John Lis

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Fuda Nicholas J; Ardehali M Behfar; Lis John T
Defining mechanisms that regulate RNA polymerase II transcription in vivo.
Core Leighton J; Lis John T
Paused Pol II captures enhancer activity and acts as a potent insulator.
Park Seung-Min; Ahn Ji-Young; Jo Minjoung; Lee Dong-Ki; Lis John T; Craighead Harold G; Kim Soyoun
Selection and elution of aptamers using nanoporous sol-gel arrays with integrated microheaters.

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All Publications

2009: Fuda Nicholas J; Ardehali M Behfar; Lis John T
Defining mechanisms that regulate RNA polymerase II transcription in vivo.
Nature 2009;461(7261):186-92.
2009: Core Leighton J; Lis John T
Paused Pol II captures enhancer activity and acts as a potent insulator.
Genes & development 2009;23(14):1606-12.
2009: Park Seung-Min; Ahn Ji-Young; Jo Minjoung; Lee Dong-Ki; Lis John T; Craighead Harold G; Kim Soyoun
Selection and elution of aptamers using nanoporous sol-gel arrays with integrated microheaters.
Lab on a chip 2009;9(9):1206-12.
2009: Ardehali M Behfar; Yao Jie; Adelman Karen; Fuda Nicholas J; Petesch Steven J; Webb Watt W; Lis John T
Spt6 enhances the elongation rate of RNA polymerase II in vivo.
The EMBO journal 2009;28(8):1067-77.
2008: Petesch Steven J; Lis John T
Rapid, transcription-independent loss of nucleosomes over a large chromatin domain at Hsp70 loci.
Cell 2008;134(1):74-84.
2008: Yao Jie; Zobeck Katie L; Lis John T; Webb Watt W
Imaging transcription dynamics at endogenous genes in living Drosophila tissues.
Methods (San Diego, Calif.) 2008;45(3):233-41.
2008: Sevilimedu Aarti; Shi Hua; Lis John T
TFIIB aptamers inhibit transcription by perturbing PIC formation at distinct stages.
Nucleic acids research 2008;36(9):3118-27.
2008: Core Leighton J; Lis John T
Transcription regulation through promoter-proximal pausing of RNA polymerase II.
Science (New York, N.Y.) 2008;319(5871):1791-2.
2008: Ni Zhuoyu; Saunders Abbie; Fuda Nicholas J; Yao Jie; Suarez Jose-Ramon; Webb Watt W; Lis John T
P-TEFb is critical for the maturation of RNA polymerase II into productive elongation in vivo.
Molecular and cellular biology 2008;28(3):1161-70.
2007: Yao Jie; Ardehali M Behfar; Fecko Christopher J; Webb Watt W; Lis John T
Intranuclear distribution and local dynamics of RNA polymerase II during transcription activation.
Molecular cell 2007;28(6):978-90.
2007: Fecko Christopher J; Munson Katherine M; Saunders Abbie; Sun Guangxing; Begley Tadhg P; Lis John T; Webb Watt W
Comparison of femtosecond laser and continuous wave UV sources for protein-nucleic acid crosslinking.
Photochemistry and photobiology 2007;83(6):1394-404.
2007: Shi Hua; Fan Xiaochun; Sevilimedu Aarti; Lis John T
RNA aptamers directed to discrete functional sites on a single protein structural domain.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(10):3742-6.
2006: Saunders Abbie; Core Leighton J; Lis John T
Breaking barriers to transcription elongation.
Nature reviews. Molecular cell biology 2006;7(8):557-67.
2006: Yao Jie; Munson Katherine M; Webb Watt W; Lis John T
Dynamics of heat shock factor association with native gene loci in living cells.
Nature 2006;442(7106):1050-3.
2006: Lis John T; Kraus W Lee
Promoter cleavage: a topoIIbeta and PARP-1 collaboration.
Cell 2006;125(7):1225-7.
2006: Adelman Karen; Wei Wenxiang; Ardehali M Behfar; Werner Janis; Zhu Bing; Reinberg Danny; Lis John T
Drosophila Paf1 modulates chromatin structure at actively transcribed genes.
Molecular and cellular biology 2006;26(1):250-60.
2006: Zhao Xiaoching; Shi Hua; Sevilimedu Aarti; Liachko Nicole; Nelson Hillary C M; Lis John T
An RNA aptamer that interferes with the DNA binding of the HSF transcription activator.
Nucleic acids research 2006;34(13):3755-61.
2005: Yeh Richard C; Hyun Jerome K; Boehm Amber K; Lis John T; Franck Carl
Improving slide-based assays by stirring: application of liquid-on-liquid mixing to immunofluorescence staining of polytene chromosomes.
Journal of biochemical and biophysical methods 2005;64(1):59-68.
2005: Brower-Toland Brent; Wacker David A; Fulbright Robert M; Lis John T; Kraus W Lee; Wang Michelle D
Specific contributions of histone tails and their acetylation to the mechanical stability of nucleosomes.
Journal of molecular biology 2005;346(1):135-46.
2005: Adelman Karen; Marr Michael T; Werner Janis; Saunders Abbie; Ni Zhuoyu; Andrulis Erik D; Lis John T
Efficient release from promoter-proximal stall sites requires transcript cleavage factor TFIIS.
Molecular cell 2005;17(1):103-12.
2005: Fan Xiaochun; Shi Hua; Lis John T
Distinct transcriptional responses of RNA polymerases I, II and III to aptamers that bind TBP.
Nucleic acids research 2005;33(3):838-45.
2004: Kim Mi Young; Mauro Steven; Gévry Nicolas; Lis John T; Kraus W Lee
NAD+-dependent modulation of chromatin structure and transcription by nucleosome binding properties of PARP-1.
Cell 2004;119(6):803-14.
2004: Adelman Karen; Yuzenkova Julia; La Porta Arthur; Zenkin Nikolay; Lee Jookyung; Lis John T; Borukhov Sergei; Wang Michelle D; Severinov Konstantin
Molecular mechanism of transcription inhibition by peptide antibiotic Microcin J25.
Molecular cell 2004;14(6):753-62.
2004: Fan Xiaochun; Shi Hua; Adelman Karen; Lis John T
Probing TBP interactions in transcription initiation and reinitiation with RNA aptamers that act in distinct modes.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(18):6934-9.
2004: Belotserkovskaya Rimma; Saunders Abbie; Lis John T; Reinberg Danny
Transcription through chromatin: understanding a complex FACT.
Biochimica et biophysica acta 2004;1677(1-3):87-99.
2004: Ni Zhuoyu; Schwartz Brian E; Werner Janis; Suarez Jose-Ramon; Lis John T
Coordination of transcription, RNA processing, and surveillance by P-TEFb kinase on heat shock genes.
Molecular cell 2004;13(1):55-65.
2004: Schwartz Brian E; Werner Janis K; Lis John T
Indirect immunofluorescent labeling of Drosophila polytene chromosomes: visualizing protein interactions with chromatin in vivo.
Methods in enzymology 2004;376():393-404.
2003: Boehm Amber K; Saunders Abbie; Werner Janis; Lis John T
Transcription factor and polymerase recruitment, modification, and movement on dhsp70 in vivo in the minutes following heat shock.
Molecular and cellular biology 2003;23(21):7628-37.
2003: Schwartz Brian E; Larochelle Stephane; Suter Beat; Lis John T
Cdk7 is required for full activation of Drosophila heat shock genes and RNA polymerase II phosphorylation in vivo.
Molecular and cellular biology 2003;23(19):6876-86.
2003: Saunders Abbie; Werner Janis; Andrulis Erik D; Nakayama Takahiro; Hirose Susumu; Reinberg Danny; Lis John T
Tracking FACT and the RNA polymerase II elongation complex through chromatin in vivo.
Science (New York, N.Y.) 2003;301(5636):1094-6.
2003: Kraus W Lee; Lis John T
PARP goes transcription.
Cell 2003;113(6):677-83.
2003: Kim Soyoun; Shi Hua; Lee Dong-Ki; Lis John T
Specific SR protein-dependent splicing substrates identified through genomic SELEX.
Nucleic acids research 2003;31(7):1955-61.
2002: Andrulis Erik D; Werner Janis; Nazarian Arpi; Erdjument-Bromage Hediye; Tempst Paul; Lis John T
The RNA processing exosome is linked to elongating RNA polymerase II in Drosophila.
Nature 2002;420(6917):837-41.
2002: Adelman Karen; La Porta Arthur; Santangelo Thomas J; Lis John T; Roberts Jeffrey W; Wang Michelle D
Single molecule analysis of RNA polymerase elongation reveals uniform kinetic behavior.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(21):13538-43.
2002: Nishioka Kenichi; Rice Judd C; Sarma Kavitha; Erdjument-Bromage Hediye; Werner Janis; Wang Yanming; Chuikov Sergei; Valenzuela Pablo; Tempst Paul; Steward Ruth; Lis John T; Allis C David; Reinberg Danny
PR-Set7 is a nucleosome-specific methyltransferase that modifies lysine 20 of histone H4 and is associated with silent chromatin.
Molecular cell 2002;9(6):1201-13.
2002: Adelman Karen; Lis John T
How does Pol II overcome the nucleosome barrier?
Molecular cell 2002;9(3):451-2.
2002: Brower-Toland Brent D; Smith Corey L; Yeh Richard C; Lis John T; Peterson Craig L; Wang Michelle D
Mechanical disruption of individual nucleosomes reveals a reversible multistage release of DNA.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(4):1960-5.
2000: Andrulis E D; Guzmán E; Döring P; Werner J; Lis J T
High-resolution localization of Drosophila Spt5 and Spt6 at heat shock genes in vivo: roles in promoter proximal pausing and transcription elongation.
Genes & development 2000;14(20):2635-49.
2000: Lis J T; Mason P; Peng J; Price D H; Werner J
P-TEFb kinase recruitment and function at heat shock loci.
Genes & development 2000;14(7):792-803.
2000: Hoffman B E; Lis J T
Pre-mRNA splicing by the essential Drosophila protein B52: tissue and target specificity.
Molecular and cellular biology 2000;20(1):181-6.
1999: Lee D K; Kim S; Lis J T
Different upstream transcriptional activators have distinct coactivator requirements.
Genes & development 1999;13(22):2934-9.
1999: Shi H; Hoffman B E; Lis J T
RNA aptamers as effective protein antagonists in a multicellular organism.
Proceedings of the National Academy of Sciences of the United States of America 1999;96(18):10033-8.
1999: Guzmán E; Lis J T
Transcription factor TFIIH is required for promoter melting in vivo.
Molecular and cellular biology 1999;19(8):5652-8.
1999: Lin J T; Lis J T
Glycogen synthase phosphatase interacts with heat shock factor to activate CUP1 gene transcription in Saccharomyces cerevisiae.
Molecular and cellular biology 1999;19(5):3237-45.
1999: Wilkins R C; Lis J T
DNA distortion and multimerization: novel functions of the glutamine-rich domain of GAGA factor.
Journal of molecular biology 1999;285(2):515-25.
1999: Hirayoshi K; Lis J T
Nuclear run-on assays: assessing transcription by measuring density of engaged RNA polymerases.
Methods in enzymology 1999;304():351-62.
1998: Ulrich H; Ippolito J E; Pagán O R; Eterovic V A; Hann R M; Shi H; Lis J T; Eldefrawi M E; Hess G P
In vitro selection of RNA molecules that displace cocaine from the membrane-bound nicotinic acetylcholine receptor.
Proceedings of the National Academy of Sciences of the United States of America 1998;95(24):14051-6.
1998: Wilkins R C; Lis J T
GAGA factor binding to DNA via a single trinucleotide sequence element.
Nucleic acids research 1998;26(11):2672-8.
1998: Lee D; Lis J T
Transcriptional activation independent of TFIIH kinase and the RNA polymerase II mediator in vivo.
Nature 1998;393(6683):389-92.
1998: Law A; Hirayoshi K; O'Brien T; Lis J T
Direct cloning of DNA that interacts in vivo with a specific protein: application to RNA polymerase II and sites of pausing in Drosophila.
Nucleic acids research 1998;26(4):919-24.
1998: Lis J
Promoter-associated pausing in promoter architecture and postinitiation transcriptional regulation.
Cold Spring Harbor symposia on quantitative biology 1998;63():347-56.
1997: Wilkins R C; Lis J T
Dynamics of potentiation and activation: GAGA factor and its role in heat shock gene regulation.
Nucleic acids research 1997;25(20):3963-8.
1997: Shi H; Hoffman B E; Lis J T
A specific RNA hairpin loop structure binds the RNA recognition motifs of the Drosophila SR protein B52.
Molecular and cellular biology 1997;17(5):2649-57.
1996: Shopland L S; Lis J T
HSF recruitment and loss at most Drosophila heat shock loci is coordinated and depends on proximal promoter sequences.
Chromosoma 1996;105(3):158-71.
1995: Fernandes M; Xiao H; Lis J T
Binding of heat shock factor to and transcriptional activation of heat shock genes in Drosophila.
Nucleic acids research 1995;23(23):4799-804.
1995: Shopland L S; Hirayoshi K; Fernandes M; Lis J T
HSF access to heat shock elements in vivo depends critically on promoter architecture defined by GAGA factor, TFIID, and RNA polymerase II binding sites.
Genes & development 1995;9(22):2756-69.
1995: Xiao H; Friesen J D; Lis J T
Recruiting TATA-binding protein to a promoter: transcriptional activation without an upstream activator.
Molecular and cellular biology 1995;15(10):5757-61.
1995: O'Brien T; Wilkins R C; Giardina C; Lis J T
Distribution of GAGA protein on Drosophila genes in vivo.
Genes & development 1995;9(9):1098-110.
1995: Giardina C; Lis J T
Dynamic protein-DNA architecture of a yeast heat shock promoter.
Molecular and cellular biology 1995;15(5):2737-44.
1995: Giardina C; Lis J T
Sodium salicylate and yeast heat shock gene transcription.
The Journal of biological chemistry 1995;270(18):10369-72.
1994: Ring H Z; Lis J T
The SR protein B52/SRp55 is essential for Drosophila development.
Molecular and cellular biology 1994;14(11):7499-506.
1994: Kraus M E; Lis J T
The concentration of B52, an essential splicing factor and regulator of splice site choice in vitro, is critical for Drosophila development.
Molecular and cellular biology 1994;14(8):5360-70.
1994: O'Brien T; Hardin S; Greenleaf A; Lis J T
Phosphorylation of RNA polymerase II C-terminal domain and transcriptional elongation.
Nature 1994;370(6484):75-7.
1994: Champlin D T; Lis J T
Distribution of B52 within a chromosomal locus depends on the level of transcription.
Molecular biology of the cell 1994;5(1):71-9.
1994: Fernandes M; Xiao H; Lis J T
Fine structure analyses of the Drosophila and Saccharomyces heat shock factor--heat shock element interactions.
Nucleic acids research 1994;22(2):167-73.
1993: Giardina C; Lis J T
Polymerase processivity and termination on Drosophila heat shock genes.
The Journal of biological chemistry 1993;268(32):23806-11.
1993: Rasmussen E B; Lis J T
In vivo transcriptional pausing and cap formation on three Drosophila heat shock genes.
Proceedings of the National Academy of Sciences of the United States of America 1993;90(17):7923-7.
1993: Giardina C; Lis J T
DNA melting on yeast RNA polymerase II promoters.
Science (New York, N.Y.) 1993;261(5122):759-62.
1993: Lis J; Wu C
Protein traffic on the heat shock promoter: parking, stalling, and trucking along.
Cell 1993;74(1):1-4.
1993: O'Brien T; Lis J T
Rapid changes in Drosophila transcription after an instantaneous heat shock.
Molecular and cellular biology 1993;13(6):3456-63.
1992: Giardina C; Pérez-Riba M; Lis J T
Promoter melting and TFIID complexes on Drosophila genes in vivo.
Genes & development 1992;6(11):2190-200.
1992: Lu Q; Wallrath L L; Allan B D; Glaser R L; Lis J T; Elgin S C
Promoter sequence containing (CT)n.(GA)n repeats is critical for the formation of the DNase I hypersensitive sites in the Drosophila hsp26 gene.
Journal of molecular biology 1992;225(4):985-98.
1992: Lee H; Kraus K W; Wolfner M F; Lis J T
DNA sequence requirements for generating paused polymerase at the start of hsp70.
Genes & development 1992;6(2):284-95.
1991: O'Brien T; Lis J T
RNA polymerase II pauses at the 5' end of the transcriptionally induced Drosophila hsp70 gene.
Molecular and cellular biology 1991;11(10):5285-90.
1991: Champlin D T; Frasch M; Saumweber H; Lis J T
Characterization of a Drosophila protein associated with boundaries of transcriptionally active chromatin.
Genes & development 1991;5(9):1611-21.
1991: Xiao H; Perisic O; Lis J T
Cooperative binding of Drosophila heat shock factor to arrays of a conserved 5 bp unit.
Cell 1991;64(3):585-93.
1991: Gilmour D S; Rougvie A E; Lis J T
Protein-DNA cross-linking as a means to determine the distribution of proteins on DNA in vivo.
Methods in cell biology 1991;35():369-81.
1990: Rougvie A E; Lis J T
Postinitiation transcriptional control in Drosophila melanogaster.
Molecular and cellular biology 1990;10(11):6041-5.
1990: Xiao H; Lis J T
Closely related DNA sequences specify distinct patterns of developmental expression in Drosophila melanogaster.
Molecular and cellular biology 1990;10(6):3272-6.
1990: Glaser R L; Thomas G H; Siegfried E; Elgin S C; Lis J T
Optimal heat-induced expression of the Drosophila hsp26 gene requires a promoter sequence containing (CT)n.(GA)n repeats.
Journal of molecular biology 1990;211(4):751-61.
1990: Glaser R L; Lis J T
Multiple, compensatory regulatory elements specify spermatocyte-specific expression of the Drosophila melanogaster hsp26 gene.
Molecular and cellular biology 1990;10(1):131-7.
1989: Perisic O; Xiao H; Lis J T
Stable binding of Drosophila heat shock factor to head-to-head and tail-to-tail repeats of a conserved 5 bp recognition unit.
Cell 1989;59(5):797-806.
1989: Xiao H; Lis J T
Heat shock and developmental regulation of the Drosophila melanogaster hsp83 gene.
Molecular and cellular biology 1989;9(4):1746-53.
1988: Sun X H; Tso J Y; Lis J; Wu R
Differential regulation of the two glyceraldehyde-3-phosphate dehydrogenase genes during Drosophila development.
Molecular and cellular biology 1988;8(12):5200-5.
1988: Kraus K W; Lee Y H; Lis J T; Wolfner M F
Sex-specific control of Drosophila melanogaster yolk protein 1 gene expression is limited to transcription.
Molecular and cellular biology 1988;8(11):4756-64.
1988: Lee H S; Simon J A; Lis J T
Structure and expression of ubiquitin genes of Drosophila melanogaster.
Molecular and cellular biology 1988;8(11):4727-35.
1988: Rougvie A E; Lis J T
The RNA polymerase II molecule at the 5' end of the uninduced hsp70 gene of D. melanogaster is transcriptionally engaged.
Cell 1988;54(6):795-804.
1988: Sun X H; Lis J T; Wu R
The positive and negative transcriptional regulation of the Drosophila Gapdh-2 gene.
Genes & development 1988;2(6):743-53.
1988: Xiao H; Lis J T
Germline transformation used to define key features of heat-shock response elements.
Science (New York, N.Y.) 1988;239(4844):1139-42.
1987: Gilmour D S; Lis J T
Protein-DNA cross-linking reveals dramatic variation in RNA polymerase II density on different histone repeats of Drosophila melanogaster.
Molecular and cellular biology 1987;7(9):3341-4.
1985: Simon J A; Sutton C A; Lobell R B; Glaser R L; Lis J T
Determinants of heat shock-induced chromosome puffing.
Cell 1985;40(4):805-17.
1985: Simon J A; Sutton C A; Lis J T
Localization and expression of transformed DNA sequences within heat shock puffs of Drosophila melanogaster.
Chromosoma 1985;93(1):26-30.
1983: Lis J T; Simon J A; Sutton C A
New heat shock puffs and beta-galactosidase activity resulting from transformation of Drosophila with an hsp70-lacZ hybrid gene.
Cell 1983;35(2 Pt 1):403-10.

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John Lis

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