John T Lis

John T Lis

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Chemical roadblocking of DNA transcription for nascent RNA display.

J Biol Chem 2020 Mar 24. Epub 2020 Mar 24.

Chemical and Biological Engineering, Northwestern University, United States.

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http://dx.doi.org/10.1074/jbc.RA120.012641DOI Listing
March 2020

Nascent RNA analyses: tracking transcription and its regulation.

Nat Rev Genet 2019 12 9;20(12):705-723. Epub 2019 Aug 9.

Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.

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http://dx.doi.org/10.1038/s41576-019-0159-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6858503PMC
December 2019

A 50 year history of technologies that drove discovery in eukaryotic transcription regulation.

Authors:
John T Lis

Nat Struct Mol Biol 2019 09 22;26(9):777-782. Epub 2019 Aug 22.

Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.

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http://dx.doi.org/10.1038/s41594-019-0288-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7106917PMC
September 2019

Chromatin conformation remains stable upon extensive transcriptional changes driven by heat shock.

Proc Natl Acad Sci U S A 2019 09 10;116(39):19431-19439. Epub 2019 Sep 10.

Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853;

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http://dx.doi.org/10.1073/pnas.1901244116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6765289PMC
September 2019

Molecular mechanisms driving transcriptional stress responses.

Nat Rev Genet 2018 06;19(6):385-397

Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.

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http://dx.doi.org/10.1038/s41576-018-0001-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6036639PMC
June 2018

A Cdk9-PP1 switch regulates the elongation-termination transition of RNA polymerase II.

Nature 2018 06 13;558(7710):460-464. Epub 2018 Jun 13.

Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.

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http://dx.doi.org/10.1038/s41586-018-0214-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6021199PMC
June 2018

Dynamic evolution of regulatory element ensembles in primate CD4 T cells.

Nat Ecol Evol 2018 03 29;2(3):537-548. Epub 2018 Jan 29.

Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.

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http://dx.doi.org/10.1038/s41559-017-0447-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5957490PMC
March 2018

Cdk9 regulates a promoter-proximal checkpoint to modulate RNA polymerase II elongation rate in fission yeast.

Nat Commun 2018 02 7;9(1):543. Epub 2018 Feb 7.

Department of Molecular Biology and Genetics, Cornell University, 107 Biotechnology Building, 526 Campus Road, Ithaca, NY, 14853-2703, USA.

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http://dx.doi.org/10.1038/s41467-018-03006-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5803247PMC
February 2018

Enhancer transcription: what, where, when, and why?

Genes Dev 2018 01;32(1):1-3

Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA.

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http://genesdev.cshlp.org/lookup/doi/10.1101/gad.311605.118
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http://dx.doi.org/10.1101/gad.311605.118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5828389PMC
January 2018

Nascent RNA sequencing reveals a dynamic global transcriptional response at genes and enhancers to the natural medicinal compound celastrol.

Genome Res 2017 11 12;27(11):1816-1829. Epub 2017 Oct 12.

Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.

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http://dx.doi.org/10.1101/gr.222935.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5668940PMC
November 2017

CBP Regulates Recruitment and Release of Promoter-Proximal RNA Polymerase II.

Mol Cell 2017 Nov 19;68(3):491-503.e5. Epub 2017 Oct 19.

Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2017.09.031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5826544PMC
November 2017

The 4D nucleome project.

Nature 2017 09;549(7671):219-226

Department of Bioengineering, University of California San Diego, La Jolla, California 92093, USA.

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http://dx.doi.org/10.1038/nature23884DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5617335PMC
September 2017

Transcriptional response to stress is pre-wired by promoter and enhancer architecture.

Nat Commun 2017 08 15;8(1):255. Epub 2017 Aug 15.

Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, 20520, Finland.

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http://www.nature.com/articles/s41467-017-00151-0
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http://dx.doi.org/10.1038/s41467-017-00151-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5557961PMC
August 2017

Use of conditioned media is critical for studies of regulation in response to rapid heat shock.

Cell Stress Chaperones 2017 01 3;22(1):155-162. Epub 2016 Nov 3.

Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14850, USA.

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http://dx.doi.org/10.1007/s12192-016-0737-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5225056PMC
January 2017

Cotranscriptional folding of a riboswitch at nucleotide resolution.

Nat Struct Mol Biol 2016 Dec 31;23(12):1124-1131. Epub 2016 Oct 31.

Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York, USA.

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http://dx.doi.org/10.1038/nsmb.3316DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5497173PMC
December 2016

Transcription factors GAF and HSF act at distinct regulatory steps to modulate stress-induced gene activation.

Genes Dev 2016 08 4;30(15):1731-46. Epub 2016 Aug 4.

Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14835, USA;

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http://dx.doi.org/10.1101/gad.284430.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5002978PMC
August 2016

High-Resolution Mapping of RNA Polymerases Identifies Mechanisms of Sensitivity and Resistance to BET Inhibitors in t(8;21) AML.

Cell Rep 2016 08 4;16(7):2003-16. Epub 2016 Aug 4.

Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2016.07.032DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4996374PMC
August 2016

Highly Multiplexed RNA Aptamer Selection using a Microplate-based Microcolumn Device.

Sci Rep 2016 07 19;6:29771. Epub 2016 Jul 19.

School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA.

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http://dx.doi.org/10.1038/srep29771DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4949599PMC
July 2016

Divergence of a conserved elongation factor and transcription regulation in budding and fission yeast.

Genome Res 2016 06 12;26(6):799-811. Epub 2016 May 12.

Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703, USA;

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http://dx.doi.org/10.1101/gr.204578.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4889974PMC
June 2016

Discovering aptamers by cell-SELEX against human soluble growth factors ectopically expressed on yeast cell surface.

PLoS One 2014 27;9(3):e93052. Epub 2014 Mar 27.

Department of Biomedical Engineering, Cornell University, Ithaca, New York, United States of America; Department of Radiology, Weill Cornell Medical College, New York, New York, United States of America; Department of Biomedical Engineering, Dongguk University, Seoul, South Korea.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0093052PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3968096PMC
December 2015

Human Gene Promoters Are Intrinsically Bidirectional.

Mol Cell 2015 Nov;60(3):346-7

Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology and Genetics, C.F. Møllers Alle 3, Building 1130, 8000 Aarhus, Denmark. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2015.10.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5485825PMC
November 2015

Chromatin Architecture of the Pitx2 Locus Requires CTCF- and Pitx2-Dependent Asymmetry that Mirrors Embryonic Gut Laterality.

Cell Rep 2015 Oct 24;13(2):337-49. Epub 2015 Sep 24.

Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2015.08.075DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4617833PMC
October 2015

Quantitative assessment of RNA-protein interactions with high-throughput sequencing-RNA affinity profiling.

Nat Protoc 2015 Aug 16;10(8):1212-33. Epub 2015 Jul 16.

Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA.

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http://www.nature.com/articles/nprot.2015.074
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http://dx.doi.org/10.1038/nprot.2015.074DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4714542PMC
August 2015

Identification of active transcriptional regulatory elements from GRO-seq data.

Nat Methods 2015 May 23;12(5):433-8. Epub 2015 Mar 23.

Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, USA.

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http://dx.doi.org/10.1038/nmeth.3329DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4507281PMC
May 2015

RAPID-SELEX for RNA aptamers.

PLoS One 2013 20;8(12):e82667. Epub 2013 Dec 20.

School of Applied and Engineering Physics, Cornell University, Ithaca, New York, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0082667PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3869713PMC
March 2015

Getting up to speed with transcription elongation by RNA polymerase II.

Nat Rev Mol Cell Biol 2015 Mar 18;16(3):167-77. Epub 2015 Feb 18.

Department of Molecular Biology and Genetics, Cornell University, 416 Biotechnology Building, 14853, Ithaca, New York, USA.

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http://dx.doi.org/10.1038/nrm3953DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4782187PMC
March 2015

GAGA factor maintains nucleosome-free regions and has a role in RNA polymerase II recruitment to promoters.

PLoS Genet 2015 Mar 27;11(3):e1005108. Epub 2015 Mar 27.

Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1005108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4376892PMC
March 2015

Inhibiting heat shock factor 1 in human cancer cells with a potent RNA aptamer.

PLoS One 2014 6;9(5):e96330. Epub 2014 May 6.

Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America; Department of Biomedical Engineering, Dongguk University, Seoul, South Korea.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0096330PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4011729PMC
January 2015

Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers.

Nat Genet 2014 Dec 10;46(12):1311-20. Epub 2014 Nov 10.

Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA.

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http://dx.doi.org/10.1038/ng.3142DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4254663PMC
December 2014

Targeted H3R26 deimination specifically facilitates estrogen receptor binding by modifying nucleosome structure.

PLoS Genet 2014 Sep 11;10(9):e1004613. Epub 2014 Sep 11.

Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1004613DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4161307PMC
September 2014

New Technologies Provide Quantum Changes in the Scale, Speed, and Success of SELEX Methods and Aptamer Characterization.

Mol Ther Nucleic Acids 2014 Aug 5;3:e183. Epub 2014 Aug 5.

Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA.

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https://linkinghub.elsevier.com/retrieve/pii/S21622531163032
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http://dx.doi.org/10.1038/mtna.2014.34DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4221594PMC
August 2014

Comprehensive analysis of RNA-protein interactions by high-throughput sequencing-RNA affinity profiling.

Nat Methods 2014 Jun 8;11(6):683-8. Epub 2014 May 8.

Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA.

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http://www.nature.com/articles/nmeth.2970
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http://dx.doi.org/10.1038/nmeth.2970DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073888PMC
June 2014

Control of transcriptional elongation.

Annu Rev Genet 2013 11;47:483-508. Epub 2013 Sep 11.

Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703; email: ,

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http://dx.doi.org/10.1146/annurev-genet-110711-155440DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3974797PMC
April 2014

High-throughput binding characterization of RNA aptamer selections using a microplate-based multiplex microcolumn device.

Anal Bioanal Chem 2014 Apr 20;406(11):2727-32. Epub 2014 Feb 20.

School of Applied and Engineering Physics, Cornell University, Ithaca, NY, 14853, USA.

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http://dx.doi.org/10.1007/s00216-014-7661-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3975076PMC
April 2014

Imaging RNA Polymerase II transcription sites in living cells.

Curr Opin Genet Dev 2014 Apr 8;25:126-30. Epub 2014 May 8.

Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA. Electronic address:

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http://dx.doi.org/10.1016/j.gde.2014.01.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5497218PMC
April 2014

Genome-wide dynamics of Pol II elongation and its interplay with promoter proximal pausing, chromatin, and exons.

Elife 2014 Apr 29;3:e02407. Epub 2014 Apr 29.

Department of Molecular Biology and Genetics, Cornell University, Ithaca, United States

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4001325PMC
http://dx.doi.org/10.7554/eLife.02407DOI Listing
April 2014

RNA-DNA differences are generated in human cells within seconds after RNA exits polymerase II.

Cell Rep 2014 Mar 20;6(5):906-15. Epub 2014 Feb 20.

Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Departments of Pediatrics and Genetics, University of Michigan, Ann Arbor, MI 48109, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2014.01.037DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4918108PMC
March 2014

Pol II docking and pausing at growth and stress genes in C. elegans.

Cell Rep 2014 Feb 30;6(3):455-66. Epub 2014 Jan 30.

Department of Biology, Duke Center for Systems Biology, Duke University, Durham, NC 27708, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2014.01.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4026043PMC
February 2014

Defining NELF-E RNA binding in HIV-1 and promoter-proximal pause regions.

PLoS Genet 2014 Jan 16;10(1):e1004090. Epub 2014 Jan 16.

Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America.

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http://dx.plos.org/10.1371/journal.pgen.1004090
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http://dx.doi.org/10.1371/journal.pgen.1004090DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3894171PMC
January 2014

A universal DNA-based protein detection system.

J Am Chem Soc 2013 Sep 11;135(38):14008-11. Epub 2013 Sep 11.

Department of Biological & Environmental Engineering, ∥Department of Molecular Biology and Genetics, and ⊥Kavli Institute at Cornell for Nanoscale Science, Cornell University , Ithaca, New York 14853, United States.

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http://dx.doi.org/10.1021/ja405872gDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4237005PMC
September 2013

Density-dependent cooperative non-specific binding in solid-phase SELEX affinity selection.

Nucleic Acids Res 2013 Aug 3;41(14):7167-75. Epub 2013 Jun 3.

Department of Molecular Biology and Genetics, Cornell University, Biotechnology Building, Ithaca, NY 14853,USA.

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https://academic.oup.com/nar/article/41/14/7167/1750061
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http://dx.doi.org/10.1093/nar/gkt477DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3737557PMC
August 2013

A new player in Pol II pausing.

EMBO J 2013 Jul 7;32(13):1796-8. Epub 2013 Jun 7.

Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, NY, USA.

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http://dx.doi.org/10.1038/emboj.2013.138DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3981171PMC
July 2013

A systematic study of the features critical for designing a high avidity multivalent aptamer.

Nucleic Acid Ther 2013 Jun 3;23(3):238-42. Epub 2013 Apr 3.

Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA.

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http://dx.doi.org/10.1089/nat.2012.0410DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3660072PMC
June 2013

Condensin controls recruitment of RNA polymerase II to achieve nematode X-chromosome dosage compensation.

Elife 2013 Jun 18;2:e00808. Epub 2013 Jun 18.

Department of Molecular and Cell Biology , Howard Hughes Medical Institute, University of California, Berkeley , Berkeley , United States.

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http://dx.doi.org/10.7554/eLife.00808DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3687364PMC
June 2013

Extensive polymerase pausing during Drosophila axis patterning enables high-level and pliable transcription.

Genes Dev 2013 May;27(10):1146-58

Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom.

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http://dx.doi.org/10.1101/gad.215459.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3672648PMC
May 2013

Mechanisms by which transcription factors gain access to target sequence elements in chromatin.

Curr Opin Genet Dev 2013 Apr 19;23(2):116-23. Epub 2012 Dec 19.

Department of Molecular Biology and Genetics, Cornell University, United States.

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http://dx.doi.org/10.1016/j.gde.2012.11.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3651763PMC
April 2013

Development of temperature-sensitive mutants of the Drosophila melanogaster P-TEFb (Cyclin T/CDK9) heterodimer using yeast two-hybrid screening.

Biochem Biophys Res Commun 2013 Apr 7;433(2):243-8. Epub 2013 Mar 7.

Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.

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http://dx.doi.org/10.1016/j.bbrc.2013.02.091DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4014677PMC
April 2013

Multiplexed microcolumn-based process for efficient selection of RNA aptamers.

Anal Chem 2013 Mar 27;85(6):3417-24. Epub 2013 Feb 27.

School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, United States.

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http://pubs.acs.org/doi/10.1021/ac400105e
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http://dx.doi.org/10.1021/ac400105eDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3753675PMC
March 2013

Genome-wide control of RNA polymerase II activity by cohesin.

PLoS Genet 2013 Mar 21;9(3):e1003382. Epub 2013 Mar 21.

Edward A Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1003382DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3605059PMC
March 2013

Precise maps of RNA polymerase reveal how promoters direct initiation and pausing.

Science 2013 Feb;339(6122):950-3

Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.

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http://dx.doi.org/10.1126/science.1229386DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3974810PMC
February 2013

Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans.

Nat Rev Genet 2012 Oct;13(10):720-31

Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA.

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http://www.nature.com/articles/nrg3293
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http://dx.doi.org/10.1038/nrg3293DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3552498PMC
October 2012

Defining the status of RNA polymerase at promoters.

Cell Rep 2012 Oct 10;2(4):1025-35. Epub 2012 Oct 10.

Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.

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http://dx.doi.org/10.1016/j.celrep.2012.08.034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3483431PMC
October 2012

Accurate prediction of inducible transcription factor binding intensities in vivo.

PLoS Genet 2012 29;8(3):e1002610. Epub 2012 Mar 29.

Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1002610DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3315474PMC
September 2012

The Drosophila 7SK snRNP and the essential role of dHEXIM in development.

Nucleic Acids Res 2012 Jul 29;40(12):5283-97. Epub 2012 Feb 29.

Université Paris-Sud 11, UMR-S757, Bât. 443, Orsay, F-91405, INSERM, Orsay, F-91405, France.

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http://dx.doi.org/10.1093/nar/gks191DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3384314PMC
July 2012

Overcoming the nucleosome barrier during transcript elongation.

Trends Genet 2012 Jun 31;28(6):285-94. Epub 2012 Mar 31.

Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.

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http://dx.doi.org/10.1016/j.tig.2012.02.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3466053PMC
June 2012

RNA aptamers that functionally interact with green fluorescent protein and its derivatives.

Nucleic Acids Res 2012 Mar 20;40(5):e39. Epub 2011 Dec 20.

Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA.

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http://dx.doi.org/10.1093/nar/gkr1264DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3300005PMC
March 2012

Activator-induced spread of poly(ADP-ribose) polymerase promotes nucleosome loss at Hsp70.

Mol Cell 2012 Jan 15;45(1):64-74. Epub 2011 Dec 15.

Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.

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http://dx.doi.org/10.1016/j.molcel.2011.11.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3473076PMC
January 2012

Profile of John T. Lis. Interviewed by Kristie Nybo.

Authors:
John T Lis

Biotechniques 2012 Jan;52(1):15

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http://dx.doi.org/10.2144/000113795DOI Listing
January 2012

Minichromosome maintenance helicase paralog MCM9 is dispensible for DNA replication but functions in germ-line stem cells and tumor suppression.

Proc Natl Acad Sci U S A 2011 Oct 10;108(43):17702-7. Epub 2011 Oct 10.

Department of Biomedical Sciences and Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.

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http://dx.doi.org/10.1073/pnas.1113524108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3203795PMC
October 2011

An RNA aptamer perturbs heat shock transcription factor activity in Drosophila melanogaster.

Nucleic Acids Res 2011 Aug 16;39(15):6729-40. Epub 2011 May 16.

Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.

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http://dx.doi.org/10.1093/nar/gkr206DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159435PMC
August 2011

Drosophila Set1 is the major histone H3 lysine 4 trimethyltransferase with role in transcription.

EMBO J 2011 Jun 21;30(14):2817-28. Epub 2011 Jun 21.

Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA; Department of Molecular Biology and Biochemistry, Rutgers, State University of New Jersey, Piscataway, NJ, USA.

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http://dx.doi.org/10.1038/emboj.2011.194DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3160253PMC
June 2011

The polycomb group mutant esc leads to augmented levels of paused Pol II in the Drosophila embryo.

Mol Cell 2011 Jun;42(6):837-44

Department of Molecular and Cell Biology, Division of Genetics, Genomics, and Development, University of California, Berkeley, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1016/j.molcel.2011.05.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3130001PMC
June 2011

A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells.

Cell 2011 May 5;145(4):622-34. Epub 2011 May 5.

Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.

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http://dx.doi.org/10.1016/j.cell.2011.03.042DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3099127PMC
May 2011

X chromosome dosage compensation via enhanced transcriptional elongation in Drosophila.

Nature 2011 Mar;471(7336):115-8

Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA.

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http://www.nature.com/articles/nature09757
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http://dx.doi.org/10.1038/nature09757DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3076316PMC
March 2011

Recruitment timing and dynamics of transcription factors at the Hsp70 loci in living cells.

Mol Cell 2010 Dec;40(6):965-75

Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.

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http://dx.doi.org/10.1016/j.molcel.2010.11.022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3021954PMC
December 2010

Chromatin landscape dictates HSF binding to target DNA elements.

PLoS Genet 2010 Sep 9;6(9):e1001114. Epub 2010 Sep 9.

Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1001114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936546PMC
September 2010

Knocking down gene function with an RNA aptamer expressed as part of an intron.

Nucleic Acids Res 2010 Aug 11;38(15):e154. Epub 2010 Jun 11.

Department of Biological Sciences, University at Albany, State University of New York, Albany, NY 12222, USA.

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http://dx.doi.org/10.1093/nar/gkq529DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2926621PMC
August 2010

Tracking rates of transcription and splicing in vivo.

Nat Struct Mol Biol 2009 Nov;16(11):1123-4

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http://dx.doi.org/10.1038/nsmb1109-1123DOI Listing
November 2009

Defining mechanisms that regulate RNA polymerase II transcription in vivo.

Nature 2009 Sep;461(7261):186-92

Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA.

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http://dx.doi.org/10.1038/nature08449DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2833331PMC
September 2009

Divergent transcription: a new feature of active promoters.

Cell Cycle 2009 Aug 19;8(16):2557-64. Epub 2009 Aug 19.

Koch Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.4161/cc.8.16.9305DOI Listing
August 2009

Phosphorylation of the RNA polymerase II C-terminal domain by TFIIH kinase is not essential for transcription of Saccharomyces cerevisiae genome.

Proc Natl Acad Sci U S A 2009 Aug 7;106(34):14276-80. Epub 2009 Aug 7.

Department of Chemistry, Global Research Laboratory for RNAi Medicine, BK21 School of Chemical Materials Science, Sungkyunkwan University, Suwon 440-746, Korea.

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http://dx.doi.org/10.1073/pnas.0903642106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2732804PMC
August 2009

Paused Pol II captures enhancer activity and acts as a potent insulator.

Genes Dev 2009 Jul;23(14):1606-12

Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA.

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http://dx.doi.org/10.1101/gad.1827709DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3959990PMC
July 2009

Selection and elution of aptamers using nanoporous sol-gel arrays with integrated microheaters.

Lab Chip 2009 May 13;9(9):1206-12. Epub 2009 Feb 13.

Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA.

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http://dx.doi.org/10.1039/b814993cDOI Listing
May 2009

Spt6 enhances the elongation rate of RNA polymerase II in vivo.

EMBO J 2009 Apr 12;28(8):1067-77. Epub 2009 Mar 12.

Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.

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http://dx.doi.org/10.1038/emboj.2009.56DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2683705PMC
April 2009

High-resolution dynamic mapping of histone-DNA interactions in a nucleosome.

Nat Struct Mol Biol 2009 Feb 11;16(2):124-9. Epub 2009 Jan 11.

Department of Physics-Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, New York 14853, USA.

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http://dx.doi.org/10.1038/nsmb.1526DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2635915PMC
February 2009

Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters.

Science 2008 Dec 4;322(5909):1845-8. Epub 2008 Dec 4.

Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.

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http://dx.doi.org/10.1126/science.1162228DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2833333PMC
December 2008

Imaging transcription dynamics at endogenous genes in living Drosophila tissues.

Methods 2008 Jul 27;45(3):233-41. Epub 2008 Jun 27.

School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA.

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http://dx.doi.org/10.1016/j.ymeth.2008.06.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2613026PMC
July 2008

Rapid, transcription-independent loss of nucleosomes over a large chromatin domain at Hsp70 loci.

Cell 2008 Jul;134(1):74-84

Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.

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http://dx.doi.org/10.1016/j.cell.2008.05.029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2527511PMC
July 2008

TFIIB aptamers inhibit transcription by perturbing PIC formation at distinct stages.

Nucleic Acids Res 2008 May 10;36(9):3118-27. Epub 2008 Apr 10.

Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.

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http://dx.doi.org/10.1093/nar/gkn163DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2396426PMC
May 2008

Transcription regulation through promoter-proximal pausing of RNA polymerase II.

Science 2008 Mar;319(5871):1791-2

Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.

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http://www.sciencemag.org/cgi/doi/10.1126/science.1150843
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http://dx.doi.org/10.1126/science.1150843DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2833332PMC
March 2008

Comparison of femtosecond laser and continuous wave UV sources for protein-nucleic acid crosslinking.

Photochem Photobiol 2007 Nov-Dec;83(6):1394-404

School of Applied and Engineering Physics, Cornell University, Ithaca, NY, USA.

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http://dx.doi.org/10.1111/j.1751-1097.2007.00179.xDOI Listing
February 2008

P-TEFb is critical for the maturation of RNA polymerase II into productive elongation in vivo.

Mol Cell Biol 2008 Feb 10;28(3):1161-70. Epub 2007 Dec 10.

Department of Molecular Biology and Genetics,1 School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, USA.

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http://dx.doi.org/10.1128/MCB.01859-07DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2223398PMC
February 2008

Intranuclear distribution and local dynamics of RNA polymerase II during transcription activation.

Mol Cell 2007 Dec;28(6):978-90

School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA.

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http://dx.doi.org/10.1016/j.molcel.2007.10.017DOI Listing
December 2007

Imaging Drosophila gene activation and polymerase pausing in vivo.

Authors:
John T Lis

Nature 2007 Nov;450(7167):198-202

Molecular Biology and Genetics, 416 Biotechnology Building, Cornell University, Ithaca, New York 14853, USA.

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http://dx.doi.org/10.1038/nature06324DOI Listing
November 2007