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Zarmik Moqtaderi, Ph.D., D.E.A.

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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.
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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. 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. PMID: 36421680; PMCID: PMC9721619.
    Citations: 1     Fields:    Translation:HumansAnimalsCells
  2. 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. PMID: 35972270; PMCID: PMC9476944.
    Citations: 1     Fields:    Translation:AnimalsCells
  3. Moqtaderi Z, Geisberg JV, Struhl K. 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). PMID: 35058367; PMCID: PMC8794773.
    Citations: 3     Fields:    Translation:AnimalsCells
  4. Moqtaderi Z, Brown S, Bender W. Genome-wide oscillations in G + C density and sequence conservation. Genome Res. 2021 11; 31(11):2050-2057. PMID: 34649930; PMCID: PMC8559709.
    Citations:    Fields:    Translation:Cells
  5. Geisberg JV, Moqtaderi Z, Struhl K. The transcriptional elongation rate regulates alternative polyadenylation in yeast. Elife. 2020 08 26; 9. PMID: 32845240.
    Citations: 9     Fields:    Translation:AnimalsCells
  6. Moqtaderi Z, Geisberg JV. Probing In Vivo Structure of Individual mRNA 3' Isoforms Using Dimethyl Sulfate. Curr Protoc Mol Biol. 2019 09; 128(1):e99. PMID: 31503415.
    Citations:    Fields:    Translation:AnimalsCells
  7. Geisberg JV, Moqtaderi Z. Protein Binding to mRNA 3' Isoforms. Curr Protoc Mol Biol. 2019 09; 128(1):e101. PMID: 31503412.
    Citations:    Fields:    Translation:AnimalsCells
  8. Moqtaderi Z, Geisberg JV, Struhl K. 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. PMID: 30318446; PMCID: PMC6289678.
    Citations: 17     Fields:    Translation:AnimalsCells
  9. Geisberg JV, Moqtaderi Z. Genome-Wide Study of mRNA Isoform Half-Lives. Methods Mol Biol. 2016; 1358:317-23. PMID: 26463393.
    Citations:    Fields:    Translation:AnimalsCells
  10. 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. PMID: 25827089.
    Citations: 9     Fields:    
  11. Moqtaderi Z, Geisberg JV, Struhl K. 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. PMID: 25279376.
    Citations: 7     
  12. 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. PMID: 24529382.
    Citations: 122     Fields:    Translation:AnimalsCells
  13. Moqtaderi Z, Geisberg JV. 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. PMID: 24510296.
    Citations: 2     Fields:    Translation:Animals
  14. 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. PMID: 23776204.
    Citations: 28     Fields:    Translation:AnimalsCells
  15. Wong KH, Jin Y, Moqtaderi Z. Multiplex Illumina sequencing using DNA barcoding. Curr Protoc Mol Biol. 2013; Chapter 7:Unit 7.11.. PMID: 23288465.
    Citations: 30     Fields:    
  16. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 06; 489(7414):57-74. PMID: 22955616; PMCID: PMC3439153.
    Citations: 7598     Fields:    Translation:HumansAnimalsCells
  17. 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. PMID: 22722849.
    Citations: 258     Fields:    Translation:HumansAnimalsCells
  18. 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. PMID: 21695216.
    Citations: 11     Fields:    Translation:AnimalsCells
  19. 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. PMID: 21084631.
    Citations: 41     Fields:    Translation:HumansCells
  20. Fan X, Moqtaderi Z, Jin Y, Zhang Y, Liu XS, Struhl K. 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. PMID: 20921369.
    Citations: 53     Fields:    Translation:Cells
  21. Zhang Y, Moqtaderi Z, Rattner BP, Euskirchen G, Snyder M, Kadonaga JT, Liu XS, Struhl K. 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. PMID: 20683474.
    Citations: 31     Fields:    Translation:HumansAnimalsCells
  22. 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. PMID: 20418883.
    Citations: 126     Fields:    Translation:HumansCells
  23. 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. PMID: 20139302.
    Citations: 120     Fields:    Translation:HumansCells
  24. 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. PMID: 19706456.
    Citations: 112     Fields:    Translation:HumansAnimalsCells
  25. 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. PMID: 19620965.
    Citations: 214     Fields:    Translation:AnimalsCells
  26. Moqtaderi Z, Struhl K. Expanding the repertoire of plasmids for PCR-mediated epitope tagging in yeast. Yeast. 2008 Apr; 25(4):287-92. PMID: 18338317.
    Citations: 21     Fields:    Translation:AnimalsCells
  27. 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. PMID: 18258921.
    Citations: 77     Fields:    Translation:HumansCells
  28. 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. PMID: 17571346; PMCID: PMC2212820.
    Citations: 2604     Fields:    Translation:HumansCells
  29. Sekinger EA, Moqtaderi Z, Struhl K. 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. PMID: 15949447.
    Citations: 194     Fields:    Translation:AnimalsCells
  30. 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. PMID: 18265358.
    Citations: 66     Fields:    Translation:HumansAnimalsCells
  31. Moqtaderi Z, Struhl K. Defining in vivo targets of nuclear proteins by chromatin immunoprecipitation and microarray analysis. Curr Protoc Mol Biol. 2004 Nov; Chapter 21:Unit 21.9. PMID: 18265347.
    Citations: 1     Fields:    Translation:Animals
  32. Moqtaderi Z, Struhl K. 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. PMID: 15121834.
    Citations: 85     Fields:    Translation:AnimalsCells
  33. Reid JL, Moqtaderi Z, Struhl K. Eaf3 regulates the global pattern of histone acetylation in Saccharomyces cerevisiae. Mol Cell Biol. 2004 Jan; 24(2):757-64. PMID: 14701747.
    Citations: 38     Fields:    Translation:AnimalsCells
  34. 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. PMID: 12417716.
    Citations: 37     Fields:    Translation:AnimalsCells
  35. 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. PMID: 11983173.
    Citations: 78     Fields:    Translation:AnimalsCells
  36. Lundblad V, Hartzog G, Moqtaderi Z. Manipulation of cloned yeast DNA. Curr Protoc Mol Biol. 2001 May; Chapter 13:Unit13.10. PMID: 18265094.
    Citations: 7     Fields:    Translation:Animals
  37. 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. PMID: 10777519.
    Citations: 8     Fields:    Translation:AnimalsCells
  38. Moqtaderi Z, Keaveney M, Struhl K. The histone H3-like TAF is broadly required for transcription in yeast. Mol Cell. 1998 Nov; 2(5):675-82. PMID: 9844639.
    Citations: 44     Fields:    Translation:AnimalsCells
  39. Struhl K, Moqtaderi Z. The TAFs in the HAT. Cell. 1998 Jul 10; 94(1):1-4. PMID: 9674419.
    Citations: 39     Fields:    Translation:HumansAnimalsCells
  40. Struhl K, Kadosh D, Keaveney M, Kuras L, Moqtaderi Z. Activation and repression mechanisms in yeast. Cold Spring Harb Symp Quant Biol. 1998; 63:413-21. PMID: 10384306.
    Citations: 16     Fields:    Translation:AnimalsCells
  41. 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. PMID: 8962109; PMCID: PMC26190.
    Citations: 44     Fields:    Translation:HumansAnimalsCells
  42. 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. PMID: 8774887.
    Citations: 119     Fields:    Translation:AnimalsCells
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