|Waksman Institute 335|
|190 Frelinghuysen Road Piscataway, NJ, 08854|
Proper control of gene expression is essential for organismal development, cellular response to environmental signals, and the prevention of disease states. Transcription is the first step in gene expression and thus is highly regulated. Transcription in all cells is performed by multi-subunit RNA polymerases (RNAPs) that are conserved in sequence, structure and function from bacteria to humans. Our lab utilizes a range of approaches including molecular biology, genetics, biochemistry and high-throughput sequencing to obtain a detailed understanding of the mechanism and regulation of transcription. To facilitate our studies, we use bacterial RNAP as a model for understanding gene expression paradigms in all organisms.
Transcriptomes are dynamic and responsive to alterations in environmental conditions or growth state. According to the classical model, transcription is regulated primarily through the action of DNA-binding proteins that activate or repress transcription initiation, with a few long-studied exceptions. However, it is now abundantly apparent that cells employ a highly diverse range of mechanisms to control gene expression during all three phases of transcription: initiation, elongation and termination. An overarching goal of our studies is to understand the diversity of regulatory mechanisms that link changes to cellular state to changes in RNAP activity.
5'-end Nicotinamide Adenine Dinucleotide cap in human cells promotes RNA decay through DXO-mediated deNADding. Jiao X, Doamekpor S, Bird JG, Nickels BE, Tong L, Hart RP, & Kiledjian M. Cell (2017) 168, 1015-1027.
Garner AL, Rammohan J, Huynh JP, Onder LM, Chen J, Bae B, Jensen D, Weiss LA, Manzano AR, Darst SA, Campbell EA, Nickels BE, Galburt EA, & Stallings CL. Effects of Increasing the Affinity of CarD for RNA Polymerase on Mycobacterium tuberculosis Growth, rRNA Transcription, and Virulence. Journal of Bacteriology (2017) 199, pii: e00698-16.
Bird JG, Zhang Y, Tian Y, Panova N, Barvík I, Greene L, Liu M, Buckley B, Krásný L, Lee JK, Kaplan CD, Ebright RH, and Nickels BE. The mechanism of RNA 5' capping with NAD+, NADH, and desphospho-CoA. Nature (2016) 535, 444–447.
Vvedenskaya IO, Vahedian-Movahed H, Zhang Y, Taylor DM, Ebright RH, and Nickels BE. Interactions between RNA polymerase and the core recognition element are a determinant of transcription start site selection. Proc. Natl. Acad. Sci. U.S.A. (2016) 113, E2899-2905.
Winkelman JT, Vvedenskaya IO, Zhang Y, Zhang Y, Bird JG, Taylor DM, Gourse RL, Ebright RH, and Nickels BE. Multiplexed protein-DNA crosslinking: scrunching in transcription start site selection. Science (2016) 351, 1090-1093.
Schifano JM, Cruz JW, Edifor R, Vvedenskaya IO, Ouyang M, Husson RN, Nickels BE, and Woychik NA. tRNA is a new target for cleavage by a MazF toxin. Nucleic Acids Research (2016) 44, 1256-1270.
Vvedenskaya IO, Zhang Y, Goldman SR, Valenti A, Visone V, Taylor DM, Ebright RH, and Nickels BE. Massively systematic transcript end readout, “MASTER”: transcription start site selection, transcriptional slippage, and transcript yields. Molecular Cell (2015) 60, 953-965.
Goldman SR, Nair N, Wells C, Nickels BE, and Hochschild A. The primary sigma factor in Escherichia coli can access the transcription elongation complex from solution in vivo. eLife (2015) 4:e10514
Cruz JW, Sharp JD, Hoffer ED, Maehigashi T, Vvedenskaya IO, Konkimalla A, Husson RN, Nickels BE, Dunham CM, and Woychik NA. Growth-regulating Mycobacterium tuberculosis VapC-mt4 toxin is an isoacceptor-specific tRNase. Nature Communications (2015) 6, 7480.
Druzhinin SY, Tran NT, Skalenko KS, Goldman SR, Knoblauch JG, Dove SL, and Nickels BE. A conserved pattern of primer-dependent transcription initiation in Escherichia coli and Vibrio cholerae revealed by 5' RNA-seq. PLOS Genetics (2015) 11(7):e1005348.
Ramsey KM, Osborne ML, Vvedenskaya IO, Su C, Nickels BE, and Dove SL. Ubiquitous promoter-localization of essential virulence regulators in Francisella tularensis. PLOS Pathogens (2015) 11(4):e1004793.
Vvedenskaya IO, Goldman SR, and Nickels BE. Preparation of cDNA libraries for high-throughput RNA sequencing analysis of RNA 5' ends. Methods in Molecular Biology (2015) 1276, 211-228.
Vvedenskaya IO, Vahedian-Movahed H, Bird JG, Knoblauch JG, Goldman SR, Zhang Y, Ebright RH, and Nickels BE. Interactions between RNA polymerase and the "core recognition element" counteract pausing. Science (2014) 344, 1285-1289.
Schifano JM, Vvedenskaya IO, Knoblauch JG, Ouyang M, Nickels BEandWoychik NA. An RNA-seq method for defining endoribonuclease cleavage specificity identifies dual rRNA substrates for toxin MazF-mt3. Nature Communications (2014) 5, 3538.
Vorobiev SM, Gensler Y, Vahedian-Movahed H, Seetharaman J, Su M, Huang JY, Xiao R, Kornhaber G, Montelione GT, Tong L, Ebright RH, and Nickels BE. Structure of the DNA-binding and RNA polymerase-binding region of transcription antitermination factor lambda Q. Structure (2014) 22, 488-495.
Nickels BE. A new way to start: nanoRNA-mediated priming of transcription initiation. Transcription (2012) 3, 300-304.
Bao X, Nickels BE, and Fan H. Chlamydia trachomatis protein GrgA activates transcription by contacting the non-conserved region of sigma-66. Proc. Natl. Acad. Sci. U.S.A. (2012) 109, 16870-16875.
Weiss LA, Harrison PG, Nickels BE, Darst SA, Glickman MS, and Stallings CL. The interaction of CarD with RNAP mediates Mycobacterium tuberculosis viability, rifampicin resistance, and persistence. Journal of Bacteriology (2012) 194, 5621-5631.
Vvedenskaya IO, Sharp JS, Goldman SR, Kanabar PN, Livny J, Dove SL, and Nickels BE. Growth phase-dependent control of transcription start site selection and gene expression by nanoRNAs. Genes and Development (2012) 26, 1498-1507.
Berdygulova Z, Esyunina D, Miropolskaya N, Mukhamedyarov D, Kuznedelov K, Nickels BE, Severinov K, Kulbachinskiy A, and Minakhin L. A novel phage transcription antiterminator acts by suppressing pausing by bacterial RNA polymerase. Nucleic Acids Research (2012) 40, 4052-4063.
Nickels BE and Dove SL. NanoRNAs: a class of small RNAs that can prime transcription initiation in bacteria. Journal of Molecular Biology (2011) 412, 772-781.
Bao X, Pachikara ND, Oey CB, Westblade LF, Tan M, Chase T, Nickels BE, and Fan H. Noncoding Nucleotides and Amino Acids near the Active Site Regulate Peptide Deformylase Expression and Inhibitor Susceptibility in Chlamydia trachomatis. Microbiology (2011) 157, 2569-2581.
Goldman SR, Sharp JS, Vvedenskaya IO, Livny J., Dove SL, and Nickels BE. NanoRNAs prime transcription initiation in vivo. Molecular Cell (2011) 42, 817-825
Westblade LF, Campbell EA, Pukhrambam C, Padovan JC, Nickels BE, Lamour V, and Darst SA. Structural basis for the bacterial transcription-repair coupling factor/RNA polymerase interaction. Nucleic Acids Research (2010) 38, 8357-69.
Nickels BE. A new twist on a classic paradigm: illumination of a "genetic switch" in Vibrio cholerae phage CTX Phi. Journal of Bacteriology (2009) 191, 6779-6781.
Deighan P, Montero Diez C, Leibman M, Hochschild A, and Nickels BE. The bacteriophage lambda Q antiterminator protein contacts the Beta flap domain of RNA polymerase. Proc. Natl. Acad. Sci. U.S.A. (2008) 105, 15305-15310.