. in Biochemistry, University of Wisconsin-Madison Research Experience: Dissertation title: Discovering unexpected connections and developing tools to define the CTD code of Pol II. Dissertation advisor: Dr. Aseem Z. Ansari, Ph.D. Dissertation Summary: In all eukaryotes, transcription of mrna genes is accompanied by the recruitment of factors that regulate transcription rate, modify chromatin and process the pre-mrna. The C- terminal domain (CTD) of the largest subunit of RNA Polymerase II is the central interaction hub for these factors. The CTD is comprised of a highly repetitive heptapeptide, Tyr 1 -Ser 2 - Pro 3 -Thr 4 -Ser 5 -Pro 6 -Ser 7, and orderly phosphorylation and dephosphorylation of the tyrosines, threonines and serines serve as signals that recruit CTD binding proteins. In my research I employed next-generation kinase inhibition strategies to understand the role of the essential kinase Kin28/CDK7 which phosphorylates the Ser 5 position. I also identified Bur1/CDK9 as a novel Ser 7 kinase and contributed to understanding the importance of removing the phospho-ser 7 mark in vivo. Finally, I explored the physical distribution of CTD binding proteins along the repetitive array of CTD heptapeptides by employing mutational analyses and genetically encoded unnatural amino acids. Previous Research Experience: Undergraduate research at UPRM Isolation and characterization of bioluminescent bacteria from marine environments of Puerto Rico. Under the guidance of Dr. Carlos Rios-Velazquez. Summer internship at University of Wisconsin-Madison June-August 2006 Generating amino acid substitutions to alter the activity and response specificity of the antisigma factor, ChrR. Under the guidance of Dr. Timothy Donohue. Summer internship at Pfizer Global Research and Development June-August 2005 Validation of primer combinations for implementation of RT-PCR-based technology for rapid microbial contaminant identification.

2 Under the guidance of Dr. Claudio Denoya. Summer internship at University of Colorado-Boulder June-August 2004 Determining the importance of the Cys residues in the Luecyl-Phenylalanyl-tRNA-protein transferase. Under the guidance of Dr. Alexey Wolfson. Publications: Rodríguez-Molina JB, Tseng SC, Taunton J, Ansari AZ. Covalent inhibition of the TFIIH kinase reveals its role in post transcriptional processing and mrna stability. Manuscript in preparation. Rodríguez-Molina JB, Zhang DW, Gilmore JR, Washburn MP, Ansari AZ. Nascent RNA and Pol II CTD interactions instruct recruitment of the Nrd1-Nab3-Sen1 complex. Manuscript in preparation. Zhang DW, Rodríguez-Molina JB, Tietjen JR, Nemec CM, Ansari AZ. Emerging views on the CTD code. Genet Res Int. (2012), 2012: Chinchilla K, Rodriguez-Molina JB, Ursic D, Finkel JS, Ansari AZ, Culbertson MR. Interactions of Sen1, Nrd1, and Nab3 with Multiple Phosphorylated Forms of the Rpb1 C- Terminal Domain in Saccharomyces cerevisiae. Eukaryot Cell. (2012), 11(4): Zhang DW, Mosley AL, Ramisetty SR, Rodríguez-Molina JB, Washburn MP, Ansari AZ. Ssu72 phosphatase-dependent erasure of phospho-ser7 marks on the RNA polymerase II C-terminal domain is essential for viability and transcription termination. J Biol Chem. (2012), 287(11): Tietjen JR, Rodríguez-Molina JB*, Zhang DW*,White BE*, Akhtar MS, Heidemann M, Li X, Chapman RD, Shokat K, Keles S, Eick D, Ansari AZ. Chemical Dissection of the CTD code. Nat Struct Mol Biol. (2010), 17(9): (*These authors contributed equally). Research Highlights Nat Chem Biol. (2010), 6, Awards and Fellowships: American Society for Biochemistry and Molecular Biology Travel Award Biochemistry WARF Research Assistant Award Genomic Sciences Predoctoral Traineeship Advance Opportunity Fellowship. 2007, 2013 Sloan Undergraduate Research Fellow. 2006, 2007 American Society for Cell Biology MAC Travel Award Pfizer Global Research and Development & Connecticut Business Industry Association Undergraduate Research Fellowship Puerto Rico Louis Stokes Access for Minority Participation (PR-LSAMP) Fellowship. 2004, 2005

3 Talks: Chemical-genomic (re)dissection of the RNA Polymerase II CTD code Student elected speaker at Biochemistry Department Retreat, University of Wisconsin- Madison. Chemical-genomic dissection of Pol II phospho-ctd marks Transcription and chromatin regulation seminar, University of Wisconsin-Madison. Poster Presentations: A novel chemical-genomic approach for the dissection of the CTD code American Society for Biochemistry and Molecular Biology, San Diego, CA. Unexpected gene-class specific differences in Nrd1 recruitment Mechanisms of Eukaryotic Transcription, Cold Spring Harbor Laboratory, Cold Spring Harbor NY. Global Nrd1 distribution is regulated by dynamic phosphorylation states of the C-terminal domain of RNA Polymeraes II The Biology of Genomes Annual Conference, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY. A novel chemical-genomic approach for the dissection of the CTD code Mechanisms of Eukaryotic Transcription, Cold Spring Harbor Laboratory, Cold Spring Harbor NY. Chemical-genomic analysis reveals Bur1 as an unexpected Ser7 CTD kinase EMBO Gene Transcription in Yeast, San Feliu de Guixols, Spain. Genome-wide analysis of RNA Pol II CTD phosphorylation patterns upon chemical inhibition of Bur The Biology of Genomes Annual Conference, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY. Generating Amino Acids Substitutions to Alter the Activity and Response Specificity of the Anti-Sigma Factor, ChrR Annual Biomedical Conference for Minority Students, Anaheim, CA. Mentoring Shane Simonett Fall 2014-present Under my guidance, Shane is pioneering genetic interaction studies between Pol II CTD variants and Kin28 activity. He is finding many interesting interactions which have sparked new areas of research currently being pursued in the lab. Jiayue Liu Fall 2012-present I trained Jiayue in basic molecular biology techniques such as protein immunoblots, immunoprecipitation, cloning, and genetic manipulation in budding yeast. She has been

4 instrumental in testing a covalent inhibition strategy aimed at inactivating the Pol II CTD kinase Bur1 in vivo. She performed chromatin immunoprecipitation (ChIP), qpcr and immunoblot analysis to resolve the contentious function of Bur1 in cells. She has also helped in optimizing ChIP-seq protocols for their long-term use in the Ansari lab. Alex Burford Spring 2012-Spring 2014 I trained Alex in cloning, site directed mutagenesis, immunoblotting, protein purification and genetic manipulation in yeast. With these tools in hand, Alex helped me develop a custom photo-crosslinking system that utilizes genetically encode unnatural amino acids at various positions along the length of the CTD of Pol II. By site specifically incorporating photocrosslinkers along the highly repetitive array of CTD heptads, Alex was able to capture and identify CTD-binding factors using affinity purification and mass spectrometry analysis. Currently: University of Wisconsin-Madison Medical School. Laura Dattilo Fall 2009-Spring 2010 As her first experience in a research laboratory, I trained Laura in basic biochemical protocols. Her project focused on developing double mutant kinase yeast strains for simultaneous chemical-genetic inhibition of Kin28 and Bur1 in vivo. She created double mutant strains using the two-step gene replacement approach. She also performed preliminary ChIP experiments and qpcr analysis to determine the effect of Kin28/Bur1 inhibition on the phosphorylation states of Pol II. Currently: Genetic Counseling Intern, University of Wisconsin-Madison Genetic Counselor Training Program. Teaching Experience: Eukaryotic Molecular Biology (Biochem 620), Teaching Assistant Graduate/advanced undergraduate course. In charge of study sections before exams and grading exams and assignments. University of Wisconsin-Madison. General Biochemistry (Biochem 507), Teaching Assistant Undergraduate course. In charge of weekly study sections and grading exams. University of Wisconsin-Madison. Pre-College Enrichment Opportunity Program for Learning Excellence (PEOPLE), Instructor 2009 Short course (1 week) for high school students. Independently designed a basic course on evolution which included lectures and simple experiments illustrating the power of natural selection. University of Wisconsin-Madison. Outreach and Volunteer work: Science Night Resource (in collaboration with the Science and Medicine Graduate Research Scholars) Science Expeditions/Explorando las ciencias English-Spanish Translator Resource Science Fair Judge at Capital Science and Engineering Fair ,

5 Graduate student recruiting on behalf of the University of Wisconsin-Madison Graduate School and the Department of Biochemistry: Annual Biomedical Research Conference for Minority Students (ABRCMS), Orlando FL Department of Industrial Biotechnology, University of Puerto Rico-Mayagüez, Mayagüez PR Technical Skills: Chromatin immunoprecipitation (ChIP) of RNA Polymerase II, its various phosphorylation states and other chromatin-associated proteins from the yeast Saccharomyces cerevisiae. Use of high density DNA microarrays for genomic analysis of chromatin binding factors. Basic computational proficiency (in R and Python) for the extraction of novel biological insight from vast genomic data. Rational design of kinase active sites for targeted inhibition using bulky ATP analogs. Affinity purification of active protein kinase complexes from yeast. In vitro kinase assays. Encoding unnatural amino acids for protein-protein photo-crosslinking in yeast. Site directed mutagenesis. Genetic manipulation in yeast. Recombinant protein expression and purification from E. coli. Northern blots and Western blots. Quantitative PCR. Electrophoretic mobility shift assays (EMSA) of DNA and RNA binding proteins. Languages: Spanish (native) English (native) References upon request from the following: Dr. Aseem Z. Ansari, University of Wisconsin-Madison ansari@biochem.wisc.edu Phone: Dr. Audrey P. Gasch, University of Wisconsin-Madison. agasch@wisc.edu Phone: Dr. David C. Schwartz, University of Wisconsin-Madison. schwartz@chem.wisc.edu Phone: Dr. Michael R. Culbertson, University of Wisconsin-Madison. mrculber@wisc.edu Phone: