Kevin Struhl

Kevin Struhl

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Kevin Struhl

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Promoter-specific dynamics of TATA-binding protein association with the human genome.

Genome Res 2019 12 15;29(12):1939-1950. Epub 2019 Nov 15.

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

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http://dx.doi.org/10.1101/gr.254466.119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6886507PMC
December 2019

Inflammatory regulatory network mediated by the joint action of NF-kB, STAT3, and AP-1 factors is involved in many human cancers.

Proc Natl Acad Sci U S A 2019 May 25;116(19):9453-9462. Epub 2019 Mar 25.

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

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http://dx.doi.org/10.1073/pnas.1821068116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6511065PMC
May 2019

Requirements for RNA polymerase II preinitiation complex formation in vivo.

Elife 2019 01 25;8. Epub 2019 Jan 25.

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

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http://dx.doi.org/10.7554/eLife.43654DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6366898PMC
January 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:

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

Targeted profiling of RNA translation reveals mTOR-4EBP1/2-independent translation regulation of mRNAs encoding ribosomal proteins.

Proc Natl Acad Sci U S A 2018 10 17;115(40):E9325-E9332. Epub 2018 Sep 17.

Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215;

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http://dx.doi.org/10.1073/pnas.1805782115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6176620PMC
October 2018

Nutrient Deprivation Elicits a Transcriptional and Translational Inflammatory Response Coupled to Decreased Protein Synthesis.

Cell Rep 2018 08;24(6):1415-1424

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

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http://dx.doi.org/10.1016/j.celrep.2018.07.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6419098PMC
August 2018

Genome-scale identification of transcription factors that mediate an inflammatory network during breast cellular transformation.

Nat Commun 2018 05 25;9(1):2068. Epub 2018 May 25.

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

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http://www.nature.com/articles/s41467-018-04406-2
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http://dx.doi.org/10.1038/s41467-018-04406-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5970197PMC
May 2018

The Ground State and Evolution of Promoter Region Directionality.

Cell 2017 Aug 10;170(5):889-898.e10. Epub 2017 Aug 10.

Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2017.07.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5576552PMC
August 2017

Evidence that Mediator is essential for Pol II transcription, but is not a required component of the preinitiation complex in vivo.

Elife 2017 07 12;6. Epub 2017 Jul 12.

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

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http://dx.doi.org/10.7554/eLife.28447DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5529107PMC
July 2017

Mediator Undergoes a Compositional Change during Transcriptional Activation.

Mol Cell 2016 11 20;64(3):443-454. Epub 2016 Oct 20.

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

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http://dx.doi.org/10.1016/j.molcel.2016.09.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5096951PMC
November 2016

Selectivity of ORC binding sites and the relation to replication timing, fragile sites, and deletions in cancers.

Proc Natl Acad Sci U S A 2016 08 19;113(33):E4810-9. Epub 2016 Jul 19.

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

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http://dx.doi.org/10.1073/pnas.1609060113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4995967PMC
August 2016

Transcriptome-scale RNase-footprinting of RNA-protein complexes.

Nat Biotechnol 2016 Apr 22;34(4):410-3. Epub 2016 Feb 22.

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

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http://www.nature.com/articles/nbt.3441
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http://dx.doi.org/10.1038/nbt.3441DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4824641PMC
April 2016

Many lncRNAs, 5'UTRs, and pseudogenes are translated and some are likely to express functional proteins.

Elife 2015 Dec 19;4:e08890. Epub 2015 Dec 19.

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

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http://dx.doi.org/10.7554/eLife.08890DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4739776PMC
December 2015

Alternative to the soft-agar assay that permits high-throughput drug and genetic screens for cellular transformation.

Proc Natl Acad Sci U S A 2015 May 20;112(18):5708-13. Epub 2015 Apr 20.

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

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http://dx.doi.org/10.1073/pnas.1505979112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4426412PMC
May 2015

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.

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

STAT3 acts through pre-existing nucleosome-depleted regions bound by FOS during an epigenetic switch linking inflammation to cancer.

Epigenetics Chromatin 2015 14;8. Epub 2015 Feb 14.

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

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http://dx.doi.org/10.1186/1756-8935-8-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4362815PMC
March 2015

TFIIH phosphorylation of the Pol II CTD stimulates mediator dissociation from the preinitiation complex and promoter escape.

Mol Cell 2014 May 17;54(4):601-12. Epub 2014 Apr 17.

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

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http://dx.doi.org/10.1016/j.molcel.2014.03.024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4035452PMC
May 2014

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.

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

Is DNA methylation of tumour suppressor genes epigenetic?

Authors:
Kevin Struhl

Elife 2014 Mar 12;3:e02475. Epub 2014 Mar 12.

Kevin Struhl is an eLife reviewing editor, and is in the Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3949415PMC
http://dx.doi.org/10.7554/eLife.02475DOI Listing
March 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:

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

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.

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

Determinants of nucleosome positioning.

Nat Struct Mol Biol 2013 Mar;20(3):267-73

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

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http://dx.doi.org/10.1038/nsmb.2506DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3740156PMC
March 2013

Metformin inhibits the inflammatory response associated with cellular transformation and cancer stem cell growth.

Proc Natl Acad Sci U S A 2013 Jan 31;110(3):972-7. Epub 2012 Dec 31.

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

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http://dx.doi.org/10.1073/pnas.1221055110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3549132PMC
January 2013

A functional evolutionary approach to identify determinants of nucleosome positioning: a unifying model for establishing the genome-wide pattern.

Mol Cell 2012 Oct 9;48(1):5-15. Epub 2012 Aug 9.

Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School,Worcester, MA 01605, USA.

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http://dx.doi.org/10.1016/j.molcel.2012.07.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3472102PMC
October 2012

An integrated transcriptional regulatory circuit that reinforces the breast cancer stem cell state.

Proc Natl Acad Sci U S A 2012 Sep 20;109(36):14470-5. Epub 2012 Aug 20.

Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, MA 02215, USA.

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http://dx.doi.org/10.1073/pnas.1212811109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3437881PMC
September 2012

The Cyc8-Tup1 complex inhibits transcription primarily by masking the activation domain of the recruiting protein.

Genes Dev 2011 Dec;25(23):2525-39

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

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http://genesdev.cshlp.org/cgi/doi/10.1101/gad.179275.111
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http://dx.doi.org/10.1101/gad.179275.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3243062PMC
December 2011

SAGA and ATAC histone acetyl transferase complexes regulate distinct sets of genes and ATAC defines a class of p300-independent enhancers.

Mol Cell 2011 Nov;44(3):410-423

Program of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique UMR 7104, Institut National de la Santé et de la Recherche Médicale U964, Université de Strasbourg, BP 10142, 67404 Illkirch Cedex, CU de Strasbourg, France.

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http://linkinghub.elsevier.com/retrieve/pii/S109727651100789
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http://dx.doi.org/10.1016/j.molcel.2011.08.037DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4641564PMC
November 2011

JNK1 phosphorylation of Cdt1 inhibits recruitment of HBO1 histone acetylase and blocks replication licensing in response to stress.

Mol Cell 2011 Oct;44(1):62-71

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

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http://linkinghub.elsevier.com/retrieve/pii/S109727651100497
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http://dx.doi.org/10.1016/j.molcel.2011.06.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3190045PMC
October 2011

Extensive divergence of yeast stress responses through transitions between induced and constitutive activation.

Proc Natl Acad Sci U S A 2011 Oct 19;108(40):16693-8. Epub 2011 Sep 19.

Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.

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http://www.pnas.org/cgi/doi/10.1073/pnas.1113718108
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http://dx.doi.org/10.1073/pnas.1113718108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3189053PMC
October 2011

Inhibition of miR-193a expression by Max and RXRα activates K-Ras and PLAU to mediate distinct aspects of cellular transformation.

Cancer Res 2011 Aug 13;71(15):5144-53. Epub 2011 Jun 13.

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

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http://cancerres.aacrjournals.org/cgi/doi/10.1158/0008-5472.
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http://dx.doi.org/10.1158/0008-5472.CAN-11-0425DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3148313PMC
August 2011

Metformin decreases the dose of chemotherapy for prolonging tumor remission in mouse xenografts involving multiple cancer cell types.

Cancer Res 2011 May 17;71(9):3196-201. Epub 2011 Mar 17.

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

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http://cancerres.aacrjournals.org/cgi/doi/10.1158/0008-5472.
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http://dx.doi.org/10.1158/0008-5472.CAN-10-3471DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3085572PMC
May 2011

Splitting of H3-H4 tetramers at transcriptionally active genes undergoing dynamic histone exchange.

Proc Natl Acad Sci U S A 2011 Jan 10;108(4):1296-301. Epub 2011 Jan 10.

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

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http://dx.doi.org/10.1073/pnas.1018308108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3029712PMC
January 2011

Inducible formation of breast cancer stem cells and their dynamic equilibrium with non-stem cancer cells via IL6 secretion.

Proc Natl Acad Sci U S A 2011 Jan 10;108(4):1397-402. Epub 2011 Jan 10.

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

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http://dx.doi.org/10.1073/pnas.1018898108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3029760PMC
January 2011

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.

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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.

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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.

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

STAT3 activation of miR-21 and miR-181b-1 via PTEN and CYLD are part of the epigenetic switch linking inflammation to cancer.

Mol Cell 2010 Aug;39(4):493-506

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

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http://dx.doi.org/10.1016/j.molcel.2010.07.023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2929389PMC
August 2010

Genome-wide mapping indicates that p73 and p63 co-occupy target sites and have similar dna-binding profiles in vivo.

PLoS One 2010 Jul 14;5(7):e11572. Epub 2010 Jul 14.

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

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0011572PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2904373PMC
July 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.

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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.

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

HBO1 histone acetylase activity is essential for DNA replication licensing and inhibited by Geminin.

Mol Cell 2010 Jan;37(1):57-66

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

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http://dx.doi.org/10.1016/j.molcel.2009.12.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2818871PMC
January 2010

An epigenetic switch involving NF-kappaB, Lin28, Let-7 MicroRNA, and IL6 links inflammation to cell transformation.

Cell 2009 Nov 29;139(4):693-706. Epub 2009 Oct 29.

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

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https://linkinghub.elsevier.com/retrieve/pii/S00928674090130
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http://dx.doi.org/10.1016/j.cell.2009.10.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2783826PMC
November 2009

Metformin selectively targets cancer stem cells, and acts together with chemotherapy to block tumor growth and prolong remission.

Cancer Res 2009 Oct 14;69(19):7507-11. Epub 2009 Sep 14.

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Molecular Oncology Research Institute, Tufts Medical Center, Boston, MA 02115, USA.

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http://cancerres.aacrjournals.org/cgi/doi/10.1158/0008-5472.
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http://dx.doi.org/10.1158/0008-5472.CAN-09-2994DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2756324PMC
October 2009

MicroRNAs differentially regulated by Akt isoforms control EMT and stem cell renewal in cancer cells.

Sci Signal 2009 Oct 13;2(92):ra62. Epub 2009 Oct 13.

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

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http://dx.doi.org/10.1126/scisignal.2000356DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2862216PMC
October 2009

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.

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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.

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

Where does mediator bind in vivo?

PLoS One 2009 3;4(4):e5029. Epub 2009 Apr 3.

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

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0005029PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2661142PMC
May 2009

Extensive chromatin fragmentation improves enrichment of protein binding sites in chromatin immunoprecipitation experiments.

Nucleic Acids Res 2008 Nov 2;36(19):e125. Epub 2008 Sep 2.

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

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkn535DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2577354PMC
November 2008

HBO1 histone acetylase is a coactivator of the replication licensing factor Cdt1.

Genes Dev 2008 Oct;22(19):2633-8

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

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http://genesdev.cshlp.org/cgi/doi/10.1101/gad.1674108
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http://dx.doi.org/10.1101/gad.1674108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2559906PMC
October 2008

The hisB463 mutation and expression of a eukaryotic protein in Escherichia coli.

Authors:
Kevin Struhl

Genetics 2008 Oct;180(2):709-14

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

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http://dx.doi.org/10.1534/genetics.104.96693DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2567374PMC
October 2008

The transition from transcriptional initiation to elongation.

Curr Opin Genet Dev 2008 Apr 20;18(2):130-6. Epub 2008 Feb 20.

Wadsworth Center, New York State Department of Health, Albany, NY 12208, United States.

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http://dx.doi.org/10.1016/j.gde.2007.12.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2563432PMC
April 2008

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.

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

Kevin Struhl. Interview.

Authors:
Kevin Struhl

Curr Biol 2008 Jan;18(1):R7-9

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http://dx.doi.org/10.1016/j.cub.2007.10.060DOI Listing
January 2008

[Histone H4 lysine 16 acetylation: from genome regulation to tumoral progression].

Med Sci (Paris) 2007 Aug-Sep;23(8-9):735-40

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

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http://dx.doi.org/10.1051/medsci/20072389735DOI Listing
November 2007

The Swi/Snf complex is important for histone eviction during transcriptional activation and RNA polymerase II elongation in vivo.

Mol Cell Biol 2007 Oct 20;27(20):6987-95. Epub 2007 Aug 20.

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

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http://mcb.asm.org/cgi/doi/10.1128/MCB.00717-07
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http://dx.doi.org/10.1128/MCB.00717-07DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168902PMC
October 2007

Differential analysis for high density tiling microarray data.

BMC Bioinformatics 2007 Sep 24;8:359. Epub 2007 Sep 24.

Affymetrix Inc,, Santa Clara, CA 95051, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2231405PMC
September 2007

Nucleosome positioning signals in genomic DNA.

Genome Res 2007 Aug 9;17(8):1170-7. Epub 2007 Jul 9.

Bioinformatics Program, Boston University, Boston, MA 02215, USA.

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http://www.genome.org/cgi/doi/10.1101/gr.6101007
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933512PMC
August 2007

Genomic analysis of protein-DNA interactions in bacteria: insights into transcription and chromosome organization.

Mol Microbiol 2007 Jul;65(1):21-6

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

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http://doi.wiley.com/10.1111/j.1365-2958.2007.05781.x
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July 2007

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

Transcriptional noise and the fidelity of initiation by RNA polymerase II.

Authors:
Kevin Struhl

Nat Struct Mol Biol 2007 Feb;14(2):103-5

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

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February 2007

The transition between transcriptional initiation and elongation in E. coli is highly variable and often rate limiting.

Mol Cell 2006 Dec;24(5):747-757

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

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http://dx.doi.org/10.1016/j.molcel.2006.10.030DOI Listing
December 2006

Genome-wide location analysis of the stress-activated MAP kinase Hog1 in yeast.

Methods 2006 Nov;40(3):272-8

Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universidad Politécnica de Valencia, 46022 Valencia, Spain.

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http://dx.doi.org/10.1016/j.ymeth.2006.06.007DOI Listing
November 2006

Relationships between p63 binding, DNA sequence, transcription activity, and biological function in human cells.

Mol Cell 2006 Nov;24(4):593-602

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

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http://dx.doi.org/10.1016/j.molcel.2006.10.018DOI Listing
November 2006

Extensive functional overlap between sigma factors in Escherichia coli.

Nat Struct Mol Biol 2006 Sep 6;13(9):806-14. Epub 2006 Aug 6.

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

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http://dx.doi.org/10.1038/nsmb1130DOI Listing
September 2006

Differential gene regulation by selective association of transcriptional coactivators and bZIP DNA-binding domains.

Mol Cell Biol 2006 Aug;26(16):5969-82

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

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http://mcb.asm.org/cgi/doi/10.1128/MCB.00696-06
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1592802PMC
August 2006

The stress-activated Hog1 kinase is a selective transcriptional elongation factor for genes responding to osmotic stress.

Mol Cell 2006 Jul;23(2):241-50

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

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July 2006

Chipper: discovering transcription-factor targets from chromatin immunoprecipitation microarrays using variance stabilization.

Genome Biol 2005 1;6(11):R96. Epub 2005 Nov 1.

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

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http://genomebiology.biomedcentral.com/articles/10.1186/gb-2
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1297652PMC
June 2006

An HMG protein, Hmo1, associates with promoters of many ribosomal protein genes and throughout the rRNA gene locus in Saccharomyces cerevisiae.

Mol Cell Biol 2006 May;26(9):3672-9

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

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http://dx.doi.org/10.1128/MCB.26.9.3672-3679.2006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1447432PMC
May 2006

Asf1 mediates histone eviction and deposition during elongation by RNA polymerase II.

Mol Cell 2006 May;22(3):415-22

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

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May 2006

Activator-specific recruitment of Mediator in vivo.

Nat Struct Mol Biol 2006 Feb 22;13(2):117-20. Epub 2006 Jan 22.

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

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http://dx.doi.org/10.1038/nsmb1049DOI Listing
February 2006

Eaf3 chromodomain interaction with methylated H3-K36 links histone deacetylation to Pol II elongation.

Mol Cell 2005 Dec;20(6):971-8

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

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http://dx.doi.org/10.1016/j.molcel.2005.11.021DOI Listing
December 2005

Genomic analysis of LexA binding reveals the permissive nature of the Escherichia coli genome and identifies unconventional target sites.

Genes Dev 2005 Nov;19(21):2619-30

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

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http://www.genesdev.org/cgi/doi/10.1101/gad.1355605
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1276735PMC
November 2005

Heterochromatin formation involves changes in histone modifications over multiple cell generations.

EMBO J 2005 Jun 26;24(12):2138-49. Epub 2005 May 26.

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

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http://dx.doi.org/10.1038/sj.emboj.7600692DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1150886PMC
June 2005

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.

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June 2005

Analysis of protein co-occupancy by quantitative sequential chromatin immunoprecipitation.

Curr Protoc Mol Biol 2005 May;Chapter 21:Unit 21.8

Harvard Medical School, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1002/0471142727.mb2108s70DOI Listing
May 2005

Transcriptional activation: mediator can act after preinitiation complex formation.

Authors:
Kevin Struhl

Mol Cell 2005 Mar;17(6):752-4

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

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http://dx.doi.org/10.1016/j.molcel.2005.03.002DOI Listing
March 2005

Distinction and relationship between elongation rate and processivity of RNA polymerase II in vivo.

Mol Cell 2005 Mar;17(6):831-40

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

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http://dx.doi.org/10.1016/j.molcel.2005.02.017DOI Listing
March 2005

Evidence for eviction and rapid deposition of histones upon transcriptional elongation by RNA polymerase II.

Mol Cell Biol 2004 Dec;24(23):10111-7

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

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http://mcb.asm.org/cgi/doi/10.1128/MCB.24.23.10111-10117.200
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC529037PMC
December 2004

Association of RNA polymerase with transcribed regions in Escherichia coli.

Proc Natl Acad Sci U S A 2004 Dec 13;101(51):17777-82. Epub 2004 Dec 13.

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

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http://dx.doi.org/10.1073/pnas.0404305101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC539717PMC
December 2004

The transcription factor Ifh1 is a key regulator of yeast ribosomal protein genes.

Nature 2004 Dec;432(7020):1054-8

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

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http://dx.doi.org/10.1038/nature03175DOI Listing
December 2004

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.

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

Chromatin immunoprecipitation for determining the association of proteins with specific genomic sequences in vivo.

Curr Protoc Cell Biol 2004 Sep;Chapter 17:Unit 17.7

University of Southern California, Los Angeles, California, USA.

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September 2004