Thomas D. Tullius, PhD
Professor, Chemistry
Biography
Tom Tullius conducts research in genomics, structural biology, and biophysical chemistry. In addition to Chemistry, he is Professor of Pharmacology and Professor of Experimental Therapeutics in the Chobanian and Avedisian School of Medicine. He is an elected Fellow of the American Association for the Advancement of Science and he is on the Editorial Advisory Board of the Chemistry Central Journal. Professor Tullius is a faculty affiliate and Director of the Boston University Bioinformatics Program.
The Tullius Group introduced hydroxyl radical footprinting, which is widely used for the structural study of DNA, DNA-protein complexes, and RNA. They investigate the connection between structural properties of DNA and genomics, including evolutionary selection for DNA structure in the human genome. Their human genome studies were initiated with funding from the ENCODE (Encyclopedia of DNA Elements) Pilot Project, which was organized by the National Human Genome Research Institute of the NIH to discover functional elements in the human genome.
Measurement of the Deuterium Kinetic Isotope Effect on Hydroxyl Radical Cleavage of RNA aims to synthesize a complete set of nucleoside and deoxynucleoside triphosphates specifically deuterated at each sugar carbon atom. The deuterated nucleoside triphosphates are used in kinetic isotope effect experiments on hydroxyl radical cleavage of RNA, to provide more detailed information on the structural features of RNA to which the hydroxyl radical is sensitive. The goal of this work is the development of a chemical probe of RNA structure of unprecedented resolution.
Genome damage and aging: whole-genome maps of oxidative DNA lesions at single-nucleotide resolution investigates a new way to map, at single nucleotide resolution for an entire genome, the sites of oxidative damage that are induced in the DNA backbone by the hydroxyl radical. The study uses an advanced sequencing platform to comprehensively identify sites of DNA strand breaks. With these experiments it is possible to visualize, at single-nucleotide resolution, what parts of a genome are sensitive to attack by the hydroxyl radical and what parts are resistant. This work will provide unique new information on how oxidative damage affects the genome and so contributes to aging.
Techniques & Resources:
ORChID (OH Radical Cleavage Intensity Database) – Database of experimentally determined hydroxyl radical cleavage patterns of naked DNA molecules. Algorithm to predict the cleavage pattern of any DNA sequence.
ORChID in the UCSC Genome Browser – ORChID values predicted for the human genome. The data is viewable and available for download from the UCSC genome browser.
Chai regions in the UCSC Genome Browser – Chai is a structure-informed evolutionary sequence constraint detection algorithm. Chai-identified regions are available from the UCSC genome browser.
Other Positions
- Professor, Pharmacology, Physiology & Biophysics, Boston University Chobanian & Avedisian School of Medicine
- Director, Bioinformatics Graduate Program, Boston University
- Member, BU-BMC Cancer Center, Boston University
- Member, Evans Center for Interdisciplinary Biomedical Research, Boston University
- Member, Genome Science Institute, Boston University
- Graduate Faculty (Primary Mentor of Grad Students), Boston University Chobanian & Avedisian School of Medicine, Graduate Medical Sciences
Education
- Stanford University, PhD
- University of California, Los Angeles, BS
Publications
- Published on 3/16/2018
Azad RN, Zafiropoulos D, Ober D, Jiang Y, Chiu TP, Sagendorf JM, Rohs R, Tullius TD. Experimental maps of DNA structure at nucleotide resolution distinguish intrinsic from protein-induced DNA deformations. Nucleic Acids Res. 2018 03 16; 46(5):2636-2647. PMID: 29390080.
Read at: PubMed - Published on 1/1/2015
Chiu TP, Yang L, Zhou T, Main BJ, Parker SC, Nuzhdin SV, Tullius TD, Rohs R. 28 GBshape: a genome browser database for DNA shape annotations. J Biomol Struct Dyn. 2015; 33 Suppl 1:16. PMID: 26103240.
Read at: PubMed - Published on 10/17/2014
Chiu TP, Yang L, Zhou T, Main BJ, Parker SC, Nuzhdin SV, Tullius TD, Rohs R. GBshape: a genome browser database for DNA shape annotations. Nucleic Acids Res. 2015 Jan; 43(Database issue):D103-9. PMID: 25326329.
Read at: PubMed - Published on 10/13/2014
Ingle S, Azad RN, Jain SS, Tullius TD. Chemical probing of RNA with the hydroxyl radical at single-atom resolution. Nucleic Acids Res. 2014 Nov 10; 42(20):12758-67. PMID: 25313156.
Read at: PubMed - Published on 8/28/2014
Ho JW, Jung YL, Liu T, Alver BH, Lee S, Ikegami K, Sohn KA, Minoda A, Tolstorukov MY, Appert A, Parker SC, Gu T, Kundaje A, Riddle NC, Bishop E, Egelhofer TA, Hu SS, Alekseyenko AA, Rechtsteiner A, Asker D, Belsky JA, Bowman SK, Chen QB, Chen RA, Day DS, Dong Y, Dose AC, Duan X, Epstein CB, Ercan S, Feingold EA, Ferrari F, Garrigues JM, Gehlenborg N, Good PJ, Haseley P, He D, Herrmann M, Hoffman MM, Jeffers TE, Kharchenko PV, Kolasinska-Zwierz P, Kotwaliwale CV, Kumar N, Langley SA, Larschan EN, Latorre I, Libbrecht MW, Lin X, Park R, Pazin MJ, Pham HN, Plachetka A, Qin B, Schwartz YB, Shoresh N, Stempor P, Vielle A, Wang C, Whittle CM, Xue H, Kingston RE, Kim JH, Bernstein BE, Dernburg AF, Pirrotta V, Kuroda MI, Noble WS, Tullius TD, Kellis M, MacAlpine DM, Strome S, Elgin SC, Liu XS, Lieb JD, Ahringer J, Karpen GH, Park PJ. Comparative analysis of metazoan chromatin organization. Nature. 2014 Aug 28; 512(7515):449-52. PMID: 25164756.
Read at: PubMed - Published on 10/13/2011
Bishop EP, Rohs R, Parker SC, West SM, Liu P, Mann RS, Honig B, Tullius TD. A map of minor groove shape and electrostatic potential from hydroxyl radical cleavage patterns of DNA. ACS Chem Biol. 2011 Dec 16; 6(12):1314-20. PMID: 21967305.
Read at: PubMed - Published on 3/23/2011
Parker SC, Tullius TD. DNA shape, genetic codes, and evolution. Curr Opin Struct Biol. 2011 Jun; 21(3):342-7. PMID: 21439813.
Read at: PubMed - Published on 1/1/2011
Parker SC, Harlap A, Tullius TD. A computational method to search for DNA structural motifs in functional genomic elements. Methods Mol Biol. 2011; 759:367-79. PMID: 21863498.
Read at: PubMed - Published on 3/12/2009
Parker SC, Hansen L, Abaan HO, Tullius TD, Margulies EH. Local DNA topography correlates with functional noncoding regions of the human genome. Science. 2009 Apr 17; 324(5925):389-92. PMID: 19286520.
Read at: PubMed - Published on 1/1/2008
Jain SS, Tullius TD. Footprinting protein-DNA complexes using the hydroxyl radical. Nat Protoc. 2008; 3(6):1092-1100. PMID: 18546600.
Read at: PubMed
View 62 more publications: View full profile at BUMC