Aseem Z. Ansari

Photo of Aseem Z. Ansari
Professor (also with The Genome Center)
B.Sc., St. Xavier's College, Bombay University
Ph.D., Northwestern University
Post Doc Harvard University & Whitehead Institute (MIT)
Phone: (608) 265-4690
Email: ansari@biochem.wisc.edu

Publications

Nemec CM, Yang F, Gilmore JM, Hintermair C, Ho YH, Tseng SC, Heidemann M, Zhang Y, Florens L, Gasch AP, Eick D, Washburn MP, Varani G, Ansari AZ. (2017) Different phosphoisoforms of RNA polymerase II engage the Rtt103 termination factor in a structurally analogous manner. Proc Natl Acad Sci U S A. May 16;114(20):E3944-E3953.
PMCID: PMC5441780. [PubMed]

Rodríguez-Martínez JA, Reinke AW, Bhimsaria D, Keating AE, Ansari AZ. (2017) Combinatorial bZIP dimers display complex DNA-binding specificity landscapes. Elife. Feb 10;6. pii: e19272. PMCID: PMC5349851 [PubMed]

Eguchi A, Wleklinski MJ, Spurgat MC, Heiderscheit EA, Kropornicka AS, Vu CK, Bhimsaria D, Swanson SA, Stewart R, Ramanathan P, Kamp TJ, Slukvin I, Thomson JA, Dutton JR, Ansari AZ. (2016) Reprogramming cell fate with a genome-scale library of artificial transcription factors. Proc Natl Acad Sci U S A.Dec 20;113(51):E8257-E8266. PMCID: PMC5187731 [PubMed]

Erwin GS, Grieshop MP, Bhimsaria D, Do TJ, Rodríguez-Martínez JA, Mehta C, Khanna K, Swanson SA, Stewart R, Thomson JA, Ramanathan P, Ansari AZ. (2016) Synthetic genome readers target clustered binding sites across diverse chromatin states. Proc Natl Acad Sci U S A. Nov 22;113(47):E7418-E7427. PMCID: PMC5127382 [PubMed]

Xiong K, Erwin GS, Ansari AZ, Blainey PC. (2016) Sliding on DNA: From Peptides to Small Molecules. Angew Chem Int Ed Engl. Nov 21;55(48):15110-15114. PMCID: PMC5217825 [PubMed]

Rodríguez-Molina JB, Tseng SC, Simonett SP, Taunton J, Ansari AZ. (2016) Engineered Covalent Inactivation of TFIIH-Kinase Reveals an Elongation Checkpoint and Results in Widespread mRNA Stabilization. Mol Cell. Aug 4;63(3):433-44. PMCID: PMC5122673 [PubMed]

Erwin GS, Grieshop MP, Bhimsaria D, Eguchi A, Rodríguez-Martínez JA, Ansari AZ (2016) Genome-wide Mapping of Drug-DNA Interactions in Cells with COSMIC (Crosslinking of Small Molecules to Isolate Chromatin). J Vis Exp.  Jan 20;(107):e53510. PMCID: PMC4781686 [PubMed]

Chasman D, Ho YH, Berry DB, Nemec CM, MacGilvray ME, Hose J, Merrill AE, Lee MV, Will JL, Coon JJ, Ansari AZ, Craven M, Gasch AP (2014) Pathway connectivity and signaling coordination in the yeast stress-activated signaling network. Mol Syst Biol. Nov 19;10:759. PMCID: PMC4299600 [PubMed]

Eguchi A, Lee GO, Wan F, Erwin GS, Ansari AZ (2014) Controlling gene networks and cell fate with precision-targeted DNA-binding proteins and small-molecule-based genome readers. Biochem J. Sep 15;462(3):397-413.
PMCID: PMC4205157 [PubMed]

Erwin GS, Bhimsaria D, Eguchi A, Ansari AZ. (2014) Mapping polyamide-DNA interactions in human cells reveals a new design strategy for effective targeting of genomic sites. Angew Chem Int Ed Engl. Sep 15;53(38):10124-8.
PMCID: PMC4160732 [PubMed]

Park DM, Akhtar MS, Ansari AZ, Landick R, Kiley PJ (2013) The bacterial response regulator ArcA uses a diverse binding site architecture to regulate carbon oxidation globally. PLoS Genet. 9(10):e1003839. PMCID: PMC3798270 [PubMed]

Tan-Wong SM, Zaugg JB, Camblong J, Xu Z, Zhang DW, Mischo HE, Ansari AZ, Luscombe NM, Steinmetz LM, Proudfoot NJ (2012) Gene loops enhance transcriptional directionality. Science. Nov 2;338(6107):671-5. PMCID: PMC3563069 [PubMed]

Campbell ZT, Bhimsaria D, Valley CT, Rodriguez-Martinez JA, Menichelli E, Williamson JR, Ansari AZ, Wickens M (2012) Cooperativity in RNA-Protein Interactions: Global Analysis of RNA Binding Specificity. Cell Rep. May 31;1(5):570-581. PMCID: PMC3375920 [PubMed]

Zhang DW, Rodríguez-Molina JB, Tietjen JR, Nemec CM, Ansari AZ (2012) Emerging Views on the CTD Code. Genet Res Int. 2012:347214. PMCID: PMC3335543 [PubMed]

Chinchilla K, Rodriguez-Molina JB, Ursic D, Finkel JS, Ansari AZ, Culbertson MR (2012) Interactions of Sen1, Nrd1, and Nab3 with multiple phosphorylated forms of the Rpb1 C-terminal domain in Saccharomyces cerevisiae. Eukaryot Cell. Apr;11(4):417-29. PMCID: PMC3318303 [PubMed]

Zhang DW, Mosley AL, Ramisetty SR, Rodríguez-Molina JB, Washburn MP, Ansari AZ (2012) 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. Mar 9;287(11):8541-51. PMCID: PMC3318730 [PubMed]

Warren CL, Zhao J, Glass K, Rishi V, Ansari AZ, Vinson C (2012) Fabrication of duplex DNA microarrays incorporating methyl-5-cytosine. Lab Chip. Jan 21;12(2):376-80. PMCID: PMC4205155 [PubMed]

Mysliwiec MR, Carlson CD, Tietjen J, Hung H, Ansari AZ, Lee Y (2012) Jarid2 (Jumonji, AT rich interactive domain 2) regulates NOTCH1 expression via histone modification in the developing heart. J Biol Chem. Jan 6;287(2):1235-41. PMCID: PMC3256911 [PubMed]

Ansari AZ, Rosner MR, Adler J. (2011) Har Gobind Khorana 1922-2011. Cell. Dec 23;147(7):1433-5. [PubMed] [PDF]

Ansari AZ, Rosner MR, Adler J. (2011) Har Gobind Khorana 1922-2011. Mol Cell. Dec 23;44(6):841-843. [MolCell] [PDF]

Ansari AZ, Peterson-Kaufman KJ (2011) A partner evokes latent differences between Hox proteins. Cell. Dec 9;147(6):1220-1. [PubMed]

Davis SE, Mooney RA, Kanin EI, Grass J, Landick R, Ansari AZ (2011) Mapping E. coli RNA polymerase and associated transcription factors and identifying promoters genome-wide. Methods Enzymol. 498:449-71. [PubMed]

Tietjen JR, Donato LJ, Bhimisaria D, Ansari AZ (2011) Sequence-specificity and energy landscapes of DNA-binding molecules. Methods Enzymol. 497:3-30. [PubMed]

Peterson-Kaufman KJ, Carlson CD, Rodriguez-Martinez JA, Ansari AZ (2010) Nucleating the assembly of macromolecular complexes. Chembiochem 11, 1955-1962. [PubMed]

Rodriguez-Martinez JA, Peterson-Kaufman KJ, Ansari AZ (2010) Small-molecule regulators that mimic transcription factors. Biochim Biophys Acta. Oct-Dec;1799(10-12):768-74. [PubMed]

Tietjen JR, Zhang DW, Rodriguez-Molina JB, White BE. Akhtar MS, Heidemann M, Li X, Chapman RD, Shokat K, Keles S, Eick D, Ansari AZ (2010) Chemical-genome dissection of the CTD code. Nat Struct Mol Biol. 17, 1154-1161. [PubMed]

Müller P, Park S, Shor E, Huebert DJ, Warren CL, Ansari AZ, Weinreich M, Eaton ML, MacAlpine DM, Fox CA (2010) The conserved bromo-adjacent homology domain of yeast Orc1 functions in the selection of DNA replications origins within chromatin. Genes Dev. 24, 1418-1433. [PubMed]

Carlson CD, Warren CL, Hauschild KE, Ozers MS, Qadir N, Bhimsaria D, Lee Y, Cerrina F, Ansari AZ (2010) Specificity landscapes of DNA binding molecules elucidate biological function. Proc Natl acad Sci USA, 107, 4544-4549. [PubMed]

Shor E, Warren CL, Tietjen J, Hou Z, Müller U, Alborelli I, Gohard FH, Yemm AI, Borisov L, Broach JR, Weinreich M, Nieduszynski CA, Ansari AZ, Fox CA (2009) The origin recognition complex interacts with a subset of metabolic genes tightly linked to origins of replication. PLoS Genet. 5, e1000755. [PubMed]

Arora PS, Ansari AZ (2009) Chemical biology: A Notch above other inhibitors. Nature 12, 171-173. [PubMed]

Ozers MS, Warren CL, Ansari AZ (2009) Determining DNA sequence specificity of natural and artificial transcription factors by cognate site identifier analysis. Methods Mol Biol. 544, 637-653. [PubMed]

Stanton BC, Giles SS, Kruzel EK, Warren CL, Ansari AZ, Hull CM (2009) Cognate Site Identifier analysis reveals novel binding properties of the Sex Inducer homeodomain proteins of Cryptococcus neoformans. Mol Microbiol. 72, 1334-1347. [PubMed]

Akhtar MS, Heidemann M, Tietjen JR, Zhang DW, Chapman RD, Eick D, Ansari AZ (2009) TFIIH kinase places bivalent marks on the carboxy-terminal domain of RNA polymerase II. Mol cell. 34, 387-393. [PubMed]

Hauschild KE, Stover JS, Boger DL, Ansari AZ (2009) CSI-FID: high throughput label-free detection of DNA binding molecules. Bioorg Med Chem Lett. 19, 3779-3782. [PubMed]

Ansari AZ (2009) Riboactivators: transcription activation by noncoding RNA. Crit Rev Biochem Mol Biol. 44, 50-61. [PubMed]

Mooney RA, Davis SE, Peters JM, Rowland JL, Ansari AZ, Landick R (2009) Regulator trafficking on bacterial transcription units in vivo. Mol Cell. 33, 97-108. [PubMed]

Badis G, Chan ET, van Bakel H, Pena-Castillo L, Tillo D, Tsui K, Carlson CD, Gossett AJ, Hasinoff MJ, Warren CL, Gebbia M, Talukder S, Yang A, Mnaimneh S, Terterov D, Coburn D, Li Yeo A, Yeo ZX, Clarke ND, Lieb JD, Ansari AZ, Nislow C, Hughes TR (2008) A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters. Mol Cell. 32, 878-887. [PubMed]

Moretti R, Donato LJ, Brezinski ML, Stafford RL, Hoff H, Thorson JS, Dervan PB, Ansari AZ (2008) Targeted chemical wedges reveal the role of allosteric DNA modulation in protein-DNA assembly. ACS Chem Biol. 3, 220-229. [PubMed]

Keleş S, Warren CL, Carlson CD, Ansari AZ (2008) CSI-Tree: a regression tree approach for modeling binding properties of DNA-binding molecules based on cognate site identification (CSI) data. Nucleic Acids Res. 36, 3171-3184. [PubMed]

Moretti R, Ansari AZ (2008) Expanding the specificity of DNA targeting by harnessing cooperative assembly. Biochimie. 90, 1015-1025. [PubMed]

Puckett JW, Muzikar KA, Tietjen J, Warren CL, Ansari AZ, Dervan PB (2007) Quantitative microarray profiling of DNA-binding molecules. J Am Chem Soc. 129, 12310-12319. [PubMed]

Kanin EI, Kipp RT, Kung C, Slattery M, Viale A, Hahn S, Shokat KM, Ansari AZ (2007) Chemical inhibition of the TFIIH-associated kinase Cdk7/Kin28 does not impair global mRNA synthesis. Proc Natl Acad Sci USA 104, 5812-5817. [PubMed]

Stafford RL, Arndt HD, Brezinski ML, Ansari AZ, Dervan PB (2007) Minimization of a protein-DNA dimerizer. J Am Chem Soc. 129, 2660-2668. [PubMed]

Mapp AK, Ansari AZ (2007) A TAD further: exogenous control of gene activation. ACS Chem Biol. 2, 62-75. [PubMed]

Ansari AZ (2007) Chemical crosshairs on the central dogma. Nat Chem Biol. 3, 2-7. [PubMed]

Lum JK, Majmudar CY, Ansari AZ, Mapp AK (2006) Converting inactive peptides into potent transcriptional activators. ACS Chem Biol. 1, 639-643. [PubMed]

Steinmetz EJ, Warren CL, Kuehner JN, Panbehi B, Ansari AZ, Brow DA (2006) Genome-wide distribution of yeast RNA polymerase II and its control by Sen1 helicase. Mol Cell. 24, 735-746. [PubMed]

Warren CL, Kratochvil NC, Hauschild KE, Foister S, Brezinski ML, Dervan PB, Phillips GN Jr, Ansari AZ (2006) Defining the sequence-recognition profile of DNA-binding molecules. Proc Natl Acad Sci USA. 103, 867-872. [PubMed]

Raffaelle M, Kanin EI, Vogt J, Burgess RR, Ansari AZ (2005) Holoenzyme switching and stochastic release of sigma factors from RNA polymerase in vivo. Mol Cell. 20, 357-366. [PubMed]

Herring CD, Raffaelle M, Allen TE, Kanin EI, Landick R, Ansari AZ, Palsson BØ (2005) Immobilization of Escherichia coli RNA polymerase and location of binding sites by use of chromatin immunoprecipitation and microarrays. J Bacteriol. 187, 6166-6174. [PubMed]

Lu Z, Rowe SP, Brennan BB, Davis SE, Metzler RE, Nau JJ, Majmudar CY, Mapp AK, Ansari AZ (2005) Unraveling the mechanism of a potent transcriptional activator. J Biol Chem. 280, 29689-29698. [PubMed]

Hauschild KE, Metzler RE, Arndt HD, Moretti R, Raffaelle M, Dervan PB, Ansari AZ (2005) Temperature-sensitive protein-DNA dimerizers. Proc Natl Acad Sci USA 102, 5008-5013. [PubMed]

Ansari AZ, Ogirala A, Ptashne M (2005) Transcriptional activating regions target attached substrates to a cyclin-dependent kinase. Proc Natl Acad Sci USA 102, 2346-2349. [PubMed]

Bourbon HM, Aguilera A, Ansari AZ, Asturias FJ, Berk AJ, Bjorklund S, Blackwell TK, Borggrefe T, Carey M, Carlson M, Conaway JW, Conaway RC, Emmons SW, Fondell JD, Freedman LP, Fukasawa T, Gustafsson CM, Han M, He X, Herman PK, Hinnebusch AG, Holmberg S, Holstege FC, Jaehning JA, Kim YJ, Kuras L, Leutz A, Lis JT, Meisterernest M, Naar AM, Nasmyth K, Parvin JD, Ptashne M, Reinberg D, Ronne H, Sadowski I, Sakurai H, Sipiczki M, Sternberg PW, Stillman DJ, Strich R, Struhl K, Svejstrup JQ, Tuck S, Winston F, Roeder RG, Kornberg RD (2004) A unified nomenclature for protein subunits of mediator complexes linking transcriptional regulators to RNA polymerase II. Mol Cell. 14, 553-557. [PubMed]

Liu Y, Kung C, Fishburn J, Ansari AZ, Shokat KM, Hahn S (2004) Two cyclin-dependent kinases promote RNA polymerase II transcription and formation of the scaffold complex. Mol Cell Biol. 24, 1721-1735. [PubMed]

Arndt HD, Hauschild KE, Sullivan DP, Lake K, Dervan PB, Ansari AZ (2003) Toward artificial developmental regulators. J Am Chem Soc. 125, 13322-13323. [PubMed]

Ansari AZ (2003) Fingers reach for the genome. Nat Biotechnol. 21, 242-243. [PubMed]

Saha S, Ansari AZ, Jarrell KA, Ptashne M (2003) RNA sequences that work as transcriptional activating regions. Nucleic Acids Res. 31, 1565-1570. [PubMed]

Ansari AZ, Mapp AK (2002) Modular design of artificial transcription factors. Curr Opin Chem Biol. 6, 765-772. [PubMed]

Ansari AZ, Koh SS, Zaman Z, Bongards C, Lehming N, Young RA, Ptashne M (2002) Transcriptional activating regions target a cyclin-dependent kinase. Proc Natl Acad Sci USA 99, 14706-14709. [PubMed]

Arora PS, Ansari AZ, Best TP, Ptashne M, Dervan PB (2002) Design of artificial transcriptional activators with rigid poly-L-proline linkers. J Am Chem Soc. 124, 13067-13071. [PubMed]

Lu Z, Ansari AZ, Lu X, Ogirala A, Ptashne M (2002) A target essential for the activity of a nonacidic yeast transcriptional activator. Proc Natl Acad Sci USA 99, 8591-8596. [PubMed]

Ansari AZ, Mapp AK, Nguyen DH, Dervan PB, Ptashne M (2001) Towards a minimal motif for artificial transcriptional activators. Chem Biol. 8, 583-592. [PubMed]

Hidalgo P, Ansari AZ, Schmidt P, Hare B, Simkovich N, Farrell S, Shin EJ, Ptashne M, Wagner G (2001) Recruitment of the transcriptional machinery through GAL11P: structure and interactions of the GAL4 dimerization domain. Genes Dev. 15, 1007-1020. [PubMed]

Zaman Z, Ansari AZ, Koh SS, Young R, Ptashne M (2001) Interaction of a transcriptional repressor with the RNA polymerase II holoenzyme plays a crucial role in repression. Proc Natl Acad Sci USA 98, 2550-2554. [PubMed]

Mapp AK, Ansari AZ, Ptashne M, Dervan PB (2000) Activation of gene expression by small molecule transcription factors. Proc Natl Acad Sci USA 97, 3930-3935. [PubMed]

Lu X, Ansari AZ, Ptashne M (2000) An artificial transcriptional activating region with unusual properties. Proc Natl Acad Sci USA 97, 1988-1992. [PubMed]

Zaman Z, Ansari AZ, Gaudreau L, Nevado J, Ptashne M (1998) Gene transcription by recruitment. Cold Spring Harb Symp Quant Biol. 63, 167-171. [PubMed]

Ansari AZ, Reece RJ, Ptashne M (1998) A transcriptional activating region with two contrasting modes of protein interaction. Proc Natl Acad Sci USA 95, 13543-13548. [PubMed]

Koh SS, Ansari AZ, Ptashne M, Young RA (1998) An activator target in the RNA polymerase II holoenzyme. Mol Cell. 1, 895-904. [PubMed]

Ansari AZ, Bradner JE, O'Halloran TV (1995) DNA-bend modulation in a repressor-to-activator switching mechanism. Nature 374, 371-375. [PubMed]

Parkhill J, Ansari AZ, Wright JG, Brown NL, O'Halloran TV (1993) Construction and characterization of a mercury-independent MerR activator (MerRAC): transcriptional activation in the absence of Hg(II) is accompanied by DNA distortion. EMBO J. 12, 4131-4121. [PubMed]

Ansari AZ, Chael ML, O'Halloran TV (1992) Allosteric underwinding of DNA is a critical step in positive control of transcription by Hg-MerR. Nature 355, 87-89. [PubMed]