Publications

 2019

• Scheidegger A, Dunn CJ, Samarakkody A, Koney NK, Perley D, Saha RN, Nechaev S (2019) Genome-wide RNA pol II initiation and pausing in neural progenitors of the rat. BMC Genomics. 2019 Jun 11;20(1):477. doi: 10.1186/s12864-019-5829-4. PubMed PMID: 31185909; PubMed Central PMCID: PMC6558777. PubMed
• Schacke M, Kumar J, Colwell N, Hermanson K, Folle GA, Nechaev S, Dhasarathy A, Lafon-Hughes (2019) PARP-1/2 Inhibitor Olaparib Prevents or Partially Reverts EMT Induced by TGF-β in NMuMG Cells. Int J Mol Sci. 2019 Jan 26;20(3). doi: 10.3390/ijms20030518. PubMed PMID: 30691122; PubMed Central PMCID: PMC6387051. PubMed

2016-2017

• Casselli T, Qureshi H, Peterson E, Perley D, Blake E, Jokinen B, Abbas A, Nechaev S, Watt JA, Dhasarathy A, and Brissette CA (2017) MicroRNA and mRNA Transcriptome Profiling in Primary Human Astrocytes Infected with Borrelia burgdorferi. PloS one. 2017; 12(1):e0170961. PubMed
• Scheidegger A and Nechaev S (2016) RNA polymerase II pausing as a context-dependent reader of the genome. Biochemistry and cell biology. Biochimie et biologie cellulaire. 2016; 94(1):82-92. NIHMSID: NIHMS729237. PubMed

2015

• Scheidegger A, Burkholder A, Abbas A, Zarns K, Samarakkody A, and Nechaev S (2015) Analysis of paired end Pol II ChIP-seq and short capped RNA-seq in MCF-7 cells. Genomics data. 2015; 5:263-267. NIHMSID: NIHMS703204. PubMed
• Zarns K, Desell T, Nechaev S, and Dhasarathy A (2015) Searching the Human Genome for Snail and Slug With DNA@Home Proceedings. IEEE International Conference on eScience. IEEE International Conference on eScience. 2015; 2015:429-438. NIHMSID: NIHMS766087. PubMed
• Chauhan A, Quenum FZ, Abbas A, Bradley DS, Nechaev S, Singh BB, Sharma J, and Mishra BB (2015) Epigenetic Modulation of Microglial Inflammatory Gene Loci in Helminth-Induced Immune Suppression: Implications for Immune Regulation in Neurocysticercosis. ASN neuro. 2015;7(4). PubMed
• Scruggs BS, Gilchrist DA, Nechaev S, Muse GW, Burkholder A, Fargo DC, and Adelman K (2015) Bidirectional Transcription Arises from Two Distinct Hubs of Transcription Factor Binding and Active Chromatin Molecular cell. 2015; 58(6):1101-12. NIHMSID: NIHMS678991. PubMed
• Samarakkody A, Abbas A, Scheidegger A, Warns J, Nnoli O, Jokinen B, Zarns K, Kubat B, Dhasarathy A, and Nechaev S (2015)  RNA polymerase II pausing can be retained or acquired during activation of genes involved in the epithelial to mesenchymal transition. Nucleic acids research. 2015; 43(8):3938-49. PubMed

2011-2013

• Henriques T, Gilchrist DA, Nechaev S, Bern M, Muse GW, Burkholder A, Fargo DC, and Adelman K (2013) Stable pausing by RNA polymerase II provides an opportunity to target and integrate regulatory signals. Molecular cell. 2013; 52(4):517-28. NIHMSID: NIHMS530973. PubMed
• Twist KA, Campbell EA, Deighan P, Nechaev S, Jain V, Geiduschek EP, Hochschild A, and Darst SA (2011) Crystal structure of the bacteriophage T4 late-transcription coactivator gp33 with the β-subunit flap domain of Escherichia coli RNA polymerase. Proceedings of the National Academy of Sciences of the United States of America. 2011;108(50):19961-6. PubMed
• Nechaev S and Adelman K (2011) Pol II waiting in the starting gates: Regulating the transition from transcription initiation into productive elongation. Biochimica et biophysica acta. 2011; 1809(1):34-45. NIHMSID: NIHMS252434. PubMed

2005-2010

• 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. Journal of molecular biology. 2010; 402(1):118-26. NIHMSID: NIHMS230465. PubMed
• Nechaev S, Fargo DC, 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 (New York, N.Y.). 2010; 327(5963):335-8. NIHMSID: NIHMS401007. PubMed
• Adelman K, Kennedy MA, Nechaev S, Gilchrist DA, Muse GW, Chinenov Y, and Rogatsky I (2009) Immediate mediators of the inflammatory response are poised for gene activation through RNA polymerase II stalling. Proceedings of the National Academy of Sciences of the United States of America. 2009; 106(43):18207-12. PubMed
• Nechaev S and Severinov K (2008) RapA: completing the transcription cycle? Structure (London, England : 1993). 2008; 16(9):1294-5. PubMed
• Gilchrist DA, Nechaev S, Lee C, Ghosh SK, Collins JB, Li L, Gilmour DS, and Adelman K (2008) NELF-mediated stalling of Pol II can enhance gene expression by blocking promoter-proximal nucleosome assembly. Genes & development. 2008; 22(14):1921-33. PubMed
• Nechaev S and Geiduschek EP (2008) Dissection of the bacteriophage T4 late promoter complex. Journal of molecular biology. 2008; 379(3):402-13. NIHMSID: NIHMS49138. PubMed
• Nechaev S and Adelman K (2008) Promoter-proximal Pol II: when stalling speeds things up Cell cycle. (Georgetown, Tex.). 2008; 7(11):1539-44. PubMed
• Nechaev S and Severinov K (2008) The elusive object of desire--interactions of bacteriophages and their hosts. Current opinion in microbiology. 2008; 11(2):186-93. NIHMSID: NIHMS49056. PubMed
• Muse GW, Gilchrist DA, Nechaev S, Shah R, Parker JS, Grissom SF, Zeitlinger J, and Adelman K (2007) RNA polymerase is poised for activation across the genome. Nature genetics. 2007; 39(12):1507-11. NIHMSID: NIHMS44392. PubMed
• Zeitlinger J, Stark A, Kellis M, Hong JW, Nechaev S, Adelman K, Levine M, and Young RA (2007) RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo. Nature genetics. 2007; 39(12):1512-6. NIHMSID: NIHMS44576. PubMed
• Nechaev S and Geiduschek EP (2006) The role of an upstream promoter interaction in initiation of bacterial transcription. The EMBO journal. 2006; 25(8):1700-9. PubMed

2001-2004

• Nechaev S, Kamali-Moghaddam M, André E, Léonetti JP, and Geiduschek EP (2004) The bacteriophage T4 late-transcription coactivator gp33 binds the flap domain of Escherichia coli RNA polymerase. Proceedings of the National Academy of Sciences of the United States of America. 2004; 101(50):17365-70. PubMed
• Wigneshweraraj SR, Burrows PC, Nechaev S, Zenkin N, Severinov K, and Buck M (2004) Regulated communication between the upstream face of RNA polymerase and the beta' subunit jaw domain. The EMBO journal. 2004; 23(21):4264-74. PubMed
• Yuzenkova J, Nechaev S, Berlin J, Rogulja D, Kuznedelov K, Inman R, Mushegian A, and Severinov K (2003) Genome of Xanthomonas oryzae bacteriophage Xp10: an odd T-odd phage. Journal of molecular biology. 2003; 330(4):735-48. PubMed
• Wigneshweraraj SR, Nechaev S, Bordes P, Jones S, Cannon W, Severinov K, and 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 in enzymology. 2003; 370:646-57. PubMed
• Nechaev S, Imburgio D, and Severinov K (2003) Purification and characterization of bacteriophage-encoded inhibitors of host RNA polymerase: T-odd phage gp2-like proteins. Methods in enzymology. 2003; 370:212-25. PubMed
• Nechaev S and Severinov K (2003) Bacteriophage-induced modifications of host RNA polymerase. Annual review of microbiology. 2003; 57:301-22. PubMed
• Yuzenkova J, Delgado M, Nechaev S, Savalia D, Epshtein V, Artsimovitch I, Mooney RA, Landick R, Farias RN, Salomon R, and Severinov K (2002) Mutations of bacterial RNA polymerase leading to resistance to microcin j25. The Journal of biological chemistry. 2002; 277(52):50867-75. PubMed
• Nechaev S, Yuzenkova Y, Niedziela-Majka A, Heyduk T, and Severinov K (2002) A novel bacteriophage-encoded RNA polymerase binding protein inhibits transcription initiation and abolishes transcription termination by host RNA polymerase. Journal of molecular biology. 2002; 320(1):11-22. PubMed
• Wigneshweraraj SR, Nechaev S, Severinov K, and 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. Journal of molecular biology. 2002; 319(5):1067-83. PubMed
• Minakhin L, Nechaev S, Campbell EA, and Severinov K (2001) Recombinant Thermus aquaticus RNA polymerase, a new tool for structure-based analysis of transcription. Journal of bacteriology. 2001; 183(1):716. PubMed

1999-2000

• Nechaev S, Chlenov M, and Severinov K (2000) Dissection of two hallmarks of the open promoter complex by mutation in an RNA polymerase core subunit. The Journal of biological chemistry. 2000; 275(33):25516-22. PubMed
• Sharp MM, Chan CL, Lu CZ, Marr MT, Nechaev S, Merritt EW, Severinov K, Roberts JW, and Gross CA (1999) The interface of sigma with core RNA polymerase is extensive, conserved, and functionally specialized. Genes & development. 1999; 13(22):3015-26. PubMed
• Lohrke SM, Nechaev S, Yang H, Severinov K, and Jin SJ (1999) Transcriptional activation of Agrobacterium tumefaciens virulence gene promoters in Escherichia coli requires the A. tumefaciens RpoA gene, encoding the alpha subunit of RNA polymerase. Journal of bacteriology. 1999; 181(15):4533-9. PubMed
• Nechaev S and Severinov K (1999) Inhibition of Escherichia coli RNA polymerase by bacteriophage T7 gene 2 protein. Journal of molecular biology. 1999; 289(4):815-26. PubMed

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, and 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