Interactions between RNA polymerase and the "core recognition element" counteract pausing
Vvedenskaya, Irina O., Vahedian-Movahed, Hanif, Bird, Jeremy G., Knoblauch, Jared G., Goldman, Seth R., Zhang, Yu, Ebright, Richard H., Nickels, Bryce E.
Published in Science (American Association for the Advancement of Science) (13.06.2014)
Published in Science (American Association for the Advancement of Science) (13.06.2014)
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Journal Article
Massively Systematic Transcript End Readout, “MASTER”: Transcription Start Site Selection, Transcriptional Slippage, and Transcript Yields
Vvedenskaya, Irina O., Zhang, Yuanchao, Goldman, Seth R., Valenti, Anna, Visone, Valeria, Taylor, Deanne M., Ebright, Richard H., Nickels, Bryce E.
Published in Molecular cell (17.12.2015)
Published in Molecular cell (17.12.2015)
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Journal Article
tRNA is a new target for cleavage by a MazF toxin
Schifano, Jason M, Cruz, Jonathan W, Vvedenskaya, Irina O, Edifor, Regina, Ouyang, Ming, Husson, Robert N, Nickels, Bryce E, Woychik, Nancy A
Published in Nucleic acids research (18.02.2016)
Published in Nucleic acids research (18.02.2016)
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Journal Article
NanoRNAs Prime Transcription Initiation In Vivo
Goldman, Seth R., Sharp, Josh S., Vvedenskaya, Irina O., Livny, Jonathan, Dove, Simon L., Nickels, Bryce E.
Published in Molecular cell (24.06.2011)
Published in Molecular cell (24.06.2011)
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Journal Article
XACT-Seq Comprehensively Defines the Promoter-Position and Promoter-Sequence Determinants for Initial-Transcription Pausing
Winkelman, Jared T., Pukhrambam, Chirangini, Vvedenskaya, Irina O., Zhang, Yuanchao, Taylor, Deanne M., Shah, Premal, Ebright, Richard H., Nickels, Bryce E.
Published in Molecular cell (03.09.2020)
Published in Molecular cell (03.09.2020)
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Journal Article
Toxin-mediated ribosome stalling reprograms the Mycobacterium tuberculosis proteome
Barth, Valdir C, Zeng, Ju-Mei, Vvedenskaya, Irina O, Ouyang, Ming, Husson, Robert N, Woychik, Nancy A
Published in Nature communications (10.07.2019)
Published in Nature communications (10.07.2019)
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Journal Article
An RNA-seq method for defining endoribonuclease cleavage specificity identifies dual rRNA substrates for toxin MazF-mt3
Schifano, Jason M, Vvedenskaya, Irina O, Knoblauch, Jared G, Ouyang, Ming, Nickels, Bryce E, Woychik, Nancy A
Published in Nature communications (08.04.2014)
Published in Nature communications (08.04.2014)
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Journal Article
Growth-regulating Mycobacterium tuberculosis VapC-mt4 toxin is an isoacceptor-specific tRNase
Cruz, Jonathan W, Sharp, Jared D, Hoffer, Eric D, Maehigashi, Tatsuya, Vvedenskaya, Irina O, Konkimalla, Arvind, Husson, Robert N, Nickels, Bryce E, Dunham, Christine M, Woychik, Nancy A
Published in Nature communications (09.07.2015)
Published in Nature communications (09.07.2015)
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Journal Article
Detection of spacer precursors formed in vivo during primed CRISPR adaptation
Shiriaeva, Anna A, Savitskaya, Ekaterina, Datsenko, Kirill A, Vvedenskaya, Irina O, Fedorova, Iana, Morozova, Natalia, Metlitskaya, Anastasia, Sabantsev, Anton, Nickels, Bryce E, Severinov, Konstantin, Semenova, Ekaterina
Published in Nature communications (10.10.2019)
Published in Nature communications (10.10.2019)
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Journal Article
Ubiquitous promoter-localization of essential virulence regulators in Francisella tularensis
Ramsey, Kathryn M, Osborne, Melisa L, Vvedenskaya, Irina O, Su, Cathy, Nickels, Bryce E, Dove, Simon L
Published in PLoS pathogens (01.04.2015)
Published in PLoS pathogens (01.04.2015)
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Journal Article
Quantitative analysis of transcription start site selection reveals control by DNA sequence, RNA polymerase II activity and NTP levels
Zhu, Yunye, Vvedenskaya, Irina O, Sze, Sing-Hoi, Nickels, Bryce E, Kaplan, Craig D
Published in Nature structural & molecular biology (01.01.2024)
Published in Nature structural & molecular biology (01.01.2024)
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Journal Article
CapZyme-Seq Comprehensively Defines Promoter-Sequence Determinants for RNA 5′ Capping with NAD
Vvedenskaya, Irina O., Bird, Jeremy G., Zhang, Yuanchao, Zhang, Yu, Jiao, Xinfu, Barvík, Ivan, Krásný, Libor, Kiledjian, Megerditch, Taylor, Deanne M., Ebright, Richard H., Nickels, Bryce E.
Published in Molecular cell (03.05.2018)
Published in Molecular cell (03.05.2018)
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Journal Article
Interactions between RNA polymerase and the core recognition element are a determinant of transcription start site selection
Vvedenskaya, Irina O., Vahedian-Movahed, Hanif, Zhang, Yuanchao, Taylor, Deanne M., Ebright, Richard H., Nickels, Bryce E.
Published in Proceedings of the National Academy of Sciences - PNAS (24.05.2016)
Published in Proceedings of the National Academy of Sciences - PNAS (24.05.2016)
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Journal Article
Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli
Skalenko, Kyle S, Li, Lingting, Zhang, Yuanchao, Vvedenskaya, Irina O, Winkelman, Jared T, Cope, Alexander L, Taylor, Deanne M, Shah, Premal, Ebright, Richard H, Kinney, Justin B, Zhang, Yu, Nickels, Bryce E
Published in Proceedings of the National Academy of Sciences - PNAS (06.07.2021)
Published in Proceedings of the National Academy of Sciences - PNAS (06.07.2021)
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Journal Article
Multiplexed protein-DNA cross-linking: Scrunching in transcription start site selection
Winkelman, Jared T., Vvedenskaya, Irina O., Zhang, Yuanchao, Zhang, Yu, Bird, Jeremy G., Taylor, Deanne M., Gourse, Richard L., Ebright, Richard H., Nickels, Bryce E.
Published in Science (American Association for the Advancement of Science) (04.03.2016)
Published in Science (American Association for the Advancement of Science) (04.03.2016)
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Journal Article