Publications by authors named "Zarmik Moqtaderi"

30Publications

The transcriptional elongation rate regulates alternative polyadenylation in yeast.

Elife 2020 08 26;9. Epub 2020 Aug 26.

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.7554/eLife.59810DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7532003PMC
August 2020

Probing In Vivo Structure of Individual mRNA 3' Isoforms Using Dimethyl Sulfate.

Curr Protoc Mol Biol 2019 09;128(1):e99

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/cpmb.99DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6777956PMC
September 2019

Protein Binding to mRNA 3' Isoforms.

Curr Protoc Mol Biol 2019 09;128(1):e101

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/cpmb.101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6741434PMC
September 2019

Extensive Structural Differences of Closely Related 3' mRNA Isoforms: Links to Pab1 Binding and mRNA Stability.

Mol Cell 2018 12 11;72(5):849-861.e6. Epub 2018 Oct 11.

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.molcel.2018.08.044DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6289678PMC
December 2018

Genome-Wide Study of mRNA Isoform Half-Lives.

Methods Mol Biol 2016 ;1358:317-23

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/978-1-4939-3067-8_20DOI Listing
July 2016

Mapping 3' mRNA isoforms on a genomic scale.

Curr Protoc Mol Biol 2015 Apr 1;110:4.23.1-4.23.17. Epub 2015 Apr 1.

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/0471142727.mb0423s110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4397975PMC
April 2015

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

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115.

View Article

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4178928PMC
http://dx.doi.org/10.15698/mic2014.04.140DOI Listing
April 2014

Global analysis of mRNA isoform half-lives reveals stabilizing and destabilizing elements in yeast.

Cell 2014 Feb;156(4):812-24

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.cell.2013.12.026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3939777PMC
February 2014

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. Epub 2013 Oct 11.

Harvard Medical School, Boston, Massachusetts.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/0471142727.mb1310cs104DOI Listing
October 2013

Species-specific factors mediate extensive heterogeneity of mRNA 3' ends in yeasts.

Proc Natl Acad Sci U S A 2013 Jul 17;110(27):11073-8. Epub 2013 Jun 17.

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1309384110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3703967PMC
July 2013

Multiplex Illumina sequencing using DNA barcoding.

Curr Protoc Mol Biol 2013 ;Chapter 7:Unit 7.11.

Harvard Medical School, Boston, Massachusetts, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/0471142727.mb0711s101DOI Listing
May 2013

High-throughput sequencing reveals a simple model of nucleosome energetics.

Proc Natl Acad Sci U S A 2010 Dec 17;107(49):20998-1003. Epub 2010 Nov 17.

Department of Physics and Astronomy and BioMaPS Institute for Quantitative Biology, Rutgers University, Piscataway, NJ 08854, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1003838107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3000311PMC
December 2010

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 4;107(42):17945-50. Epub 2010 Oct 4.

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1012674107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2964211PMC
October 2010

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

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, Massachusetts, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nsmb0810-920DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4742340PMC
August 2010

Genomic binding profiles of functionally distinct RNA polymerase III transcription complexes in human cells.

Nat Struct Mol Biol 2010 May 25;17(5):635-40. Epub 2010 Apr 25.

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nsmb.1794DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3350333PMC
May 2010

Close association of RNA polymerase II and many transcription factors with Pol III genes.

Proc Natl Acad Sci U S A 2010 Feb 5;107(8):3639-44. Epub 2010 Feb 5.

Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA.

View Article

Download full-text PDF

Source
http://archive.gersteinlab.org/papers/e-print/20139302/prepr
Web Search
http://www.pnas.org/cgi/doi/10.1073/pnas.0911315106
Publisher Site
http://dx.doi.org/10.1073/pnas.0911315106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2840497PMC
February 2010

Mapping accessible chromatin regions using Sono-Seq.

Proc Natl Acad Sci U S A 2009 Sep 18;106(35):14926-31. Epub 2009 Aug 18.

Program in Computational Biology, Yale University, New Haven, CT 06520, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.0905443106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2736440PMC
September 2009

Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo.

Nat Struct Mol Biol 2009 Aug 20;16(8):847-52. Epub 2009 Jul 20.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, Massachusetts, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nsmb.1636DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2823114PMC
August 2009

Expanding the repertoire of plasmids for PCR-mediated epitope tagging in yeast.

Yeast 2008 Apr;25(4):287-92

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/yea.1581DOI Listing
April 2008

Defining in vivo targets of nuclear proteins by chromatin immunoprecipitation and microarray analysis.

Curr Protoc Mol Biol 2004 Nov;Chapter 21:Unit 21.9

Harvard Medical School, Boston, Massachusetts, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/0471142727.mb2109s68DOI Listing
November 2004

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

Authors:
Ewan Birney John A Stamatoyannopoulos Anindya Dutta Roderic Guigó Thomas R Gingeras Elliott H Margulies Zhiping Weng Michael Snyder Emmanouil T Dermitzakis Robert E Thurman Michael S Kuehn Christopher M Taylor Shane Neph Christoph M Koch Saurabh Asthana Ankit Malhotra Ivan Adzhubei Jason A Greenbaum Robert M Andrews Paul Flicek Patrick J Boyle Hua Cao Nigel P Carter Gayle K Clelland Sean Davis Nathan Day Pawandeep Dhami Shane C Dillon Michael O Dorschner Heike Fiegler Paul G Giresi Jeff Goldy Michael Hawrylycz Andrew Haydock Richard Humbert Keith D James Brett E Johnson Ericka M Johnson Tristan T Frum Elizabeth R Rosenzweig Neerja Karnani Kirsten Lee Gregory C Lefebvre Patrick A Navas Fidencio Neri Stephen C J Parker Peter J Sabo Richard Sandstrom Anthony Shafer David Vetrie Molly Weaver Sarah Wilcox Man Yu Francis S Collins Job Dekker Jason D Lieb Thomas D Tullius Gregory E Crawford Shamil Sunyaev William S Noble Ian Dunham France Denoeud Alexandre Reymond Philipp Kapranov Joel Rozowsky Deyou Zheng Robert Castelo Adam Frankish Jennifer Harrow Srinka Ghosh Albin Sandelin Ivo L Hofacker Robert Baertsch Damian Keefe Sujit Dike Jill Cheng Heather A Hirsch Edward A Sekinger Julien Lagarde Josep F Abril Atif Shahab Christoph Flamm Claudia Fried Jörg Hackermüller Jana Hertel Manja Lindemeyer Kristin Missal Andrea Tanzer Stefan Washietl Jan Korbel Olof Emanuelsson Jakob S Pedersen Nancy Holroyd Ruth Taylor David Swarbreck Nicholas Matthews Mark C Dickson Daryl J Thomas Matthew T Weirauch James Gilbert Jorg Drenkow Ian Bell XiaoDong Zhao K G Srinivasan Wing-Kin Sung Hong Sain Ooi Kuo Ping Chiu Sylvain Foissac Tyler Alioto Michael Brent Lior Pachter Michael L Tress Alfonso Valencia Siew Woh Choo Chiou Yu Choo Catherine Ucla Caroline Manzano Carine Wyss Evelyn Cheung Taane G Clark James B Brown Madhavan Ganesh Sandeep Patel Hari Tammana Jacqueline Chrast Charlotte N Henrichsen Chikatoshi Kai Jun Kawai Ugrappa Nagalakshmi Jiaqian Wu Zheng Lian Jin Lian Peter Newburger Xueqing Zhang Peter Bickel John S Mattick Piero Carninci Yoshihide Hayashizaki Sherman Weissman Tim Hubbard Richard M Myers Jane Rogers Peter F Stadler Todd M Lowe Chia-Lin Wei Yijun Ruan Kevin Struhl Mark Gerstein Stylianos E Antonarakis Yutao Fu Eric D Green Ulaş Karaöz Adam Siepel James Taylor Laura A Liefer Kris A Wetterstrand Peter J Good Elise A Feingold Mark S Guyer Gregory M Cooper George Asimenos Colin N Dewey Minmei Hou Sergey Nikolaev Juan I Montoya-Burgos Ari Löytynoja Simon Whelan Fabio Pardi Tim Massingham Haiyan Huang Nancy R Zhang Ian Holmes James C Mullikin Abel Ureta-Vidal Benedict Paten Michael Seringhaus Deanna Church Kate Rosenbloom W James Kent Eric A Stone Serafim Batzoglou Nick Goldman Ross C Hardison David Haussler Webb Miller Arend Sidow Nathan D Trinklein Zhengdong D Zhang Leah Barrera Rhona Stuart David C King Adam Ameur Stefan Enroth Mark C Bieda Jonghwan Kim Akshay A Bhinge Nan Jiang Jun Liu Fei Yao Vinsensius B Vega Charlie W H Lee Patrick Ng Atif Shahab Annie Yang Zarmik Moqtaderi Zhou Zhu Xiaoqin Xu Sharon Squazzo Matthew J Oberley David Inman Michael A Singer Todd A Richmond Kyle J Munn Alvaro Rada-Iglesias Ola Wallerman Jan Komorowski Joanna C Fowler Phillippe Couttet Alexander W Bruce Oliver M Dovey Peter D Ellis Cordelia F Langford David A Nix Ghia Euskirchen Stephen Hartman Alexander E Urban Peter Kraus Sara Van Calcar Nate Heintzman Tae Hoon Kim Kun Wang Chunxu Qu Gary Hon Rosa Luna Christopher K Glass M Geoff Rosenfeld Shelley Force Aldred Sara J Cooper Anason Halees Jane M Lin Hennady P Shulha Xiaoling Zhang Mousheng Xu Jaafar N S Haidar Yong Yu Yijun Ruan Vishwanath R Iyer Roland D Green Claes Wadelius Peggy J Farnham Bing Ren Rachel A Harte Angie S Hinrichs Heather Trumbower Hiram Clawson Jennifer Hillman-Jackson Ann S Zweig Kayla Smith Archana Thakkapallayil Galt Barber Robert M Kuhn Donna Karolchik Lluis Armengol Christine P Bird Paul I W de Bakker Andrew D Kern Nuria Lopez-Bigas Joel D Martin Barbara E Stranger Abigail Woodroffe Eugene Davydov Antigone Dimas Eduardo Eyras Ingileif B Hallgrímsdóttir Julian Huppert Michael C Zody Gonçalo R Abecasis Xavier Estivill Gerard G Bouffard Xiaobin Guan Nancy F Hansen Jacquelyn R Idol Valerie V B Maduro Baishali Maskeri Jennifer C McDowell Morgan Park Pamela J Thomas Alice C Young Robert W Blakesley Donna M Muzny Erica Sodergren David A Wheeler Kim C Worley Huaiyang Jiang George M Weinstock Richard A Gibbs Tina Graves Robert Fulton Elaine R Mardis Richard K Wilson Michele Clamp James Cuff Sante Gnerre David B Jaffe Jean L Chang Kerstin Lindblad-Toh Eric S Lander Maxim Koriabine Mikhail Nefedov Kazutoyo Osoegawa Yuko Yoshinaga Baoli Zhu Pieter J de Jong
June 2007

Intrinsic histone-DNA interactions and low nucleosome density are important for preferential accessibility of promoter regions in yeast.

Mol Cell 2005 Jun;18(6):735-48

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA.

View Article

Download full-text PDF

Source
http://linkinghub.elsevier.com/retrieve/pii/S109727650501309
Publisher Site
http://dx.doi.org/10.1016/j.molcel.2005.05.003DOI Listing
June 2005

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

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA.

View Article

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC400477PMC
http://dx.doi.org/10.1128/mcb.24.10.4118-4127.2004DOI Listing
May 2004

Eaf3 regulates the global pattern of histone acetylation in Saccharomyces cerevisiae.

Mol Cell Biol 2004 Jan;24(2):757-64

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.

View Article

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC343795PMC
http://dx.doi.org/10.1128/mcb.24.2.757-764.2004DOI Listing
January 2004

Mot1 associates with transcriptionally active promoters and inhibits association of NC2 in Saccharomyces cerevisiae.

Mol Cell Biol 2002 Dec;22(23):8122-34

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA.

View Article

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC134071PMC
http://dx.doi.org/10.1128/mcb.22.23.8122-8134.2002DOI Listing
December 2002

Activator-specific recruitment of TFIID and regulation of ribosomal protein genes in yeast.

Mol Cell 2002 Apr;9(4):823-33

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/s1097-2765(02)00490-2DOI Listing
April 2002