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Items: 1 to 50 of 79

1.

The anti-cancer drugs curaxins target spatial genome organization.

Kantidze OL, Luzhin AV, Nizovtseva EV, Safina A, Valieva ME, Golov AK, Velichko AK, Lyubitelev AV, Feofanov AV, Gurova KV, Studitsky VM, Razin SV.

Nat Commun. 2019 Mar 29;10(1):1441. doi: 10.1038/s41467-019-09500-7.

2.

Time-resolved analysis of transcription through chromatin.

Chang HW, Hsieh FK, Patel SS, Studitsky VM.

Methods. 2019 Apr 15;159-160:90-95. doi: 10.1016/j.ymeth.2019.01.016. Epub 2019 Jan 29.

PMID:
30707952
3.

Mechanism of FACT removal from transcribed genes by anticancer drugs curaxins.

Chang HW, Valieva ME, Safina A, Chereji RV, Wang J, Kulaeva OI, Morozov AV, Kirpichnikov MP, Feofanov AV, Gurova KV, Studitsky VM.

Sci Adv. 2018 Nov 7;4(11):eaav2131. doi: 10.1126/sciadv.aav2131. eCollection 2018 Nov.

4.

[HMGB Proteins as DNA Chaperones That Modulate Chromatin Activity].

Kozlova AL, Valieva ME, Maluchenko NV, Studitsky VM.

Mol Biol (Mosk). 2018 Sep-Oct;52(5):737-749. doi: 10.1134/S0026898418050099. Review. Russian.

5.

Structural interpretation of DNA-protein hydroxyl-radical footprinting experiments with high resolution using HYDROID.

Shaytan AK, Xiao H, Armeev GA, Gaykalova DA, Komarova GA, Wu C, Studitsky VM, Landsman D, Panchenko AR.

Nat Protoc. 2018 Nov;13(11):2535-2556. doi: 10.1038/s41596-018-0048-z.

6.

Structure and function of the histone chaperone FACT - Resolving FACTual issues.

Gurova K, Chang HW, Valieva ME, Sandlesh P, Studitsky VM.

Biochim Biophys Acta Gene Regul Mech. 2018 Jul 25. pii: S1874-9399(18)30159-7. doi: 10.1016/j.bbagrm.2018.07.008. [Epub ahead of print] Review.

PMID:
30055319
7.

Functional roles of the DNA-binding HMGB domain in the histone chaperone FACT in nucleosome reorganization.

McCullough LL, Connell Z, Xin H, Studitsky VM, Feofanov AV, Valieva ME, Formosa T.

J Biol Chem. 2018 Apr 20;293(16):6121-6133. doi: 10.1074/jbc.RA117.000199. Epub 2018 Mar 7.

8.

Unfolding of core nucleosomes by PARP-1 revealed by spFRET microscopy.

Sultanov DC, Gerasimova NS, Kudryashova KS, Maluchenko NV, Kotova EY, Langelier MF, Pascal JM, Kirpichnikov MP, Feofanov AV, Studitsky VM.

AIMS Genet. 2017;4(1):21-31. doi: 10.3934/genet.2017.1.21. Epub 2017 Jan 5.

9.

Towards quantitative analysis of gene regulation by enhancers.

Nizovtseva EV, Todolli S, Olson WK, Studitsky VM.

Epigenomics. 2017 Sep;9(9):1219-1231. doi: 10.2217/epi-2017-0061. Epub 2017 Aug 11. Review.

10.

Chromatin replication: TRANSmitting the histone code.

Chang HW, Studitsky VM.

J Nat Sci. 2017 Feb;3(2). pii: e322.

11.

Stabilization of Nucleosomes by Histone Tails and by FACT Revealed by spFRET Microscopy.

Valieva ME, Gerasimova NS, Kudryashova KS, Kozlova AL, Kirpichnikov MP, Hu Q, Botuyan MV, Mer G, Feofanov AV, Studitsky VM.

Cancers (Basel). 2017 Jan 6;9(1). pii: E3. doi: 10.3390/cancers9010003.

12.

[Structural studies of chromatin remodeling factors].

Volokh OI, Derkacheva NI, Studitsky VM, Sokolova OS.

Mol Biol (Mosk). 2016 Nov-Dec;50(6):922-934. doi: 10.7868/S0026898416060215. Review. Russian.

13.

Nucleosome-free DNA regions differentially affect distant communication in chromatin.

Nizovtseva EV, Clauvelin N, Todolli S, Polikanov YS, Kulaeva OI, Wengrzynek S, Olson WK, Studitsky VM.

Nucleic Acids Res. 2017 Apr 7;45(6):3059-3067. doi: 10.1093/nar/gkw1240.

14.

Overcoming a nucleosomal barrier to replication.

Chang HW, Pandey M, Kulaeva OI, Patel SS, Studitsky VM.

Sci Adv. 2016 Nov 11;2(11):e1601865. eCollection 2016 Nov.

15.

Large-scale ATP-independent nucleosome unfolding by a histone chaperone.

Valieva ME, Armeev GA, Kudryashova KS, Gerasimova NS, Shaytan AK, Kulaeva OI, McCullough LL, Formosa T, Georgiev PG, Kirpichnikov MP, Studitsky VM, Feofanov AV.

Nat Struct Mol Biol. 2016 Dec;23(12):1111-1116. doi: 10.1038/nsmb.3321. Epub 2016 Nov 7.

16.

Nucleosomal Barrier to Transcription: Structural Determinants and Changes in Chromatin Structure.

Studitsky VM, Nizovtseva EV, Shaytan AK, Luse DS.

Biochem Mol Biol J. 2016;2(2). pii: 8. Epub 2016 May 30.

17.

[Inhibiting the pro-tumor and transcription factor FACT: Mechanisms].

Maluchenko NV, Chang HW, Kozinova MT, Valieva ME, Gerasimova NS, Kitashov AV, Kirpichnikov MP, Georgiev PG, Studitsky VM.

Mol Biol (Mosk). 2016 Jul-Aug;50(4):599-610. Russian.

18.

Structure and Functions of Linker Histones.

Lyubitelev AV, Nikitin DV, Shaytan AK, Studitsky VM, Kirpichnikov MP.

Biochemistry (Mosc). 2016 Mar;81(3):213-23. doi: 10.1134/S0006297916030032. Review.

PMID:
27262190
19.

Transcription-induced DNA supercoiling: New roles of intranucleosomal DNA loops in DNA repair and transcription.

Gerasimova NS, Pestov NA, Kulaeva OI, Clark DJ, Studitsky VM.

Transcription. 2016 May 26;7(3):91-5. doi: 10.1080/21541264.2016.1182240. Epub 2016 Apr 26.

20.

[Structure and function of histone chaperone FACT].

Bondarenko MT, Maluchenko NV, Valieva ME, Gerasimova NS, Kulaeva OI, Georgiev PG, Studitsky VM.

Mol Biol (Mosk). 2015 Nov-Dec;49(6):891-904. doi: 10.7868/S0026898415060026. Review. Russian.

21.

Structure of transcribed chromatin is a sensor of DNA damage.

Pestov NA, Gerasimova NS, Kulaeva OI, Studitsky VM.

Sci Adv. 2015 Jul 3;1(6):e1500021. doi: 10.1126/sciadv.1500021. eCollection 2015 Jul.

22.

Structural analysis of nucleosomal barrier to transcription.

Gaykalova DA, Kulaeva OI, Volokh O, Shaytan AK, Hsieh FK, Kirpichnikov MP, Sokolova OS, Studitsky VM.

Proc Natl Acad Sci U S A. 2015 Oct 27;112(43):E5787-95. doi: 10.1073/pnas.1508371112. Epub 2015 Oct 12.

23.

Preparation of mononucleosomal templates for analysis of transcription with RNA polymerase using spFRET.

Kudryashova KS, Chertkov OV, Nikitin DV, Pestov NA, Kulaeva OI, Efremenko AV, Solonin AS, Kirpichnikov MP, Studitsky VM, Feofanov AV.

Methods Mol Biol. 2015;1288:395-412. doi: 10.1007/978-1-4939-2474-5_23.

24.

Preparation and analysis of positioned mononucleosomes.

Kulaeva OI, Studitsky VM.

Methods Mol Biol. 2015;1288:15-26. doi: 10.1007/978-1-4939-2474-5_2.

25.

Experimental analysis of hFACT action during Pol II transcription in vitro.

Hsieh FK, Kulaeva OI, Studitsky VM.

Methods Mol Biol. 2015;1276:315-26. doi: 10.1007/978-1-4939-2392-2_19.

26.

Nucleosome positioning and composition modulate in silico chromatin flexibility.

Clauvelin N, Lo P, Kulaeva OI, Nizovtseva EV, Diaz-Montes J, Zola J, Parashar M, Studitsky VM, Olson WK.

J Phys Condens Matter. 2015 Feb 18;27(6):064112. doi: 10.1088/0953-8984/27/6/064112. Epub 2015 Jan 7.

27.

Transcription through enhancers suppresses their activity in Drosophila.

Erokhin M, Davydova A, Parshikov A, Studitsky VM, Georgiev P, Chetverina D.

Epigenetics Chromatin. 2013 Sep 26;6(1):31. doi: 10.1186/1756-8935-6-31.

28.

Analysis of the mechanism of nucleosome survival during transcription.

Chang HW, Kulaeva OI, Shaytan AK, Kibanov M, Kuznedelov K, Severinov KV, Kirpichnikov MP, Clark DJ, Studitsky VM.

Nucleic Acids Res. 2014 Feb;42(3):1619-27. doi: 10.1093/nar/gkt1120. Epub 2013 Nov 13.

29.

Effective blocking of the white enhancer requires cooperation between two main mechanisms suggested for the insulator function.

Kyrchanova O, Maksimenko O, Stakhov V, Ivlieva T, Parshikov A, Studitsky VM, Georgiev P.

PLoS Genet. 2013;9(7):e1003606. doi: 10.1371/journal.pgen.1003606. Epub 2013 Jul 4.

30.

Histone chaperone FACT action during transcription through chromatin by RNA polymerase II.

Hsieh FK, Kulaeva OI, Patel SS, Dyer PN, Luger K, Reinberg D, Studitsky VM.

Proc Natl Acad Sci U S A. 2013 May 7;110(19):7654-9. doi: 10.1073/pnas.1222198110. Epub 2013 Apr 22.

31.

Structural Analysis of the Key Intermediate Formed during Transcription through a Nucleosome.

Chang HW, Shaytan AK, Hsieh FK, Kulaeva OI, Kirpichnikov MP, Studitsky VM.

Trends Cell Mol Biol. 2013;8:13-23.

32.

Distant activation of transcription: mechanisms of enhancer action.

Kulaeva OI, Nizovtseva EV, Polikanov YS, Ulianov SV, Studitsky VM.

Mol Cell Biol. 2012 Dec;32(24):4892-7. doi: 10.1128/MCB.01127-12. Epub 2012 Oct 8. Review.

33.

Mechanism of transcription through a nucleosome by RNA polymerase II.

Kulaeva OI, Hsieh FK, Chang HW, Luse DS, Studitsky VM.

Biochim Biophys Acta. 2013 Jan;1829(1):76-83. doi: 10.1016/j.bbagrm.2012.08.015. Epub 2012 Sep 6. Review.

34.

Experimental analysis of the mechanism of chromatin remodeling by RNA polymerase II.

Gaykalova DA, Kulaeva OI, Pestov NA, Hsieh FK, Studitsky VM.

Methods Enzymol. 2012;512:293-314. doi: 10.1016/B978-0-12-391940-3.00013-5.

35.

Internucleosomal interactions mediated by histone tails allow distant communication in chromatin.

Kulaeva OI, Zheng G, Polikanov YS, Colasanti AV, Clauvelin N, Mukhopadhyay S, Sengupta AM, Studitsky VM, Olson WK.

J Biol Chem. 2012 Jun 8;287(24):20248-57. doi: 10.1074/jbc.M111.333104. Epub 2012 Apr 19.

36.

Theoretical analysis of the role of chromatin interactions in long-range action of enhancers and insulators.

Mukhopadhyay S, Schedl P, Studitsky VM, Sengupta AM.

Proc Natl Acad Sci U S A. 2011 Dec 13;108(50):19919-24. doi: 10.1073/pnas.1103845108. Epub 2011 Nov 28.

37.

FACT in Cell Differentiation and Carcinogenesis.

Hsieh FK, Kulaeva OI, Orlovsky IV, Studitsky VM.

Oncotarget. 2011 Nov;2(11):830-2. No abstract available.

38.

The mechanism of nucleosome traversal by RNA polymerase II: roles for template uncoiling and transcript elongation factors.

Luse DS, Studitsky VM.

RNA Biol. 2011 Jul-Aug;8(4):581-5. doi: 10.4161/rna.8.4.15389. Epub 2011 Jul 1.

39.

Mechanism of histone survival during transcription by RNA polymerase II.

Kulaeva OI, Studitsky VM.

Transcription. 2010 Sep-Oct;1(2):85-8. doi: 10.4161/trns.1.2.12519.

40.

A polar barrier to transcription can be circumvented by remodeler-induced nucleosome translocation.

Gaykalova DA, Nagarajavel V, Bondarenko VA, Bartholomew B, Clark DJ, Studitsky VM.

Nucleic Acids Res. 2011 May;39(9):3520-8. doi: 10.1093/nar/gkq1273. Epub 2011 Jan 17.

41.

Histone Sin mutations promote nucleosome traversal and histone displacement by RNA polymerase II.

Hsieh FK, Fisher M, Ujvári A, Studitsky VM, Luse DS.

EMBO Rep. 2010 Sep;11(9):705-10. doi: 10.1038/embor.2010.113. Epub 2010 Aug 13.

42.

RNA polymerase complexes cooperate to relieve the nucleosomal barrier and evict histones.

Kulaeva OI, Hsieh FK, Studitsky VM.

Proc Natl Acad Sci U S A. 2010 Jun 22;107(25):11325-30. doi: 10.1073/pnas.1001148107. Epub 2010 Jun 7.

43.

Mechanism of chromatin remodeling and recovery during passage of RNA polymerase II.

Kulaeva OI, Gaykalova DA, Pestov NA, Golovastov VV, Vassylyev DG, Artsimovitch I, Studitsky VM.

Nat Struct Mol Biol. 2009 Dec;16(12):1272-8. doi: 10.1038/nsmb.1689. Epub 2009 Nov 22.

44.

Using DNA mechanics to predict in vitro nucleosome positions and formation energies.

Morozov AV, Fortney K, Gaykalova DA, Studitsky VM, Widom J, Siggia ED.

Nucleic Acids Res. 2009 Aug;37(14):4707-22. doi: 10.1093/nar/gkp475. Epub 2009 Jun 9.

45.

Preparation and analysis of uniquely positioned mononucleosomes.

Gaykalova DA, Kulaeva OI, Bondarenko VA, Studitsky VM.

Methods Mol Biol. 2009;523:109-23. doi: 10.1007/978-1-59745-190-1_8.

46.

Analysis of distant communication on defined chromatin templates in vitro.

Polikanov YS, Studitsky VM.

Methods Mol Biol. 2009;543:563-76. doi: 10.1007/978-1-60327-015-1_33.

47.

Histone N-terminal tails interfere with nucleosome traversal by RNA polymerase II.

Ujvári A, Hsieh FK, Luse SW, Studitsky VM, Luse DS.

J Biol Chem. 2008 Nov 21;283(47):32236-43. doi: 10.1074/jbc.M806636200. Epub 2008 Sep 23.

48.

Probability of the site juxtaposition determines the rate of protein-mediated DNA looping.

Polikanov YS, Bondarenko VA, Tchernaenko V, Jiang YI, Lutter LC, Vologodskii A, Studitsky VM.

Biophys J. 2007 Oct 15;93(8):2726-31. Epub 2007 Jun 15.

49.

Transcription through chromatin by RNA polymerase II: histone displacement and exchange.

Kulaeva OI, Gaykalova DA, Studitsky VM.

Mutat Res. 2007 May 1;618(1-2):116-29. Epub 2007 Jan 21. Review.

50.

Biochemical analysis of enhancer-promoter communication in chromatin.

Polikanov YS, Rubtsov MA, Studitsky VM.

Methods. 2007 Mar;41(3):250-8. Review.

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