Instructor in Biological Chemistry and Molecular Pharmacology
Zhang Y, Moqtaderi Z, Rattner BP, Euskirchen G, Snyder M, Kadonaga JT, Liu XS, Struhl K
Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo. Nat Struct Mol Biol. 2009 Aug; 16(8):847-52.
Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo.
Expanding the repertoire of plasmids for PCR-mediated epitope tagging in yeast. Yeast. 2008 Apr; 25(4):287-92.
Expanding the repertoire of plasmids for PCR-mediated epitope tagging in yeast.
Extensive Structural Differences of Closely Related 3' mRNA Isoforms: Links to Pab1 Binding and mRNA Stability. Mol Cell. 2018 12 06; 72(5):849-861.e6.
Extensive Structural Differences of Closely Related 3' mRNA Isoforms: Links to Pab1 Binding and mRNA Stability.
Fan X, Moqtaderi Z, Jin Y, Zhang Y, Liu XS, Struhl K
Proceedings of the National Academy of Sciences of the United States of America
Nucleosome depletion at yeast terminators is not intrinsic and can occur by a transcriptional mechanism linked to 3'-end formation. Proc Natl Acad Sci U S A. 2010 Oct 19; 107(42):17945-50.
Nucleosome depletion at yeast terminators is not intrinsic and can occur by a transcriptional mechanism linked to 3'-end formation.
Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermüller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaöz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CW, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JN, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PI, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrímsdóttir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007 Jun 14; 447(7146):799-816.
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.
Aparicio O, Geisberg JV, Sekinger E, Yang A, Moqtaderi Z, Struhl K
Chromatin immunoprecipitation for determining the association of proteins with specific genomic sequences in vivo. Curr Protoc Mol Biol. 2005 Feb; Chapter 21:Unit 21.3.
Chromatin immunoprecipitation for determining the association of proteins with specific genomic sequences in vivo.
Eaf3 regulates the global pattern of histone acetylation in Saccharomyces cerevisiae. Mol Cell Biol. 2004 Jan; 24(2):757-64.
Eaf3 regulates the global pattern of histone acetylation in Saccharomyces cerevisiae.
Hamilton Kuhn Professor of Biological Chemistry and Molecular Pharmacology
Research Associate in Biological Chemistry and Molecular Pharmacology
David Wesley Gaiser Professor of Biological Chemistry and Molecular Pharmacology
Professor of Biological Chemistry and Molecular Pharmacology
Christopher T. Walsh, PhD Professor of Biological Chemistry and Molecular Pharmacology
Harold T. White Professor of Biological Chemistry and Molecular Pharmacology
Protein Binding to mRNA 3' Isoforms. Curr Protoc Mol Biol. 2019 09; 128(1):e101.
Probing In Vivo Structure of Individual mRNA 3' Isoforms Using Dimethyl Sulfate. Curr Protoc Mol Biol. 2019 09; 128(1):e99.
Probing In Vivo Structure of Individual mRNA 3' Isoforms Using Dimethyl Sulfate.
The transcriptional elongation rate regulates alternative polyadenylation in yeast. Elife. 2020 08 26; 9.
The transcriptional elongation rate regulates alternative polyadenylation in yeast.
Genome-wide oscillations in G + C density and sequence conservation. Genome Res. 2021 11; 31(11):2050-2057.
Genome-wide oscillations in G + C density and sequence conservation.
A compensatory link between cleavage/polyadenylation and mRNA turnover regulates steady-state mRNA levels in yeast. Proc Natl Acad Sci U S A. 2022 01 25; 119(4).
A compensatory link between cleavage/polyadenylation and mRNA turnover regulates steady-state mRNA levels in yeast.
Lui KH, Geisberg JV, Moqtaderi Z, Struhl K
3' Untranslated Regions Are Modular Entities That Determine Polyadenylation Profiles. Mol Cell Biol. 2022 09 15; 42(9):e0024422.
3' Untranslated Regions Are Modular Entities That Determine Polyadenylation Profiles.
Geisberg JV, Moqtaderi Z, Fong N, Erickson B, Bentley DL, Struhl K
Nucleotide-level linkage of transcriptional elongation and polyadenylation. Elife. 2022 11 24; 11.
Nucleotide-level linkage of transcriptional elongation and polyadenylation.
Condition-specific 3' mRNA isoform half-lives and stability elements in yeast. Proc Natl Acad Sci U S A. 2023 05 02; 120(18):e2301117120.
Condition-specific 3' mRNA isoform half-lives and stability elements in yeast.
Khitun A, Brion C, Moqtaderi Z, Geisberg JV, Churchman LS, Struhl K
Elongation rate of RNA polymerase II affects pausing patterns across 3' UTRs. J Biol Chem. 2023 11; 299(11):105289.
Elongation rate of RNA polymerase II affects pausing patterns across 3' UTRs.
Chromatin regulates alternative polyadenylation via the RNA polymerase II elongation rate. Proc Natl Acad Sci U S A. 2024 May 21; 121(21):e2405827121.
Chromatin regulates alternative polyadenylation via the RNA polymerase II elongation rate.
Moqtaderi Z, Geisberg JV, Jin Y, Fan X, Struhl K
Species-specific factors mediate extensive heterogeneity of mRNA 3' ends in yeasts. Proc Natl Acad Sci U S A. 2013 Jul 02; 110(27):11073-8.
Species-specific factors mediate extensive heterogeneity of mRNA 3' ends in yeasts.
Location of polyadenylation sites within 3' untranslated regions is linked to biological function in yeast. Genetics. 2024 10 09.
Location of polyadenylation sites within 3' untranslated regions is linked to biological function in yeast.
Construction of mutant alleles in Saccharomyces cerevisiae without cloning: overview and the delitto perfetto method. Curr Protoc Mol Biol. 2013 Oct 11; 104:13.10C.1-13.10C.17.
Construction of mutant alleles in Saccharomyces cerevisiae without cloning: overview and the delitto perfetto method.
Geisberg JV, Moqtaderi Z, Fan X, Ozsolak F, Struhl K
Global analysis of mRNA isoform half-lives reveals stabilizing and destabilizing elements in yeast. Cell. 2014 Feb 13; 156(4):812-24.
Global analysis of mRNA isoform half-lives reveals stabilizing and destabilizing elements in yeast.
Jin Y, Geisberg JV, Moqtaderi Z, Ji Z, Hoque M, Tian B, Struhl K
Mapping 3' mRNA isoforms on a genomic scale. Curr Protoc Mol Biol. 2015 Apr 01; 110:4.23.1-4.23.17.
Mapping 3' mRNA isoforms on a genomic scale.
Methods in molecular biology (Clifton, N.J.)
Genome-Wide Study of mRNA Isoform Half-Lives. Methods Mol Biol. 2016; 1358:317-23.
Genome-Wide Study of mRNA Isoform Half-Lives.
Evidence against a genomic code for nucleosome positioning. Reply to "Nucleosome sequence preferences influence in vivo nucleosome organization.". Nat Struct Mol Biol. 2010 Aug; 17(8):920-3.
Evidence against a genomic code for nucleosome positioning. Reply to "Nucleosome sequence preferences influence in vivo nucleosome organization.".
Secondary structures involving the poly(A) tail and other 3' sequences are major determinants of mRNA isoform stability in yeast. Microb Cell. 2014 Apr; 1(4):137-139.
Secondary structures involving the poly(A) tail and other 3' sequences are major determinants of mRNA isoform stability in yeast.
Moqtaderi Z, Bai Y, Poon D, Weil PA, Struhl K
TBP-associated factors are not generally required for transcriptional activation in yeast. Nature. 1996 Sep 12; 383(6596):188-91.
TBP-associated factors are not generally required for transcriptional activation in yeast.
The TAFs in the HAT. Cell. 1998 Jul 10; 94(1):1-4.
Mencía M, Moqtaderi Z, Geisberg JV, Kuras L, Struhl K
Activator-specific recruitment of TFIID and regulation of ribosomal protein genes in yeast. Mol Cell. 2002 Apr; 9(4):823-33.
Activator-specific recruitment of TFIID and regulation of ribosomal protein genes in yeast.
Struhl K, Kadosh D, Keaveney M, Kuras L, Moqtaderi Z
Cold Spring Harbor symposia on quantitative biology
Activation and repression mechanisms in yeast. Cold Spring Harb Symp Quant Biol. 1998; 63:413-21.
Activation and repression mechanisms in yeast.
Moqtaderi Z, Wang J, Raha D, White RJ, Snyder M, Weng Z, Struhl K
Genomic binding profiles of functionally distinct RNA polymerase III transcription complexes in human cells. Nat Struct Mol Biol. 2010 May; 17(5):635-40.
Genomic binding profiles of functionally distinct RNA polymerase III transcription complexes in human cells.
Esberg A, Moqtaderi Z, Fan X, Lu J, Struhl K, Byström A
Iwr1 protein is important for preinitiation complex formation by all three nuclear RNA polymerases in Saccharomyces cerevisiae. PLoS One. 2011; 6(6):e20829.
Iwr1 protein is important for preinitiation complex formation by all three nuclear RNA polymerases in Saccharomyces cerevisiae.
Geisberg JV, Moqtaderi Z, Kuras L, Struhl K
Mot1 associates with transcriptionally active promoters and inhibits association of NC2 in Saccharomyces cerevisiae. Mol Cell Biol. 2002 Dec; 22(23):8122-34.
Mot1 associates with transcriptionally active promoters and inhibits association of NC2 in Saccharomyces cerevisiae.
The histone H3-like TAF is broadly required for transcription in yeast. Mol Cell. 1998 Nov; 2(5):675-82.
The histone H3-like TAF is broadly required for transcription in yeast.
Johnson DS, Li W, Gordon DB, Bhattacharjee A, Curry B, Ghosh J, Brizuela L, Carroll JS, Brown M, Flicek P, Koch CM, Dunham I, Bieda M, Xu X, Farnham PJ, Kapranov P, Nix DA, Gingeras TR, Zhang X, Holster H, Jiang N, Green RD, Song JS, McCuine SA, Anton E, Nguyen L, Trinklein ND, Ye Z, Ching K, Hawkins D, Ren B, Scacheri PC, Rozowsky J, Karpikov A, Euskirchen G, Weissman S, Gerstein M, Snyder M, Yang A, Moqtaderi Z, Hirsch H, Shulha HP, Fu Y, Weng Z, Struhl K, Myers RM, Lieb JD, Liu XS
Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Res. 2008 Mar; 18(3):393-403.
Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets.
Barber MF, Michishita-Kioi E, Xi Y, Tasselli L, Kioi M, Moqtaderi Z, Tennen RI, Paredes S, Young NL, Chen K, Struhl K, Garcia BA, Gozani O, Li W, Chua KF
SIRT7 links H3K18 deacetylation to maintenance of oncogenic transformation. Nature. 2012 Jul 05; 487(7405):114-8.
SIRT7 links H3K18 deacetylation to maintenance of oncogenic transformation.
Stargell LA, Moqtaderi Z, Dorris DR, Ogg RC, Struhl K
TFIIA has activator-dependent and core promoter functions in vivo. J Biol Chem. 2000 Apr 28; 275(17):12374-80.
TFIIA has activator-dependent and core promoter functions in vivo.
Genome-wide occupancy profile of the RNA polymerase III machinery in Saccharomyces cerevisiae reveals loci with incomplete transcription complexes. Mol Cell Biol. 2004 May; 24(10):4118-27.
Genome-wide occupancy profile of the RNA polymerase III machinery in Saccharomyces cerevisiae reveals loci with incomplete transcription complexes.
Intrinsic histone-DNA interactions and low nucleosome density are important for preferential accessibility of promoter regions in yeast. Mol Cell. 2005 Jun 10; 18(6):735-48.
Intrinsic histone-DNA interactions and low nucleosome density are important for preferential accessibility of promoter regions in yeast.
Defining in vivo targets of nuclear proteins by chromatin immunoprecipitation and microarray analysis. Curr Protoc Mol Biol. 2004 Nov; Chapter 21:Unit 21.9.
Defining in vivo targets of nuclear proteins by chromatin immunoprecipitation and microarray analysis.
Auerbach RK, Euskirchen G, Rozowsky J, Lamarre-Vincent N, Moqtaderi Z, Lefrançois P, Struhl K, Gerstein M, Snyder M
Mapping accessible chromatin regions using Sono-Seq. Proc Natl Acad Sci U S A. 2009 Sep 01; 106(35):14926-31.
Mapping accessible chromatin regions using Sono-Seq.
Manipulation of cloned yeast DNA. Curr Protoc Mol Biol. 2001 May; Chapter 13:Unit13.10.
Raha D, Wang Z, Moqtaderi Z, Wu L, Zhong G, Gerstein M, Struhl K, Snyder M
Close association of RNA polymerase II and many transcription factors with Pol III genes. Proc Natl Acad Sci U S A. 2010 Feb 23; 107(8):3639-44.
Close association of RNA polymerase II and many transcription factors with Pol III genes.
An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 06; 489(7414):57-74.
An integrated encyclopedia of DNA elements in the human genome.
Multiplex Illumina sequencing using DNA barcoding. Curr Protoc Mol Biol. 2013; Chapter 7:Unit 7.11..
Multiplex Illumina sequencing using DNA barcoding.
Locke G, Tolkunov D, Moqtaderi Z, Struhl K, Morozov AV
High-throughput sequencing reveals a simple model of nucleosome energetics. Proc Natl Acad Sci U S A. 2010 Dec 07; 107(49):20998-1003.
High-throughput sequencing reveals a simple model of nucleosome energetics.
Moqtaderi Z, Yale JD, Struhl K, Buratowski S
Yeast homologues of higher eukaryotic TFIID subunits. Proc Natl Acad Sci U S A. 1996 Dec 10; 93(25):14654-8.
Yeast homologues of higher eukaryotic TFIID subunits.