Publications

PUBLICATIONS

Cover pages of journals featuring figures of our publications (Highlighted below in the list)

Publications Cover - molecular systems biology Publications Cover - trends biochemical sciences Publications Cover - Molecular and Cellular Biology Publications Cover - biochemistry and cell biology

     We are strong proponents of the paradigm shift based on the functionality of intrinsically disordered protein regions operating at the near-noise level of interactions. This new framework requires a fundamental change of biochemical mentality.

     In 2003 and 2004 we proposed a novel mechanism of action for transcriptional activation domains functioning via promoter nucleosome distortion and triggering chromatin remodeling (updated in 2016). Our new data (2018) confirm this mechanism, which we further developed by introducing a new concept of “nucleosome detergents“.

See updated list of pubs here.

Major publications (full-size peer-reviwed research articles)

1. D. Pincus, J. Anandhakumar, P. Thiru, M. J. Guertin, A. M. Erkine, D. S Gross. Genetic and Epigenetic Determinants Establish a Continuum of Hsf1 Occupancy and Activity Across the Yeast Genome. Mol Biol Cell. 2018 Oct 17:mbcE18060353. doi: 10.1091/mbc.E18-06-0353. [Epub ahead of print]

2. A. M. Erkine “Nonlinear” biochemistry of nucleosome detergents. Trends in Biochem Sci. 2018 Dec;43(12):951-959

3. C. N. Ravarani, T.Y. Erkina, G. De Baets, D. C. Dudman, A. M. Erkine, M. M. Babu. High-throughput discovery of functional disordered regions: investigation of transactivation domains. Mol Syst Biol. 2018, 14(5):e8190. doi: 10.15252/msb.20188190.

4. T.Y. Erkina, A. M. Erkine. Nucleosome Distortion as a Possible Mechanism of Transcription Activation Domain Function. Epigenetics and Chromatin 2016, PMID: 27679670 PMCID: PMC5029090 DOI: 10.1186/s13072-016-0092-2.

5. T.Y. Erkina, A. M. Erkine. ASF1 and the SWI/SNF complex interact functionally during nucleosome displacement, while FACT is required for nucleosome reassembly at yeast heat shock gene promoters during sustained stress. Cell Stress and Chaperones 2015, 20(2):355-369.

6. L. M. Smith, D. Bhattacharya, D.J. Williams, I. Dixon, N.R. Powell, T.Y. Erkina, A.M. Erkine. High-throughput screening system for inhibitors of human Heat Shock Factor 2. Cell Stress and Chaperones 2015, 20(5):833-841.

7. T. Y. Erkina, A. M. Erkine. Detection of transcriptional activators, co-activators and chromatin remodeling by chromatin immuno-precipitation coupled with real-time PCR. 2012 Chapter in the book: Methods in Molecular Biology – Transcription regulation. Vol.809, pp.279-289.

8. T.Y. Erkina, Y. Zou, S. Freeling, V.I. Vorobyev, A. M. Erkine. Functional interplay between chromatin remodeling complexes SWI/SNF, ISWI, and RSC in regulation of yeast heat shock genes. 2010 Nucleic Acids Res. 38(5):1441-9.

9. T Y. Liu, S. Ye and A. M. Erkine. Analysis of Saccharomyces cerevisiae genome for the distributions of stress-response elements potentially affecting gene expression by transcriptional interference. 2009 In Silico Biology, 9, 0030.

10. T. Y. Erkina, M. V. Lavrova, A. M. Erkine. Alternative ways of stress regulation in cells of S. cerevisiae: transcription activators Msn2 and Msn4. 2009 Cell and Tissue Biology 51(2):121-129.

11. T. Y. Erkina, P. A. Tschetter, A. M. Erkine. 2008. Different requirement of SWI/SNF complex for the robust nucleosome displacement at promoters of HSF and Msn2/4 regulated heat shock genes. Mol. Cell. Biol. 28(4):1207-1217.

12. A. M. Erkina, A. M. Erkine. 2006. Displacement of histones at promoters of yeast heat shock genes is differentially associated with histone H3 acetylation. Mol. Cell. Biol. 26(20):7587-600. Summary figure used as a cover art for MCB v.26(20).

13. H. Singh, A. M. Erkine, S. B. Kremer, H. M. Duttweiler, D. A. Davis, J. Iqbal, R. R. Gross, D. S. Gross. 2006. A functional module of yeast mediator that governs the dynamic range of heat-shock gene expression. Genetics. 172(4):2169-84.

14. A. M. Erkine. 2004. Activation domains of gene-specific transcription factors: are histones among their targets? Biochem. Cell Biol. 82: 453-459. (Made a front cover of the issue 4 of the journal).

15. A. M. Erkine and D. S. Gross 2003. Dynamic chromatin remodeling triggered by natural and synthetic activation domains. J. Biol. Chem. 278: 7755-64.

16. C. B. Bourgeois-Venturi, A. M. Erkine and D. S. Gross. 2000. Cell Cycle-Dependent Binding of Yeast Heat Shock Factor to Nucleosomes. Mol. Cell. Biol. 20: 6435-6448.

17. Raitt, A. L. Johnson, A. M. Erkine, K. Makino, B. Morgan, D. S. Gross, L. H. Johnston. 2000. The Skn7 response regulator of Saccharomyces cerevisiae interacts with Hsf1 in vivo and is required for the induction of heat shock genes by oxidative stress. Mol. Biol. Cell 11: 2335-2347.

18. A. M. Erkine, S. F. Magrogan, E. A. Sekinger, D. S. Gross. 1999. Cooperative binding of heat shock factor to the yeast HSP82 promoter in vivo and in vitro. Mol. Cell. Biol. 19: 1627-1639.

19. Y. Lee, W. M. Wong, D. Gayer, A. M. Erkine, R. N. Nazar. 1997. In vivo analyses of upstream promoter sequence elements in the 5S rRNA gene from Saccharomyces cerevisiae. J. Mol. Biol. 269: 676-683.

20. A. M. Erkine, C. C. Adams, T. Diken, D. S. Gross. 1996. Heat shock factor gains access to the yeast HSC82 promoter independently of other sequence-specific factors and antagonizes nucleosomal repression of basal and induced transcription. Mol. Cell. Biol. 16: 7004-7017.

21. A. M. Erkine, C. C. Adams, M. Gao, D. S. Gross. 1995. Multiple protein-DNA interactions over the yeast HSC82 heat shock gene promoter. Nucleic Acids Res. 23: 1822-1829.

22. A. M. Erkine, C.Szent-Gyorgyi, S. F. Simmons, D. S. Gross. 1995. The upstream sequences of the HSP82 and HSC82 genes of Saccharomyces cerevisiae: regulatory elements and nucleosome positioning motifs. Yeast 11: 573-580.

23. Y. Lee, A. M. Erkine, D. I. Van Ryk, R. N. Nazar.1995. In vivo analyses of the internal control region in the 5S rRNA gene from Saccharomyces cerevisiae. Nucleic Acids Res. 23: 634-640.

24. M. A. Karymov, A. A. Kruchinin, Yu. A. Tarantov, I. A. Balova, L. A. Remisova, N. G. Sukhodolov, A. I. Yanklovich, A. M. Erkine *(Yorkin). 1992. Legmuir-Blodgett film based membrane for a DNA-probe biosensor. Sensors and Actuators B. 6: 208-210.

25. A. M. Erkine *(Erkin). 1992. Characterization of chromatin fibers immobilized on a polycationic surface. Biochemistry (Russ.) 57: 312-316.

26. A. M. Erkine *(Erkin). 1987. Localization of lysine-rich histones and linker DNA in the higher-order chromatin structure. Leningrad State University, PhD thesis.

27. A. M. Erkine *(Erkin). 1987. Chromatin on the membrane: analysis of histone H5 accessibility for antibodies in the higher order chromatin structure. Mol. Biol. (Russ.) 21: 688-695.

28. A. M. Erkine *(Erkin), L. G. Vodopyanova, A. A. Lipskaya, A. V. Kozlov. 1987. Some peculiarities of histone H5 limited tripsinolysis in solution and as a component of chromatin with different levels of compactization. Biochemistry (Russ.) 52: 396-404.

29. A. M. Erkine *(Erkin). 1986. DNA protection from DNase I action by supernucleosomal chromatin structure. Bulletin of Leningrad State University 3: 78-83.

30. M. I. Mosevitski, A. M. Erkine *(Erkin). 1982. About the distribution specificity of modification forms and histone subfractions in chromatin. Rep.Acad.Sci.USSR 262: 1510-1513.

31. V. A. Pospelov, A. M. Erkine *(Erkin), A. T. Khachatrian. 1981. H1 and H5 histone arrangement in chromatin of pigeon erythrocytes. FEBS Lett. 128: 315-317.

* In parenthesis is the alternative spelling of the last name due to an inconsistency of transliteration regulations in Russia during different time periods.