Journal Publications

Dr. Lis’s Google Scholar Page

All of Dr. Lis’ publications listed on PubMed

Selected Reviews:

  • Lis JT. (2019) “A 50 year history of technologies that drove discovery in eukaryotic transcription regulation.” NSMB, 26(9):777-782. (PubMed)
  • Wissink EM*, Vihervaara A*, Tippens ND, Lis JT. (2019) “Nascent RNA analyses: tracking transcription and its regulation.” Nat Rev Genet, Epub ahead of print. (PubMed)
  • Vihervaara A, Duarte FM, Lis JT. (2018) “Molecular mechanisms driving transcriptional stress responses.” Nat Rev Genet, 19(6):385-397. (PubMed)
  • Jonkers I, Lis JT. (2015) “Getting up to speed with transcription elongation by RNA polymerase II.” Nat Rev Mol Cell Biol, 16(3):167-77. (PubMed)
  • Buckley MS, Lis JT. (2014) “Imaging RNA Polymerase II transcription sites in living cells.” Curr Opin Genet Dev, 25:126-30.(PubMed)
  • Adelman K, Lis JT. (2012) “Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans.” Nat Rev Genet, 13(10):720-31. (PubMed)
  • Fuda NJ, Ardehali MB, Lis JT. (2009) “Defining mechanisms that regulate RNA polymerase II transcription in vivo.” Nature, 461(7261):186-92. (PubMed)
  • Lis, J. (1998) “Promoter-Associated Pausing in Promoter Architecture and Post-Initiation Transcriptional Regulation.” Cold Spring Harbor Symposium on Quantitative Biology. Volume LXIII. 347-56. (Article: PDF)

Selected Publications:

  • Ray J, Munn PR, Vihervaara A, Lewis JJ, Ozer A, Danko CG, Lis JT. (2019) “Chromatin conformation remains stable upon extensive transcriptional changes driven by heat shock.” Proc Natl Acad Sci, 116(39):19431-19439. (PubMed)
  • Tome JM, Tippens ND, Lis JT. (2018) “Single-molecule nascent RNA sequencing identifies regulatory domain architecture at promoters and enhancers.” Nat Genet, 50(11):1533-1541. (PubMed)
  • Booth GT, Parua PK, Sansó M, Fisher RP, Lis JT. (2018) “Cdk9 regulates a promoter-proximal checkpoint to modulate RNA polymerase II elongation rate in fission yeast.” Nat Commun, 9(1):543. (PubMed)Duarte FM, Fuda NJ, Mahat DB, Core LJ, Guertin MJ, Lis JT. (2016) “Transcription factors GAF and HSF act at distinct regulatory steps to modulate stress-induced gene activation.” Genes Dev, 30(15):1731-46. (PubMed)
  • Booth GT, Wang IX, Cheung VG, Lis JT. (2016) “Divergence of a conserved elongation factor and transcription regulation in budding and fission yeast.” Genome Res, 26(6):799-811. (PubMed)
  • Mahat DB, Salamanca HH, Duarte FM, Danko CG, Lis JT. (2016) “Mammalian Heat Shock Response and Mechanisms Underlying Its Genome-wide Transcriptional Regulation.” Mol Cell, 62(1):63-78. (PubMed)
  • Danko CG, Hyland SL, Core LJ, Martins AL, Waters CT, Lee HW, Cheung VG, Kraus WL, Lis JT, Siepel A. (2015) “Identification of active transcriptional regulatory elements from GRO-seq data.” Nat Methods, 12(5):433-8. (PubMed)
  • Fuda NJ, Guertin MJ, Sharma S, Danko CG, Martins AL, Siepel A, Lis JT. (2015) “GAGA factor maintains nucleosome-free regions and has a role in RNA polymerase II recruitment to promoters.” PLoS Genet, 11(3):e1005108. (PubMed)
  • Core LJ, Martins AL, Danko CG, Waters CT, Siepel A, Lis JT. (2014) “Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers.” Nat Genet, 46(12):1311-20. (PubMed)
  • Buckley MS, Kwak H, Zipfel WR, Lis JT. (2014) “Kinetics of promoter Pol II on Hsp70 reveal stable pausing and key insights into its regulation.” Genes Dev, 28(1):14-9. (PubMed)
  • Pagano JM, Kwak H, Waters CT, Sprouse RO, White BS, Ozer A, Szeto K, Shalloway D, Craighead HG, Lis JT. (2014) “Defining NELF-E RNA binding in HIV-1 and promoter-proximal pause regions.” PLoS Genet, 10(1):e1004090. (PubMed)
  • Tome JM, Ozer A, Pagano JM, Gheba D, Schroth GP, Lis JT. (2014) “Comprehensive analysis of RNA-protein interactions by high-throughput sequencing-RNA affinity profiling.” Nat Methods, 11(6):683-8. (PubMed)
  • Jonkers I, Kwak H, Lis JT. (2014) “Genome-wide dynamics of Pol II elongation and its interplay with promoter proximal pausing, chromatin, and exons.” Elife, 3:e02407. (PubMed)
  • Danko CG, Hah N, Luo X, Martins AL, Core L, Lis JT, Siepel A, Kraus WL. (2013) “Signaling Pathways Differentially Affect RNA Polymerase II Initiation, Pausing, and Elongation Rate in Cells.” Mol Cell, 50(2):212-22. (PubMed)
  • Kwak H, Fuda NJ, Core LJ, Lis JT. (2013) “Precise maps of RNA polymerase reveal how promoters direct initiation and pausing.” Science, 339(6122):950-3. (PubMed)
  • Core LJ, Waterfall JJ, Gilchrist DA, Fargo DC, Kwak H, Adelman K, Lis JT. (2012) “Defining the status of RNA polymerase at promoters.” Cell Reports, 2(4):1025-35. (PubMed)
  • Petesch SJ, Lis JT. (2012) “Activator-induced spread of poly(ADP-ribose) polymerase promotes nucleosome loss at Hsp70.” Mol Cell, 45(1):64-74. (PubMed)
  • Guertin MJ, Martins AL, Siepel A, Lis JT. (2012) “Accurate prediction of inducible transcription factor binding intensities in vivo.” PLoS Genet, 8(3):e1002610. (PubMed)
  • Min IM, Waterfall JJ, Core LJ, Munroe RJ, Schimenti J, Lis JT. (2011) “Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells.” Genes Dev, 25(7):742-54. (PubMed)
  • Zobeck KL, Buckley MS, Zipfel WR, Lis JT. (2010) “Recruitment timing and dynamics of transcription factors at the Hsp70 loci in living cells.” Mol Cell, 40(6):965-75. (PubMed)
  • Guertin MJ, Lis JT. (2010) “Chromatin landscape dictates HSF binding to target DNA elements.” PLoS Genet, 6(9). pii: e1001114. (PubMed)
  • Ardehali MB, Lis JT. (2009) “Tracking rates of transcription and splicing in vivo.” Nat Struct Mol Biol, 16(11):1123-4. (PubMed)