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Michael Tolstorukov, Ph.D.

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  1. Kaye EG, Booker M, Kurland JV, Conicella AE, Fawzi NL, Bulyk ML, Tolstorukov MY, Larschan E. Differential Occupancy of Two GA-Binding Proteins Promotes Targeting of the Drosophila Dosage Compensation Complex to the Male X Chromosome. Cell Rep. 2018 Mar 20; 22(12):3227-3239. PMID: 29562179.
    View in: PubMed
  2. Mieczkowski J, Tolstorukov MY. Bioinformatic Analysis of Nucleosome and Histone Variant Positioning. Methods Mol Biol. 2018; 1832:185-203. PMID: 30073528.
    View in: PubMed
  3. Urban J, Kuzu G, Bowman S, Scruggs B, Henriques T, Kingston R, Adelman K, Tolstorukov M, Larschan E. Enhanced chromatin accessibility of the dosage compensated Drosophila male X-chromosome requires the CLAMP zinc finger protein. PLoS One. 2017; 12(10):e0186855. PMID: 29077765.
    View in: PubMed
  4. Cook A, Mieczkowski J, Tolstorukov MY. Single-Assay Profiling of Nucleosome Occupancy and Chromatin Accessibility. Curr Protoc Mol Biol. 2017 10 02; 120:21.34.1-21.34.18. PMID: 28967996.
    View in: PubMed
  5. Rieder LE, Koreski KP, Boltz KA, Kuzu G, Urban JA, Bowman SK, Zeidman A, Jordan WT, Tolstorukov MY, Marzluff WF, Duronio RJ, Larschan EN. Histone locus regulation by the Drosophila dosage compensation adaptor protein CLAMP. Genes Dev. 2017 07 15; 31(14):1494-1508. PMID: 28838946.
    View in: PubMed
  6. Mueller B, Mieczkowski J, Kundu S, Wang P, Sadreyev R, Tolstorukov MY, Kingston RE. Widespread changes in nucleosome accessibility without changes in nucleosome occupancy during a rapid transcriptional induction. Genes Dev. 2017 03 01; 31(5):451-462. PMID: 28356342.
    View in: PubMed
  7. Goldman JA, Kuzu G, Lee N, Karasik J, Gemberling M, Foglia MJ, Karra R, Dickson AL, Sun F, Tolstorukov MY, Poss KD. Resolving Heart Regeneration by Replacement Histone Profiling. Dev Cell. 2017 02 27; 40(4):392-404.e5. PMID: 28245924.
    View in: PubMed
  8. Wang X, Lee RS, Alver BH, Haswell JR, Wang S, Mieczkowski J, Drier Y, Gillespie SM, Archer TC, Wu JN, Tzvetkov EP, Troisi EC, Pomeroy SL, Biegel JA, Tolstorukov MY, Bernstein BE, Park PJ, Roberts CW. SMARCB1-mediated SWI/SNF complex function is essential for enhancer regulation. Nat Genet. 2017 Feb; 49(2):289-295. PMID: 27941797.
    View in: PubMed
  9. Pulivarthy SR, Lion M, Kuzu G, Matthews AG, Borowsky ML, Morris J, Kingston RE, Dennis JH, Tolstorukov MY, Oettinger MA. Regulated large-scale nucleosome density patterns and precise nucleosome positioning correlate with V(D)J recombination. Proc Natl Acad Sci U S A. 2016 10 18; 113(42):E6427-E6436. PMID: 27698124.
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  10. Kuzu G, Kaye EG, Chery J, Siggers T, Yang L, Dobson JR, Boor S, Bliss J, Liu W, Jogl G, Rohs R, Singh ND, Bulyk ML, Tolstorukov MY, Larschan E. Expansion of GA Dinucleotide Repeats Increases the Density of CLAMP Binding Sites on the X-Chromosome to Promote Drosophila Dosage Compensation. PLoS Genet. 2016 07; 12(7):e1006120. PMID: 27414415; PMCID: PMC4945028.
  11. Deaton AM, Gómez-Rodríguez M, Mieczkowski J, Tolstorukov MY, Kundu S, Sadreyev RI, Jansen LE, Kingston RE. Enhancer regions show high histone H3.3 turnover that changes during differentiation. Elife. 2016 06 15; 5. PMID: 27304074; PMCID: PMC4965263.
  12. Mieczkowski J, Cook A, Bowman SK, Mueller B, Alver BH, Kundu S, Deaton AM, Urban JA, Larschan E, Park PJ, Kingston RE, Tolstorukov MY. MNase titration reveals differences between nucleosome occupancy and chromatin accessibility. Nat Commun. 2016 05 06; 7:11485. PMID: 27151365.
    View in: PubMed
  13. Tolstorukov MY, Virnik K, Zhurkin VB, Adhya S. Organization of DNA in a bacterial nucleoid. BMC Microbiol. 2016 Feb 20; 16:22. PMID: 26897370; PMCID: PMC4761138.
  14. Ho JW, Jung YL, Liu T, Alver BH, Lee S, Ikegami K, Sohn KA, Minoda A, Tolstorukov MY, Appert A, Parker SC, Gu T, Kundaje A, Riddle NC, Bishop E, Egelhofer TA, Hu SS, Alekseyenko AA, Rechtsteiner A, Asker D, Belsky JA, Bowman SK, Chen QB, Chen RA, Day DS, Dong Y, Dose AC, Duan X, Epstein CB, Ercan S, Feingold EA, Ferrari F, Garrigues JM, Gehlenborg N, Good PJ, Haseley P, He D, Herrmann M, Hoffman MM, Jeffers TE, Kharchenko PV, Kolasinska-Zwierz P, Kotwaliwale CV, Kumar N, Langley SA, Larschan EN, Latorre I, Libbrecht MW, Lin X, Park R, Pazin MJ, Pham HN, Plachetka A, Qin B, Schwartz YB, Shoresh N, Stempor P, Vielle A, Wang C, Whittle CM, Xue H, Kingston RE, Kim JH, Bernstein BE, Dernburg AF, Pirrotta V, Kuroda MI, Noble WS, Tullius TD, Kellis M, MacAlpine DM, Strome S, Elgin SC, Liu XS, Lieb JD, Ahringer J, Karpen GH, Park PJ. Comparative analysis of metazoan chromatin organization. Nature. 2014 Aug 28; 512(7515):449-52. PMID: 25164756.
    View in: PubMed
  15. West JA, Cook A, Alver BH, Stadtfeld M, Deaton AM, Hochedlinger K, Park PJ, Tolstorukov MY, Kingston RE. Nucleosomal occupancy changes locally over key regulatory regions during cell differentiation and reprogramming. Nat Commun. 2014 Aug 27; 5:4719. PMID: 25158628; PMCID: PMC4217530.
  16. West JA, Davis CP, Sunwoo H, Simon MD, Sadreyev RI, Wang PI, Tolstorukov MY, Kingston RE. The long noncoding RNAs NEAT1 and MALAT1 bind active chromatin sites. Mol Cell. 2014 Sep 04; 55(5):791-802. PMID: 25155612; PMCID: PMC4428586.
  17. Jung YL, Luquette LJ, Ho JW, Ferrari F, Tolstorukov M, Minoda A, Issner R, Epstein CB, Karpen GH, Kuroda MI, Park PJ. Impact of sequencing depth in ChIP-seq experiments. Nucleic Acids Res. 2014 May; 42(9):e74. PMID: 24598259; PMCID: PMC4027199.
  18. Soruco MM, Chery J, Bishop EP, Siggers T, Tolstorukov MY, Leydon AR, Sugden AU, Goebel K, Feng J, Xia P, Vedenko A, Bulyk ML, Park PJ, Larschan E. The CLAMP protein links the MSL complex to the X chromosome during Drosophila dosage compensation. Genes Dev. 2013 Jul 15; 27(14):1551-6. PMID: 23873939; PMCID: PMC3731544.
  19. Bowman SK, Simon MD, Deaton AM, Tolstorukov M, Borowsky ML, Kingston RE. Multiplexed Illumina sequencing libraries from picogram quantities of DNA. BMC Genomics. 2013 Jul 09; 14:466. PMID: 23837789; PMCID: PMC3711846.
  20. Tolstorukov MY, Sansam CG, Lu P, Koellhoffer EC, Helming KC, Alver BH, Tillman EJ, Evans JA, Wilson BG, Park PJ, Roberts CW. Swi/Snf chromatin remodeling/tumor suppressor complex establishes nucleosome occupancy at target promoters. Proc Natl Acad Sci U S A. 2013 Jun 18; 110(25):10165-70. PMID: 23723349; PMCID: PMC3690861.
  21. Riddle NC, Jung YL, Gu T, Alekseyenko AA, Asker D, Gui H, Kharchenko PV, Minoda A, Plachetka A, Schwartz YB, Tolstorukov MY, Kuroda MI, Pirrotta V, Karpen GH, Park PJ, Elgin SC. Enrichment of HP1a on Drosophila chromosome 4 genes creates an alternate chromatin structure critical for regulation in this heterochromatic domain. PLoS Genet. 2012 Sep; 8(9):e1002954. PMID: 23028361; PMCID: PMC3447959.
  22. Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P, Chen Y, DeSalvo G, Epstein C, Fisher-Aylor KI, Euskirchen G, Gerstein M, Gertz J, Hartemink AJ, Hoffman MM, Iyer VR, Jung YL, Karmakar S, Kellis M, Kharchenko PV, Li Q, Liu T, Liu XS, Ma L, Milosavljevic A, Myers RM, Park PJ, Pazin MJ, Perry MD, Raha D, Reddy TE, Rozowsky J, Shoresh N, Sidow A, Slattery M, Stamatoyannopoulos JA, Tolstorukov MY, White KP, Xi S, Farnham PJ, Lieb JD, Wold BJ, Snyder M. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res. 2012 Sep; 22(9):1813-31. PMID: 22955991; PMCID: PMC3431496.
  23. Tolstorukov MY, Goldman JA, Gilbert C, Ogryzko V, Kingston RE, Park PJ. Histone variant H2A.Bbd is associated with active transcription and mRNA processing in human cells. Mol Cell. 2012 Aug 24; 47(4):596-607. PMID: 22795134; PMCID: PMC3708478.
  24. Schwartz YB, Linder-Basso D, Kharchenko PV, Tolstorukov MY, Kim M, Li HB, Gorchakov AA, Minoda A, Shanower G, Alekseyenko AA, Riddle NC, Jung YL, Gu T, Plachetka A, Elgin SC, Kuroda MI, Park PJ, Savitsky M, Karpen GH, Pirrotta V. Nature and function of insulator protein binding sites in the Drosophila genome. Genome Res. 2012 Nov; 22(11):2188-98. PMID: 22767387; PMCID: PMC3483548.
  25. Alekseyenko AA, Ho JW, Peng S, Gelbart M, Tolstorukov MY, Plachetka A, Kharchenko PV, Jung YL, Gorchakov AA, Larschan E, Gu T, Minoda A, Riddle NC, Schwartz YB, Elgin SC, Karpen GH, Pirrotta V, Kuroda MI, Park PJ. Sequence-specific targeting of dosage compensation in Drosophila favors an active chromatin context. PLoS Genet. 2012; 8(4):e1002646. PMID: 22570616; PMCID: PMC3343056.
  26. Tolstorukov MY, Volfovsky N, Stephens RM, Park PJ. Impact of chromatin structure on sequence variability in the human genome. Nat Struct Mol Biol. 2011 Apr; 18(4):510-5. PMID: 21399641; PMCID: PMC3188321.
  27. Riddle NC, Minoda A, Kharchenko PV, Alekseyenko AA, Schwartz YB, Tolstorukov MY, Gorchakov AA, Jaffe JD, Kennedy C, Linder-Basso D, Peach SE, Shanower G, Zheng H, Kuroda MI, Pirrotta V, Park PJ, Elgin SC, Karpen GH. Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin. Genome Res. 2011 Feb; 21(2):147-63. PMID: 21177972; PMCID: PMC3032919.
  28. Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, Landolin JM, Bristow CA, Ma L, Lin MF, Washietl S, Arshinoff BI, Ay F, Meyer PE, Robine N, Washington NL, Di Stefano L, Berezikov E, Brown CD, Candeias R, Carlson JW, Carr A, Jungreis I, Marbach D, Sealfon R, Tolstorukov MY, Will S, Alekseyenko AA, Artieri C, Booth BW, Brooks AN, Dai Q, Davis CA, Duff MO, Feng X, Gorchakov AA, Gu T, Henikoff JG, Kapranov P, Li R, MacAlpine HK, Malone J, Minoda A, Nordman J, Okamura K, Perry M, Powell SK, Riddle NC, Sakai A, Samsonova A, Sandler JE, Schwartz YB, Sher N, Spokony R, Sturgill D, van Baren M, Wan KH, Yang L, Yu C, Feingold E, Good P, Guyer M, Lowdon R, Ahmad K, Andrews J, Berger B, Brenner SE, Brent MR, Cherbas L, Elgin SC, Gingeras TR, Grossman R, Hoskins RA, Kaufman TC, Kent W, Kuroda MI, Orr-Weaver T, Perrimon N, Pirrotta V, Posakony JW, Ren B, Russell S, Cherbas P, Graveley BR, Lewis S, Micklem G, Oliver B, Park PJ, Celniker SE, Henikoff S, Karpen GH, Lai EC, MacAlpine DM, Stein LD, White KP, Kellis M. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science. 2010 Dec 24; 330(6012):1787-97. PMID: 21177974.
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  29. Kharchenko PV, Alekseyenko AA, Schwartz YB, Minoda A, Riddle NC, Ernst J, Sabo PJ, Larschan E, Gorchakov AA, Gu T, Linder-Basso D, Plachetka A, Shanower G, Tolstorukov MY, Luquette LJ, Xi R, Jung YL, Park RW, Bishop EP, Canfield TK, Sandstrom R, Thurman RE, MacAlpine DM, Stamatoyannopoulos JA, Kellis M, Elgin SC, Kuroda MI, Pirrotta V, Karpen GH, Park PJ. Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. Nature. 2011 Mar 24; 471(7339):480-5. PMID: 21179089; PMCID: PMC3109908.
  30. Jagani Z, Mora-Blanco EL, Sansam CG, McKenna ES, Wilson B, Chen D, Klekota J, Tamayo P, Nguyen PT, Tolstorukov M, Park PJ, Cho YJ, Hsiao K, Buonamici S, Pomeroy SL, Mesirov JP, Ruffner H, Bouwmeester T, Luchansky SJ, Murtie J, Kelleher JF, Warmuth M, Sellers WR, Roberts CW, Dorsch M. Loss of the tumor suppressor Snf5 leads to aberrant activation of the Hedgehog-Gli pathway. Nat Med. 2010 Dec; 16(12):1429-33. PMID: 21076395.
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  31. Babbitt GA, Tolstorukov MY, Kim Y. The molecular evolution of nucleosome positioning through sequence-dependent deformation of the DNA polymer. J Biomol Struct Dyn. 2010 Jun; 27(6):765-80. PMID: 20232932.
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  32. Blackledge NP, Zhou JC, Tolstorukov MY, Farcas AM, Park PJ, Klose RJ. CpG islands recruit a histone H3 lysine 36 demethylase. Mol Cell. 2010 Apr 23; 38(2):179-90. PMID: 20417597; PMCID: PMC3098377.
  33. Tolstorukov MY, Kharchenko PV, Park PJ. Analysis of primary structure of chromatin with next-generation sequencing. Epigenomics. 2010 Apr; 2(2):187-197. PMID: 22022339.
    View in: PubMed
  34. Tolstorukov MY, Kharchenko PV, Goldman JA, Kingston RE, Park PJ. Comparative analysis of H2A.Z nucleosome organization in the human and yeast genomes. Genome Res. 2009 Jun; 19(6):967-77. PMID: 19246569; PMCID: PMC2694475.
  35. Kharchenko PV, Tolstorukov MY, Park PJ. Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nat Biotechnol. 2008 Dec; 26(12):1351-9. PMID: 19029915; PMCID: PMC2597701.
  36. Kharchenko PV, Woo CJ, Tolstorukov MY, Kingston RE, Park PJ. Nucleosome positioning in human HOX gene clusters. Genome Res. 2008 Oct; 18(10):1554-61. PMID: 18723689; PMCID: PMC2556261.
  37. Tolstorukov MY, Choudhary V, Olson WK, Zhurkin VB, Park PJ. nuScore: a web-interface for nucleosome positioning predictions. Bioinformatics. 2008 Jun 15; 24(12):1456-8. PMID: 18445607; PMCID: PMC3807124.
  38. Tolstorukov MY, Colasanti AV, McCandlish DM, Olson WK, Zhurkin VB. A novel roll-and-slide mechanism of DNA folding in chromatin: implications for nucleosome positioning. J Mol Biol. 2007 Aug 17; 371(3):725-38. PMID: 17585938; PMCID: PMC2000845.
  39. Tolstorukov MY, Virnik KM, Adhya S, Zhurkin VB. A-tract clusters may facilitate DNA packaging in bacterial nucleoid. Nucleic Acids Res. 2005; 33(12):3907-18. PMID: 16024741; PMCID: PMC1176013.
  40. Liu M, Tolstorukov M, Zhurkin V, Garges S, Adhya S. A mutant spacer sequence between -35 and -10 elements makes the Plac promoter hyperactive and cAMP receptor protein-independent. Proc Natl Acad Sci U S A. 2004 May 04; 101(18):6911-6. PMID: 15118087; PMCID: PMC406441.
  41. Tolstorukov MY, Jernigan RL, Zhurkin VB. Protein-DNA hydrophobic recognition in the minor groove is facilitated by sugar switching. J Mol Biol. 2004 Mar 12; 337(1):65-76. PMID: 15001352.
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  42. Virnik K, Lyubchenko YL, Karymov MA, Dahlgren P, Tolstorukov MY, Semsey S, Zhurkin VB, Adhya S. "Antiparallel" DNA loop in gal repressosome visualized by atomic force microscopy. J Mol Biol. 2003 Nov 14; 334(1):53-63. PMID: 14596799.
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  43. Tolstorukov MY, Ivanov VI, Malenkov GG, Jernigan RL, Zhurkin VB. Sequence-dependent B<-->A transition in DNA evaluated with dimeric and trimeric scales. Biophys J. 2001 Dec; 81(6):3409-21. PMID: 11721003; PMCID: PMC1301797.
  44. Tolstorukov MY, Maleev VY. Conformational transitions of DNA induced by changing water content of the sample: a theoretical study. J Biomol Struct Dyn. 2000 Apr; 17(5):913-20. PMID: 10798535.
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