Sergei Nechaev

Peer-Reviewed Publications:

• Zarns K, Desell T, Nechaev S and Dhasarathy A. (2015) Searching the Human Genome for Snail and Slug With DNA@Home. IEEE e-Science 2015 Conference Proceedings. Accepted 

• Chauhan A, Quenumzangbe F, Abbas A, Bradley D, Nechaev S, Singh B., Sharma J, Mishra B. (2015) Epigenetic Modulation of Microglial Inflammatory Gene Loci in Helminth-Induced Immune Suppression: Implications for Immune Regulation in Neurocysticercosis. ASN Neuro. 7. 

• Scheidegger A, Burkholder A, Abbas A, Zarns K, Samarakkody A and Nechaev S*. Analysis of paired end Pol II ChIP-seq and short capped RNA-seq in MCF-7 cells. Genom Data. 2015 June 25; 263-267.

• Scruggs, B. S., Gilchrist, D. A., Nechaev, S., Muse, G. W., Burkholder, A., Fargo, D. C. & Adelman, K. Bidirectional Transcription Arises from Two Distinct Hubs of Transcription Factor Binding and Active Chromatin. Mol Cell 58, 1101-1112 (2015). 

• Samarakkody, A., Abbas, A., Scheidegger, A., Warns, J., Nnoli, O., Jokinen, B., Zarns, K., Kubat, B., Dhasarathy, A. & Nechaev, S*. RNA polymerase II pausing can be retained or acquired during activation of genes involved in the epithelial to mesenchymal transition. Nucleic Acids Res 43, 3938-3949 (2015).  

• Henriques, T*., Gilchrist, D. A. *, Nechaev, S. *, Bern, M., Muse, G. W., Burkholder, A., Fargo, D. C., and Adelman, K. (2013) Stable Pausing by RNA Polymerase II Provides an Opportunity to Target and Integrate Regulatory Signals, Mol Cell 52, 517-528.
• *Co-first author 

• Twist, K. A., Campbell, E. A., Deighan, P., Nechaev, S., Jain, V., Geiduschek, E. P., Hochschild, A. & Darst, S. A. (2011). Crystal structure of the bacteriophage T4 late-transcription coactivator gp33 with the beta-subunit flap domain of Escherichia coli RNA polymerase. Proc Natl Acad Sci U S A 108, 19961-19966. 

• Savalia D, Robins W, Nechaev S, Molineux I and Severinov K (2010). The role of the T7 Gp2 inhibitor of host RNA polymerase in phage development, J Mol Biol 402 118-126

• Nechaev S, Fargo D, dos Santos G, Liu L, Gao Y and Adelman K (2010). Global Analysis of Short RNAs Reveals Widespread Promoter-Proximal Stalling and Arrest of Pol II in Drosophila. Science 327, 335-338

• Adelman K, Kennedy M, Nechaev S, Gilchrist D, Muse G, Chinenov Y and Rogatsky I (2009). Immediate mediators of the inflammatory response are poised for gene activation through RNA polymerase II stalling. Proc Natl Acad Sci U S A. 106: 18207-18212

• Gilchrist D, Nechaev S, Lee C, Collins J, Ghosh S, Gilmour D and Adelman K (2008). NELF- mediated stalling of Pol II can enhance gene expression by blocking promoter-proximal nucleosome assembly. Genes Dev. 22: 1921-1933

• Nechaev S* and Geiduschek EP (2008). Dissection of the bacteriophage T4 late promoter complex. Journal of Molecular Biology. 379: 402-413
• *corresponding author

• Zeitlinger J, Stark A, KellisM, Hong J W, Nechaev S, Adelman K, Levine M and Young R. (2007) RNA Polymerase Stalling at Developmental Control Genes in the Drosophila Embryo. Nature Genetics. 39 :1512-1516

• Muse G, Gilchrist A, Nechaev S, Shah R, Parker J, Grissom S, Zeitlinger J and Adelman K (2007) RNA polymerase is poised for activation across the genome. Nature Genetics. 39: 1507- 1511

• Nechaev S*, Geiduschek EP (2006). The role of an upstream promoter interaction in initiation of bacterial transcription. EMBO J. 25: 1700-1709
• *corresponding author 

• Nechaev S*, Kamali-Moghaddam M, Andre E, Leonetti JP, Geiduschek EP.(2004) The bacteriophage T4 late-transcription coactivator gp33 binds the flap domain of Escherichia coli RNA polymerase. Proc Natl Acad Sci U S A. 101:17365-70
• *corresponding author. 

• Wigneshweraraj SR, Burrows PC, Nechaev S, Zenkin N, Severinov K, Buck M. (2004) Regulated communication between the upstream face of RNA polymerase and the beta' subunit jaw domain. EMBO J. 23: 4264-74

• Wigneshweraraj S., Nechaev S., Bordes P., Jones S., Cannon W., Severinov K., Buck M. (2003) Enhancer-dependent transcription by bacterial RNA polymerase: the beta subunit downstream lobe is used by sigma 54 during open promoter complex formation. Methods Enzymol. 370: 646- 657

• Yuzenkova J., Nechaev S., Berlin J., Rogulja D., Kuznedelov K., Inman R., Mushegian A., Severinov K. (2003) Genome of Xanthomonas oryzae bacteriophage Xp10: an odd T-odd phage. J Mol Biol. 330: 735-748

• Yuzenkova J., Delgado M., Nechaev S., Savalia D., Epshtein V., Artsimovitch I., Mooney R., Landick R., Farias R., Salomon R., Severinov K. (2002) Mutations of bacterial RNA polymerase leading to resistance to microcin j25. J Biol Chem. 277: 50867-50875

• Wigneshweraraj S., Nechaev S., Severinov K., Buck M. (2002) Beta subunit residues 186-433 and 436-445 are commonly used by Esigma54 and Esigma70 RNA polymerase for open promoter complex formation. J Mol Biol. 319:1067-1083

• Nechaev S., Yuzenkova Y., Niedziela-Majka A., Heyduk T., Severinov K. (2002) A novel bacteriophage-encoded RNA polymerase binding protein inhibits transcription initiation and abolishes transcription termination by host RNA polymerase. J Mol Biol. 320,11-22

• Minakhin, L., Nechaev, S., Campbell, E. A., and Severinov, K. (2001) Recombinant Thermus aquaticus RNA polymerase-A new tool for structure-based analysis of transcription. J. Bacteriol., 183, 71-76

• Nechaev, S., Chlenov, M., and Severinov, K. (2000). Dissection of two hallmarks of the open promoter complex by mutation in RNA polymerase core subunit. J. Biol. Chem., 275, 25516- 25522

• Sharp, M. M., Chan, C. L., Lu, C. Z., Marr, M. T., Nechaev, S., Merritt, E. W., Severinov, K., Roberts, J. W., and Gross, C. A. (1999) The sigma interface with core RNA polymerase is extensive, functionally specialized, and conserved. Genes & Devel., 13, 3015-3026

• Lohrke, S. M., Nechaev, S., Yang, H., Severinov, K., and Jin, S. (1999) Transcriptional activation of Agrobacterium tumefaciens virulence gene promoters in Escherichia coli requires the rpoA gene from A. tumefaciens encoding the α subunit of RNA polymerase. J. Bacteriol., 181, 4533-4539

• Nechaev, S., and Severinov, K. (1999) Inhibition of E. coli RNA polymerase by bacteriophage T7 gene 2 protein. J. Mol. Biol., 289, 815-826

o   Reviews and Commentaries. 

• Scheidegger A and Nechaev S (2015). RNA Polymerase II Pausing as a Context-Dependent Reader of the Genome. Biochemistry and Cell Biology. In press.

• Nechaev, S. and K. Adelman. (2011). Pol II waiting in the starting gates: Regulating the transition from transcription initiation into productive elongation. Biochim Biophys Acta 1809: 34-45

• Nechaev S and Severinov K (2008). RapA: Completing the transcription cycle? Structure. 16: 1294-1295

• Nechaev S and Adelman K (2008). Promoter-proximal Pol II: when stalling speeds things up. Cell Cycle. 7: 1539-1544

• Nechaev S and Severinov K (2008). The Elusive Object of Desire - Interactions of Bacteriophages and Their Hosts. Current Opinion in Microbiology. 11: 186-193.

• Nechaev S., Severinov K (2003) Bacteriophage-induced modifications of host RNA polymerase. Annu Rev Microbiol. 57: 301-322

o   Book Chapters

• Nechaev S (corresponding author), Zenkin A and Severinov K (2009). Regulation of RNA polymerase through its active center. In RNA Polymerases as Molecular Motors, in Royal Society for Chemistry, Paris, France. ISBN: 978-0-85404-134-3 

• Nechaev S., Imburgio D., Severinov K (2003) Purification and characterization of bacteriophage-encoded inhibitors of host RNA polymerase: T-odd phage gp2-like proteins. Methods Enzymol. 370: 212-225