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Search life-sciences literature (45,100,050 articles, preprints and more)

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A lineage-specific nascent RNA assay unveils principles of gene regulation in tissue biology
Chovatiya G, Wang AB, Versluis P, Bai CK, Huang SY, DeBerardine M, Ray J, Ozer A, Lis JT, Tumbar T
bioRxiv, 18 Oct 2024
Cited by: 0 articles | PPR: PPR927300
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Live-cell imaging of RNA Pol II and elongation factors distinguishes competing mechanisms of transcription regulation.
Versluis P, Graham TGW, Eng V, Ebenezer J, Darzacq X, Zipfel WR, Lis JT
Mol Cell, 84(15):2856-2869.e9, 01 Aug 2024
Cited by: 1 article | PMID: 39121843
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Nanoscale photobiotinylation, pulldown and sequencing of region-specific DNA from intact cells
Roberts TC, Kushner M, Crowley JC, Ozer A, Wang J, Ray J, Lis JT, Zipfel WR
bioRxiv, 06 Dec 2023
Cited by: 0 articles | PPR: PPR770254
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PRO-IP-seq tracks molecular modifications of engaged Pol II complexes at nucleotide resolution.
Vihervaara A, Versluis P, Himanen SV, Lis JT
Nat Commun, 14(1):7039, 03 Nov 2023
Cited by: 4 articles | PMID: 37923726 | PMCID: PMC10624850
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The NELF pausing checkpoint mediates the functional divergence of Cdk9.
DeBerardine M, Booth GT, Versluis PP, Lis JT
Nat Commun, 14(1):2762, 13 May 2023
Cited by: 10 articles | PMID: 37179384 | PMCID: PMC10182999
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Evolution of promoter-proximal pausing enabled a new layer of transcription control
Chivu AG, Basso BA, Abuhashem A, Leger MM, Barshad G, Rice EJ, Vill AC, Wong W, Chou S, Chovatiya G, Brady R, Smith JJ, Wikramanayake AH, Arenas-Mena C, Brito IL, Ruiz-Trillo I, Hadjantonakis A, Lis JT, Lewis JJ, Danko CG
bioRxiv, 19 Feb 2023
Cited by: 0 articles | PPR: PPR618713
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Psi promotes Drosophila wing growth via direct transcriptional activation of cell cycle targets and repression of growth inhibitors.
Zaytseva O, Mitchell NC, Muckle D, Delandre C, Nie Z, Werner JK, Lis JT, Eyras E, Hannan RD, Levens DL, Marshall OJ, Quinn LM
Development, 150(2):dev201563, 24 Jan 2023
Cited by: 0 articles | PMID: 36692218 | PMCID: PMC10110491
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A comprehensive SARS-CoV-2-human protein-protein interactome reveals COVID-19 pathobiology and potential host therapeutic targets.
Zhou Y, Liu Y, Gupta S, Paramo MI, Hou Y, Mao C, Luo Y, Judd J, Wierbowski S, Bertolotti M, Nerkar M, Jehi L, Drayman N, Nicolaescu V, Gula H, Tay S, Randall G, Wang P, Lis JT, [...] Yu H
Nat Biotechnol, 41(1):128-139, 10 Oct 2022
Cited by: 59 articles | PMID: 36217030 | PMCID: PMC9851973
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CTCF blocks antisense transcription initiation at divergent promoters.
Luan J, Vermunt MW, Syrett CM, Coté A, Tome JM, Zhang H, Huang A, Luppino JM, Keller CA, Giardine BM, Zhang S, Dunagin MC, Zhang Z, Joyce EF, Lis JT, Raj A, Hardison RC, Blobel GA
Nat Struct Mol Biol, 29(11):1136-1144, 11 Nov 2022
Cited by: 10 articles | PMID: 36369346 | PMCID: PMC10015438
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The Drosophila BEAF insulator protein interacts with the polybromo subunit of the PBAP chromatin remodeling complex.
McKowen JK, Avva SVSP, Maharjan M, Duarte FM, Tome JM, Judd J, Wood JL, Negedu S, Dong Y, Lis JT, Hart CM
G3 (Bethesda), 12(11):jkac223, 01 Nov 2022
Cited by: 2 articles | PMID: 36029240 | PMCID: PMC9635645
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A comprehensive SARS-CoV-2-human protein-protein interactome network identifies pathobiology and host-targeting therapies for COVID-19
Zhou Y, Liu Y, Gupta S, Paramo MI, Hou Y, Mao C, Luo Y, Judd J, Wierbowski S, Bertolotti M, Nerkar M, Jehi L, Drayman N, Nicolaescu V, Gula H, Tay S, Randall G, Lis JT, Feschotte C, [...] Yu H
Research Square, 07 Jun 2022
Cited by: 0 articles | PPR: PPR503462
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Prediction of histone post-translational modification patterns based on nascent transcription data.
Wang Z, Chivu AG, Choate LA, Rice EJ, Miller DC, Chu T, Chou SP, Kingsley NB, Petersen JL, Finno CJ, Bellone RR, Antczak DF, Lis JT, Danko CG
Nat Genet, 54(3):295-305, 10 Mar 2022
Cited by: 49 articles | PMID: 35273399 | PMCID: PMC9444190
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A comparison of experimental assays and analytical methods for genome-wide identification of active enhancers.
Yao L, Liang J, Ozer A, Leung AK, Lis JT, Yu H
Nat Biotechnol, 40(7):1056-1065, 17 Feb 2022
Cited by: 28 articles | PMID: 35177836 | PMCID: PMC9288987
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CTCF blocks anti-sense transcription initiation at divergent gene promoters
Luan J, Syrett CM, Vermunt MW, Coté A, Tome JM, Zhang H, Huang A, Luppino JM, Keller CA, Giardine BM, Zhang S, Dunagin MC, Zhang Z, Joyce EF, Lis JT, Raj A, Hardison RC, Blobel GA
bioRxiv, 30 Oct 2021
Cited by: 0 articles | PPR: PPR413676
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RNA polymerase mapping in plants identifies intergenic regulatory elements enriched in causal variants.
Lozano R, Booth GT, Omar BY, Li B, Buckler ES, Lis JT, Del Carpio DP, Jannink JL
G3 (Bethesda), 11(11):jkab273, 01 Oct 2021
Cited by: 13 articles | PMID: 34499719 | PMCID: PMC8527479
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Systematic comparison of experimental assays and analytical pipelines for identification of active enhancers genome-wide
Yao L, Liang J, Ozer A, Leung AK, ENCODE Consortium, Lis JT, Yu H
bioRxiv, 03 Jun 2021
Cited by: 0 articles | PPR: PPR351784
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Glucocorticoid receptor collaborates with pioneer factors and AP-1 to execute genome-wide regulation
Wissink EM, Martinez DM, Ehmsen KT, Yamamoto KR, Lis JT
bioRxiv, 01 Jun 2021
Cited by: 0 articles | PPR: PPR350329
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EmPC-seq: Accurate RNA-sequencing and Bioinformatics Platform to Map RNA Polymerases and Remove Background Error.
Wang Y, Chong TH, Unarta IC, Xu X, Suarez GD, Wang J, Lis JT, Huang X, Cheung PP
Bio Protoc, 11(4):e3921, 20 Feb 2021
Cited by: 0 articles | PMID: 33732808 | PMCID: PMC7952946
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Stress-induced transcriptional memory accelerates promoter-proximal pause release and decelerates termination over mitotic divisions.
Vihervaara A, Mahat DB, Himanen SV, Blom MAH, Lis JT, Sistonen L
Mol Cell, 81(8):1715-1731.e6, 29 Mar 2021
Cited by: 15 articles | PMID: 33784494 | PMCID: PMC8054823
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Distinct properties and functions of CTCF revealed by a rapidly inducible degron system.
Luan J, Xiang G, Gómez-García PA, Tome JM, Zhang Z, Vermunt MW, Zhang H, Huang A, Keller CA, Giardine BM, Zhang Y, Lan Y, Lis JT, Lakadamyali M, Hardison RC, Blobel GA
Cell Rep, 34(8):108783, 01 Feb 2021
Cited by: 40 articles | PMID: 33626344 | PMCID: PMC7999233
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Pioneer-like factor GAF cooperates with PBAP (SWI/SNF) and NURF (ISWI) to regulate transcription.
Judd J, Duarte FM, Lis JT
Genes Dev, 35(1-2):147-156, 10 Dec 2020
Cited by: 40 articles | PMID: 33303640 | PMCID: PMC7778264
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An improved 4'-aminomethyltrioxsalen-based nucleic acid crosslinker for biotinylation of double-stranded DNA or RNA.
Wielenberg K, Wang M, Yang M, Ozer A, Lis JT, Lin H
RSC Adv, 10(65):39870-39874, 01 Oct 2020
Cited by: 3 articles | PMID: 35515418 | PMCID: PMC9057442
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RNA aptamer capture of macromolecular complexes for mass spectrometry analysis.
Ray J, Kruse A, Ozer A, Kajitani T, Johnson R, MacCoss M, Heck M, Lis JT
Nucleic Acids Res, 48(15):e90, 01 Sep 2020
Cited by: 3 articles | PMID: 32609809 | PMCID: PMC7470977
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Transcription imparts architecture, function and logic to enhancer units.
Tippens ND, Liang J, Leung AK, Wierbowski SD, Ozer A, Booth JG, Lis JT, Yu H
Nat Genet, 52(10):1067-1075, 21 Sep 2020
Cited by: 45 articles | PMID: 32958950 | PMCID: PMC7541647
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A rapid, sensitive, scalable method for Precision Run-On sequencing (PRO-seq)
Judd J, Wojenski LA, Wainman LM, Tippens ND, Rice EJ, Dziubek A, Villafano GJ, Wissink EM, Versluis P, Bagepalli L, Shah SR, Mahat DB, Tome JM, Danko CG, Lis JT, Core LJ
bioRxiv, 19 May 2020
Cited by: 0 articles | PPR: PPR164972
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