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

Lis JT.

Nat Struct Mol Biol. 2019 Aug 22. doi: 10.1038/s41594-019-0288-9. [Epub ahead of print] Review.


Nascent RNA analyses: tracking transcription and its regulation.

Wissink EM, Vihervaara A, Tippens ND, Lis JT.

Nat Rev Genet. 2019 Aug 9. doi: 10.1038/s41576-019-0159-6. [Epub ahead of print] Review.


Kinetics of Xist-induced gene silencing can be predicted from combinations of epigenetic and genomic features.

Barros de Andrade E Sousa L, Jonkers I, Syx L, Dunkel I, Chaumeil J, Picard C, Foret B, Chen CJ, Lis JT, Heard E, Schulz EG, Marsico A.

Genome Res. 2019 Jul;29(7):1087-1099. doi: 10.1101/gr.245027.118. Epub 2019 Jun 7.


An AR-ERG transcriptional signature defined by long-range chromatin interactomes in prostate cancer cells.

Zhang Z, Chng KR, Lingadahalli S, Chen Z, Liu MH, Do HH, Cai S, Rinaldi N, Poh HM, Li G, Sung YY, Heng CL, Core LJ, Tan SK, Ruan X, Lis JT, Kellis M, Ruan Y, Sung WK, Cheung E.

Genome Res. 2019 Feb;29(2):223-235. doi: 10.1101/gr.230243.117. Epub 2019 Jan 3.


Single-molecule nascent RNA sequencing identifies regulatory domain architecture at promoters and enhancers.

Tome JM, Tippens ND, Lis JT.

Nat Genet. 2018 Nov;50(11):1533-1541. doi: 10.1038/s41588-018-0234-5. Epub 2018 Oct 22.


Chromatin run-on and sequencing maps the transcriptional regulatory landscape of glioblastoma multiforme.

Chu T, Rice EJ, Booth GT, Salamanca HH, Wang Z, Core LJ, Longo SL, Corona RJ, Chin LS, Lis JT, Kwak H, Danko CG.

Nat Genet. 2018 Nov;50(11):1553-1564. doi: 10.1038/s41588-018-0244-3. Epub 2018 Oct 22.


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

Parua PK, Booth GT, Sansó M, Benjamin B, Tanny JC, Lis JT, Fisher RP.

Nature. 2018 Jun;558(7710):460-464. doi: 10.1038/s41586-018-0214-z. Epub 2018 Jun 13.


Molecular mechanisms driving transcriptional stress responses.

Vihervaara A, Duarte FM, Lis JT.

Nat Rev Genet. 2018 Jun;19(6):385-397. doi: 10.1038/s41576-018-0001-6. Review.


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

Tippens ND, Vihervaara A, Lis JT.

Genes Dev. 2018 Jan 1;32(1):1-3. doi: 10.1101/gad.311605.118. Review.


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

Booth GT, Parua PK, Sansó M, Fisher RP, Lis JT.

Nat Commun. 2018 Feb 7;9(1):543. doi: 10.1038/s41467-018-03006-4.


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

Danko CG, Choate LA, Marks BA, Rice EJ, Wang Z, Chu T, Martins AL, Dukler N, Coonrod SA, Tait Wojno ED, Lis JT, Kraus WL, Siepel A.

Nat Ecol Evol. 2018 Mar;2(3):537-548. doi: 10.1038/s41559-017-0447-5. Epub 2018 Jan 29.


Corrigendum: The 4D nucleome project.

Dekker J, Belmont AS, Guttman M, Leshyk VO, Lis JT, Lomvardas S, Mirny LA, O'Shea CC, Park PJ, Ren B, Politz JCR, Shendure J, Zhong S; 4D Nucleome Network.

Nature. 2017 Dec 14;552(7684):278. doi: 10.1038/nature24667. Epub 2017 Nov 22.


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

Boija A, Mahat DB, Zare A, Holmqvist PH, Philip P, Meyers DJ, Cole PA, Lis JT, Stenberg P, Mannervik M.

Mol Cell. 2017 Nov 2;68(3):491-503.e5. doi: 10.1016/j.molcel.2017.09.031. Epub 2017 Oct 19.


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

Dukler N, Booth GT, Huang YF, Tippens N, Waters CT, Danko CG, Lis JT, Siepel A.

Genome Res. 2017 Nov;27(11):1816-1829. doi: 10.1101/gr.222935.117. Epub 2017 Oct 12.


The 4D nucleome project.

Dekker J, Belmont AS, Guttman M, Leshyk VO, Lis JT, Lomvardas S, Mirny LA, O'Shea CC, Park PJ, Ren B, Politz JCR, Shendure J, Zhong S; 4D Nucleome Network.

Nature. 2017 Sep 13;549(7671):219-226. doi: 10.1038/nature23884. Erratum in: Nature. 2017 Nov 22;:.


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

Vihervaara A, Mahat DB, Guertin MJ, Chu T, Danko CG, Lis JT, Sistonen L.

Nat Commun. 2017 Aug 15;8(1):255. doi: 10.1038/s41467-017-00151-0.


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

Mahat DB, Lis JT.

Cell Stress Chaperones. 2017 Jan;22(1):155-162. doi: 10.1007/s12192-016-0737-x. Epub 2016 Nov 3.


Cotranscriptional folding of a riboswitch at nucleotide resolution.

Watters KE, Strobel EJ, Yu AM, Lis JT, Lucks JB.

Nat Struct Mol Biol. 2016 Dec;23(12):1124-1131. doi: 10.1038/nsmb.3316. Epub 2016 Oct 31.


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

Zhao Y, Liu Q, Acharya P, Stengel KR, Sheng Q, Zhou X, Kwak H, Fischer MA, Bradner JE, Strickland SA, Mohan SR, Savona MR, Venters BJ, Zhou MM, Lis JT, Hiebert SW.

Cell Rep. 2016 Aug 16;16(7):2003-16. doi: 10.1016/j.celrep.2016.07.032. Epub 2016 Aug 4.


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

Duarte FM, Fuda NJ, Mahat DB, Core LJ, Guertin MJ, Lis JT.

Genes Dev. 2016 Aug 1;30(15):1731-46. doi: 10.1101/gad.284430.116. Epub 2016 Aug 4.


Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq).

Mahat DB, Kwak H, Booth GT, Jonkers IH, Danko CG, Patel RK, Waters CT, Munson K, Core LJ, Lis JT.

Nat Protoc. 2016 Aug;11(8):1455-76. doi: 10.1038/nprot.2016.086. Epub 2016 Jul 21.


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

Reinholt SJ, Ozer A, Lis JT, Craighead HG.

Sci Rep. 2016 Jul 19;6:29771. doi: 10.1038/srep29771.


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

Booth GT, Wang IX, Cheung VG, Lis JT.

Genome Res. 2016 Jul;26(7):1010-1. doi: 10.1101/gr.210161.116. No abstract available.


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

Booth GT, Wang IX, Cheung VG, Lis JT.

Genome Res. 2016 Jun;26(6):799-811. doi: 10.1101/gr.204578.116. Epub 2016 May 12. Erratum in: Genome Res. 2016 Jul;26(7):1010-1.


Mammalian Heat Shock Response and Mechanisms Underlying Its Genome-wide Transcriptional Regulation.

Mahat DB, Salamanca HH, Duarte FM, Danko CG, Lis JT.

Mol Cell. 2016 Apr 7;62(1):63-78. doi: 10.1016/j.molcel.2016.02.025. Epub 2016 Mar 24.


Human Gene Promoters Are Intrinsically Bidirectional.

Andersson R, Chen Y, Core L, Lis JT, Sandelin A, Jensen TH.

Mol Cell. 2015 Nov 5;60(3):346-7. doi: 10.1016/j.molcel.2015.10.015. No abstract available.


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

Welsh IC, Kwak H, Chen FL, Werner M, Shopland LS, Danko CG, Lis JT, Zhang M, Martin JF, Kurpios NA.

Cell Rep. 2015 Oct 13;13(2):337-49. doi: 10.1016/j.celrep.2015.08.075. Epub 2015 Sep 24.


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

Ozer A, Tome JM, Friedman RC, Gheba D, Schroth GP, Lis JT.

Nat Protoc. 2015 Aug;10(8):1212-33. doi: 10.1038/nprot.2015.074. Epub 2015 Jul 16.


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

Fuda NJ, Guertin MJ, Sharma S, Danko CG, Martins AL, Siepel A, Lis JT.

PLoS Genet. 2015 Mar 27;11(3):e1005108. doi: 10.1371/journal.pgen.1005108. eCollection 2015 Mar.


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

Danko CG, Hyland SL, Core LJ, Martins AL, Waters CT, Lee HW, Cheung VG, Kraus WL, Lis JT, Siepel A.

Nat Methods. 2015 May;12(5):433-8. doi: 10.1038/nmeth.3329. Epub 2015 Mar 23.


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

Jonkers I, Lis JT.

Nat Rev Mol Cell Biol. 2015 Mar;16(3):167-77. doi: 10.1038/nrm3953. Epub 2015 Feb 18. Review.


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

Core LJ, Martins AL, Danko CG, Waters CT, Siepel A, Lis JT.

Nat Genet. 2014 Dec;46(12):1311-20. doi: 10.1038/ng.3142. Epub 2014 Nov 10.


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

Guertin MJ, Zhang X, Anguish L, Kim S, Varticovski L, Lis JT, Hager GL, Coonrod SA.

PLoS Genet. 2014 Sep 11;10(9):e1004613. doi: 10.1371/journal.pgen.1004613. eCollection 2014 Sep.


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

Ozer A, Pagano JM, Lis JT.

Mol Ther Nucleic Acids. 2014 Aug 5;3:e183. doi: 10.1038/mtna.2014.34.


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

Tome JM, Ozer A, Pagano JM, Gheba D, Schroth GP, Lis JT.

Nat Methods. 2014 Jun;11(6):683-8. doi: 10.1038/nmeth.2970. Epub 2014 May 8.


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

Salamanca HH, Antonyak MA, Cerione RA, Shi H, Lis JT.

PLoS One. 2014 May 6;9(5):e96330. doi: 10.1371/journal.pone.0096330. eCollection 2014.


Imaging RNA Polymerase II transcription sites in living cells.

Buckley MS, Lis JT.

Curr Opin Genet Dev. 2014 Apr;25:126-30. doi: 10.1016/j.gde.2014.01.002. Epub 2014 May 8. Review.


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

Meng HW, Pagano JM, White BS, Toyoda Y, Min IM, Craighead HG, Shalloway D, Lis JT, Xiao K, Jin MM.

PLoS One. 2014 Mar 27;9(3):e93052. doi: 10.1371/journal.pone.0093052. eCollection 2014.


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

Wang IX, Core LJ, Kwak H, Brady L, Bruzel A, McDaniel L, Richards AL, Wu M, Grunseich C, Lis JT, Cheung VG.

Cell Rep. 2014 Mar 13;6(5):906-15. doi: 10.1016/j.celrep.2014.01.037. Epub 2014 Feb 20.


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

Szeto K, Reinholt SJ, Duarte FM, Pagano JM, Ozer A, Yao L, Lis JT, Craighead HG.

Anal Bioanal Chem. 2014 Apr;406(11):2727-32. doi: 10.1007/s00216-014-7661-7. Epub 2014 Feb 20.


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

Maxwell CS, Kruesi WS, Core LJ, Kurhanewicz N, Waters CT, Lewarch CL, Antoshechkin I, Lis JT, Meyer BJ, Baugh LR.

Cell Rep. 2014 Feb 13;6(3):455-66. doi: 10.1016/j.celrep.2014.01.008. Epub 2014 Jan 30.


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

Pagano JM, Kwak H, Waters CT, Sprouse RO, White BS, Ozer A, Szeto K, Shalloway D, Craighead HG, Lis JT.

PLoS Genet. 2014 Jan;10(1):e1004090. doi: 10.1371/journal.pgen.1004090. Epub 2014 Jan 16.


Kinetics of promoter Pol II on Hsp70 reveal stable pausing and key insights into its regulation.

Buckley MS, Kwak H, Zipfel WR, Lis JT.

Genes Dev. 2014 Jan 1;28(1):14-9. doi: 10.1101/gad.231886.113.


RAPID-SELEX for RNA aptamers.

Szeto K, Latulippe DR, Ozer A, Pagano JM, White BS, Shalloway D, Lis JT, Craighead HG.

PLoS One. 2013 Dec 20;8(12):e82667. doi: 10.1371/journal.pone.0082667. eCollection 2013.


Coordinated effects of sequence variation on DNA binding, chromatin structure, and transcription.

Kilpinen H, Waszak SM, Gschwind AR, Raghav SK, Witwicki RM, Orioli A, Migliavacca E, Wiederkehr M, Gutierrez-Arcelus M, Panousis NI, Yurovsky A, Lappalainen T, Romano-Palumbo L, Planchon A, Bielser D, Bryois J, Padioleau I, Udin G, Thurnheer S, Hacker D, Core LJ, Lis JT, Hernandez N, Reymond A, Deplancke B, Dermitzakis ET.

Science. 2013 Nov 8;342(6159):744-7. doi: 10.1126/science.1242463. Epub 2013 Oct 17.


Control of transcriptional elongation.

Kwak H, Lis JT.

Annu Rev Genet. 2013;47:483-508. doi: 10.1146/annurev-genet-110711-155440. Epub 2013 Sep 11. Review.


A universal DNA-based protein detection system.

Tran TN, Cui J, Hartman MR, Peng S, Funabashi H, Duan F, Yang D, March JC, Lis JT, Cui H, Luo D.

J Am Chem Soc. 2013 Sep 25;135(38):14008-11. doi: 10.1021/ja405872g. Epub 2013 Sep 11.


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

Kruesi WS, Core LJ, Waters CT, Lis JT, Meyer BJ.

Elife. 2013 Jun 18;2:e00808. doi: 10.7554/eLife.00808.

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