Tolstorukov Lab

Michael Tolstorukov, Ph.D.

Department of Molecular Biology
Simches Research Center
Boston, MA 02114

Email

Website
Publications
    2016
  1. Wang X, Lee RS, Alver BH, Haswell JR, 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. 2016 Dec 12.

  2. 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 Oct 18; 113(42):E6427-E6436.

  3. 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 Jul; 12(7):e1006120.

  4. Deaton AM, 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 Jun 15; 5

  5. 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 May 06; 7:11485.

  6. Tolstorukov MY, Virnik K, Zhurkin VB, Adhya S. Organization of DNA in a bacterial nucleoid. BMC Microbiol. 2016 Feb 20; 16:22.

  7. 2014
  8. 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 4; 55(5):791-802.

  9. 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, 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, Lieb JD, Ahringer J, Karpen GH. Comparative analysis of metazoan chromatin organization. Nature 2014 Aug 28; 512(7515):449-52.

  10. 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; 42(9):e74.

  11. 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; 5:4719.

  12. 2013
  13. 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.

  14. 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.

  15. Bowman SK, Simon MD, Deaton AM, Tolstorukov M, Borowsky ML, Kingston RE. Multiplexed Illumina sequencing libraries from picogram quantities of DNA. BMC Genomics 2013; 14:466.

  16. 2012
  17. 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 Sep 20.

  18. 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.

  19. 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, 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.

  20. 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.

  21. 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.

  22. 2011
  23. 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.

  24. 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. Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. Nature 2011 Mar 24; 471(7339):480-5.

  25. 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.

  26. 2010
  27. modENCODE Consortium, 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, Graveley BR, Lewis S, Micklem G, Oliver B, Park PJ, Celniker SE, Karpen GH, Lai EC, Stein LD, White KP, Kellis M. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 2010 Dec 24; 330(6012):1787-97.

  28. 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.

  29. 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.

  30. 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.

  31. Tolstorukov MY, Kharchenko PV, Park PJ. Analysis of primary structure of chromatin with next-generation sequencing. Epigenomics 2010 Apr; 2(2):187-197.

  32. 2009
  33. 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.

  34. 2008
  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.

  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.

  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.

  38. 2007
  39. 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.

  40. 2005
  41. 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.

  42. 2004
  43. Semsey S, Tolstorukov MY, Virnik K, Zhurkin VB, Adhya S. DNA trajectory in the Gal repressosome. Genes Dev. 2004 Aug 1; 18(15):1898-907.

  44. 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 4; 101(18):6911-6.

  45. 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.

  46. 2003
  47. 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.

  48. 2001
  49. 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.

  50. 2000
  51. 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.

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