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Cornell University

Center for Innovative Proteomics

Publications

2024

Versluis P, Graham TGW, Eng V, Ebenezer J, Darzacq X, Zipfel WR, Lis JT. Live-cell imaging of RNA Pol II and elongation factors distinguishes competing mechanisms of transcription regulation. Mol Cell (2024)

 

2023

Chivu AG, Abuhashem A, Barshad G, Rice EJ, Leger MM, Vill AC, Wong W, Brady R, Smith JJ, Wikramanayake AH, Arenas-Mena C, Brito IL, Ruiz-Trillo I, Hadjantonakis AK, Lis JT, Lewis JJ, Danko CG. Evolution of promoter proximal pausing enabled a new layer of transcription control. Res Sq[Preprint] (2023)

DeBerardine M, Booth GT, Versluis PP, Lis JT. The NELF pausing checkpoint mediates the functional divergence of Cdk9. Nat Commun (2023)

Roberts TC, Kushner M, Crowley JC, Ozer A, Wang J, Ray J, Lis JT, Zipfel WR. Nanoscale photobiotinylation pulldown and sequencing of region-specific DNA from intact cells. bioRxiv[Preprint] (2023)

Vihervaara A, Versluis P, Lis JT. PRO-IP-seq Tracks Molecular Modifications of Engaged Pol II Complexes at Nucleotide Resolution. Nat Commun (2023)

Zaytseva O, Mitchell NC, Muckle D, Delandre C, Nie Z, Werner JK, Lis JT, Eyras E, Hannan RD, Levens DL, Marshall OJ, Quinn LM. Psi promotes Drosophila wing growth via direct transcriptional activation of cell cycle targets and repression of growth inhibitors. Development (2023)

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, Erzurum SC, Cheng F, Yu H. A comprehensive SARS-CoV-2-human protein-protein interactome network identifies pathobiology and host-targeting therapies for COVID-19. Nat Biotechnol (2023)

 

2022

Luan J, Vermunt MW, Syrett CM, Cote 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. CTCF blocks antisense transcription initiation at divergent promoters. Nat Struct Mol Bio. (2022)

McKowen JK, Avva SVSP, Maharjan M, Duarte FM, Tome JM, Judd J, Wood JL, Negedu S, Dong Y, Lis JT, Hart CM. The Drosophila BEAF insulator protein interacts with the polybromo subunit of the PBAP chromatin remodeling complex. G3 (Bethesda) (2022)

Sanford, E.J.,Smolka, M.B A field guide to the proteomics of post-translational modifications in DNA repair. Proteomics (2022)
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. Prediction of histone post-translational modification patterns based on nascent transcription data. Nat Genet (2022)

2021

Judd J, Duarte FM, Lis JT. Pioneer-like factor of GAF cooperates with PBAP (SWI/SNF) and NURF(ISWI) to regulate transcription. Genes Dev (2021)

Lanz, M.C., Yugandhar, K., Gupta, S., Sanford, E.J., Faça, V.M., Vega, S., Joiner, A.M.N., Fromme, J.C., Yu, H., Smolka, M.B. In-depth and 3-dimensional exploration of the budding yeast phosphoproteome. EMBO Rep (2021)
Lozano R, Booth GT, Omar BY, Li B, Buckler ES, Lis JT, Del Carpio DP, Jannink JL. RNA polymerase mapping in plants identifies intergenic regulatory elements enriched in causal variants. G3 (Bethesda) (2021)
Luan J, Xiang G, Gomez-Gracia PA, Tome JM, Zhang Z, Vermut MW, Zhang H, Huang A, Keller CA, Giardine BM, Zhang Y, Lan Y, Lis JT, Lakadamyali M, Hardison RC, Blobel GA. Distinct properties and functions of CTCF revealed by a rapidly inducible degron system. Cell Rep (2021)
Sanford, E.J., Smolka, M.B. Fe-nta microcolumn purification of phosphopeptides from immunoprecipitation (ip) eluates for mass spectrometry analysis. Bio-protocol (2021)
Wang Y, Chong TH, Unarta IC, Xu X, Suarez GD, Wang J, Lis JT, Huang X, Cheng PP. EmPC-seq: Accurate RNA-sequencing and Bioinformatics Platform to Map RNA Polymerases and Remove Background Error. Bio Protoc (2021)
Yugandhar, K., Zhao, Q., Gupta, S., Xiong, D., Yu, H. Progress in methodologies and quality-control strategies in protein cross-linking mass spectrometry. Proteomics (2021)

2020

Cheung PP, Jiang B, Booth GT, Chong TH, Unarta IC, Wang Y, Suarez GD, Wang J, Lis JT, Huang X. Identifying Transcription Error-Enriched Genomic Loci Using Nuclear Run-on Circular-Sequencing Coupled with Background Error Modeling. J Mol Biol (2020)

Ray J, Kruse A, Ozer A, Kajitani T, Johnson R, MacCross M, Heck M, Lis JT. RNA aptamer capture of macromolecular complexes for mass spectrometry analysis. Nucleic Acid Res (2020)

Strobel EJ, Lis JT, Lucks JB. Chemical roadblocking of DNA transcription for nascent RNA display. J Biol Chem (2020)

Tippens ND, Liang J, Leung AK, Wierbowski SD, Ozer A, Booth JG, Lis JT, Yu H. Transcription imparts architecture function and logic to enhancer units. Nat Genet (2020)

Wielenberg K, Wang M, Yang M, Ozer A, Lis JT, Lin H. An improved 4′-aminomethyltrioxsalen-based nucleic acid crosslinker for biotinylation of double-stranded DNA or RNA. RSC Adv (2020)

Yugandhar, K., Wang, T.Y., Leung, A.K., Lanz, M.C., Motorykin, I., Liang, J., Shayhidin, E.E., Smolka, M.B., Zhang, S., Yu, H. MaXLinker: Proteome-wide Cross-link Identifications with High Specificity and Sensitivity. Mol Cell Proteomics (2020)
Yugandhar, K., Wang, T.Y., Wierbowski, S.D., Shayhidin, E.E., Yu, H. Structure-based validation can drastically underestimate error rate in proteome-wide cross-linking mass spectrometry studies. Nat Methods (2020)

2019

Lis JT. A 50 year history of technologies that drove discovery in eukaryotic transcription regulation. Nat Struct Mol Bio (2019)

Ray J, Munn PR, Vihervaara A, Lewis JJ, Ozer A, Danko CG, Lis JT. Chromatin conformation remains stable upon extensive transcriptional changes driven by heat shock. Proc Natl Acad Sci USA (2019)

Wissink EM, Vihervaara A, Tippens ND, Lis JT. Nascent RNA analyses: tracking transcription and its regulation. Nature Reviews Genetic (2019)

Yugandhar, K., Gupta, S., Yu, H. Inferring Protein-Protein Interaction Networks From Mass Spectrometry-Based Proteomic Approaches: A Mini-Review. Comput Struct Biotechnol J (2019)