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  1. 1.   Robust regulation of transcription pausing in Escherichia coli by the ubiquitous elongation factor NusG
  2. Yakhnin,Alex; Bubunenko,Mikhail; Mandell, Zachary F; Lubkowska,Lucyna; Husher, Sara; Babitzke, Paul; Kashlev,Mikhail
  3. Proceedings of the National Academy of Sciences of the United States of America. 2023, Jun 13; 120(24): e2221114120.
  1. 2.   Homologs of the Escherichia coli F Element Protein TraR, Including Phage Lambda Orf73, Directly Reprogram Host Transcription
  2. Gopalkrishnan, Saumya; Ross, Wilma; Akbari, Madeline S; Li, Xintian; Haycocks, James R J; Grainger, David C; Court,Don; Gourse, Richard L
  3. mBio. 2022, May 18; e0095222.
  1. 3.   Transcriptome-Wide Effects of NusA on RNA Polymerase Pausing in Bacillus subtilis
  2. Jayasinghe, Oshadhi T; Mandell, Zachary F; Yakhnin,Alex; Kashlev,Mikhail; Babitzke, Paul
  3. Journal of Bacteriology. 2022, Mar 08; e0053421.
  1. 4.   NusG-dependent RNA polymerase pausing is a frequent function of this universally conserved transcription elongation factor
  2. Yakhnin, Alexander V; Kashlev,Mikhail; Babitzke, Paul
  3. Critical reviews in biochemistry and molecular biology. 2020, Oct 02; 1-13.
  1. 5.   NusG controls transcription pausing and RNA polymerase translocation throughout the Bacillus subtilis genome
  2. Yakhnin, Alexander V; FitzGerald, Peter C; McIntosh, Carl; Yakhnin, Helen; Kireeva, Maria; Turek-Herman, Joshua; Mandell, Zachary F; Kashlev,Mikhail; Babitzke, Paul
  3. Proceedings of the National Academy of Sciences of the United States of America. 2020, SEP 1; 117(35): 21628-21636.
  1. 6.   Targeting the RNA Polymerase I Transcription for Cancer Therapy Comes of Age
  2. Ferreira, Rita; Schneekloth,Jay; Panov, Konstantin I.; Hannan, Katherine M.; Hannan, Ross D.
  3. Cells. 2020, FEB; 9(2):
  1. 7.   NusG-Dependent RNA Polymerase Pausing and Tylosin-Dependent Ribosome Stalling Are Required for Tylosin Resistance by Inducing 23S rRNA Methylation in Bacillus subtilis
  2. Yakhnin, Helen; Yakhnin, Alexander V; Mouery, Brandon L; Mandell, Zachary F; Karbasiafshar, Catherine; Kashlev,Mikhail; Babitzke, Paul
  3. mBio. 2019, Nov; 10(6): pii: e02665-19..
  1. 8.   Spatial organization of RNA polymerase and its relationship with transcription in Escherichia coli
  2. Weng, Xiaoli; Bohrer, Christopher H; Bettridge, Kelsey; Lagda, Arvin Cesar; Cagliero, Cedric; Jin, Ding Jun; Xiao, Jie
  3. Proceedings of the National Academy of Sciences of the United States of America. 2019, OCT 1; 116(40): 20115-20123.
  1. 9.   The Role of Pyrophosphorolysis in the Initiation-to-Elongation Transition by E. coli RNA Polymerase
  2. Imashimizu, Masahiko; Kireeva, Maria L; Lubkowska,Lucyna; Kashlev,Mikhail; Shimamoto, Nobuo
  3. Journal of molecular biology. 2019, Jun 28; 431(14): 2528-2542.
  1. 10.   Extrachromosomal Nucleolus-Like Compartmentalization by a Plasmid-Borne Ribosomal RNA Operon and Its Role in Nucleoid Compaction
  2. Mata Martin, Carmen; Sun, Zhe; Zhou, Yan; Jin, Ding
  3. Frontiers in Microbiology. 2018, Jun 5; 9: 1115.
  1. 11.   Structural basis of transcriptional stalling and bypass of abasic DNA lesion by RNA polymerase II
  2. Wang, Wei; Walmacq, Celine; Chong, Jenny; Kashlev, Mikhail; Wang, Dong
  3. Proceedings of the National Academy of Sciences of the United States of America. 2018, Mar 13; 115(11): E2538-E2545.
  1. 12.   A Cre Transcription Fidelity Reporter Identifies GreA as a Major RNA Proofreading Factor in Escherichia coli
  2. Bubunenko, Mikhail; Court, Carolyn; Rattray, Alison; Gotte, Deanna; Kireeva, Maria; Irizarry Caro, Jorge; Li, Xintian; Jin, Ding; Court, Don; Strathern, Jeffrey; Kashlev, Mikhail
  3. Genetics. 2017, May; 206(1): 179-187.
  1. 13.   Nucleolus-like compartmentalization of the transcription machinery in fast-growing bacterial cells
  2. Jin, Ding; Mata Martin, Carmen; Sun, Zhe; Cagliero, Cedric; Zhou, Yan
  3. Critical reviews in biochemistry and molecular biology. 2017, Feb; 52(1): 96-106.
  1. 14.   Control of transcriptional pausing by biased thermal fluctuations on repetitive genomic sequences
  2. Imashimizu, M.; Afek, A.; Takahashi, H.; Lubkowska, Lucyna; Lukatsky, D. B.
  3. Proceedings of the National Academy of Sciences of the United States of America. 2016, Nov 22; 113(47): E7409-E7417.
  1. 15.   High-throughput single-molecule screen for small-molecule perturbation of splicing and transcription kinetics
  2. Day, C. R.; Chen, H.; Coulon, A.; Meier, J. L.; Larson, D. R.
  3. Methods (San Diego, Calif.). 2016, 1-Mar; 96: 59-68.
  1. 16.   Negative regulation of human U6 snRNA promoter by p38 kinase through Oct-1
  2. Lin, B. R.; Natarajan, V.
  3. Gene. 2012, Apr; 497(2): 200-207.
  1. 17.   Growth rate regulation in Escherichia coli
  2. Jin, D. J.; Cagliero, C.; Zhou, Y. N.
  3. FEMS Microbiology Reviews. 2012, Mar; 36(2): 269-287.
  1. 18.   Structure and function of RapA: A bacterial Swi2/Snf2 protein required for RNA polymerase recycling in transcription
  2. Jin, D. J.; Zhou, Y. N.; Shaw, G.; Ji, X. H.
  3. Biochimica Et Biophysica Acta-Gene Regulatory Mechanisms. 2011, Sep; 1809(9): 470-475.
  1. 19.   Conformational coupling, bridge helix dynamics and active site dehydration in catalysis by RNA polymerase
  2. Seibold, S. A.; Singh, B. N.; Zhang, C. F.; Kireeva, M.; Domecq, C.; Bouchard, A.; Nazione, A. M.; Feig, M.; Cukier, R. I.; Coulombe, B.; Kashlev, M.; Hampsey, M.; Burton, Z. F.
  3. Biochimica Et Biophysica Acta-Gene Regulatory Mechanisms. 2010, Aug; 1799(8): 575-587.
  1. 20.   Euprosterna elaeasa virus genome sequence and evolution of the Tetraviridae family: Emergence of bipartite genomes and conservation of the VPg signal with the dsRNA Birnaviridae family
  2. Zeddam, J. L.; Gordon, K. H. J.; Lauber, C.; Alves, C. A. F.; Luke, B. T.; Hanzlik, T. N.; Ward, V. K.; Gorbalenya, A. E.
  3. Virology. 2010, Feb; 397(1): 145-154.
  1. 21.   Translocation by multi-subunit RNA polymerases
  2. Kireeva, M.; Kashlev, M.; Burton, Z. F.
  3. Biochimica Et Biophysica Acta-Gene Regulatory Mechanisms. 2010, May-Jun; 1799(5-6): 389-401.
  1. 22.   Coupling the distribution of RNA polymerase to global gene regulation and the dynamic structure of the bacterial nucleoid in Escherichia coli
  2. Jin, D. J.; Cabrera, J. E.
  3. Journal of Structural Biology. 2006, Nov; 156(2): 284-291.
  1. 23.   Nature of the nucleosomal barrier to RNA polymerase II
  2. Kireeva, M. L.; Hancock, B.; Cremona, G. H.; Walter, W.; Studitsky, V. M.; Kashlev, M.
  3. Molecular Cell. 2005, APR 1; 18(1): 97-108.
  1. 24.   Cross-resistance of Escherichia coli RNA polymerases conferring rifarnpin resistance to different antibiotics
  2. Xu, M.; Zhou, Y. N.; Goldstein, B. P.; Jin, D. J.
  3. Journal of Bacteriology. 2005, APR; 187(8): 2783-2792.
  1. 25.   Information theory based T7-like promoter models: classification of bacteriophages and differential evolution of promoters and their polymerases
  2. Chen, Z. H.; Schneider, T. D.
  3. Nucleic Acids Research. 2005 33(19): 6172-6187.
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