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

Analysis of the mechanism of nucleosome survival during transcription.

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Department of Biochemistry and Molecular Biology, UMDNJ-Robert Wood Johnson Medical School, 675 Hoes Lane, Piscataway, NJ 08854, USA, School of Biology, Lomonosov Moscow State University, 119991 Leninskie gori, MSU, Bldg. 1, korpus 12, Moscow, Russia, Waksman Institute of Microbiology, Rutgers, the State University of New Jersey, 190 Frelinghuysen Road, Piscataway, NJ 08854, USA, Institute of Gene Biology, Russian Academy of Sciences, 1190334 34/5 Vavilova street, Moscow, Russia and Program in Genomics of Differentiation, National Institute of Child Health and Human Development, National Institutes of Health, PO Box 3006, Rockville, MD 20847, USA.


Maintenance of nucleosomal structure in the cell nuclei is essential for cell viability, regulation of gene expression and normal aging. Our previous data identified a key intermediate (a small intranucleosomal DNA loop, Ø-loop) that is likely required for nucleosome survival during transcription by RNA polymerase II (Pol II) through chromatin, and suggested that strong nucleosomal pausing guarantees efficient nucleosome survival. To evaluate these predictions, we analysed transcription through a nucleosome by different, structurally related RNA polymerases and mutant yeast Pol II having different histone-interacting surfaces that presumably stabilize the Ø-loop. The height of the nucleosomal barrier to transcription and efficiency of nucleosome survival correlate with the net negative charges of the histone-interacting surfaces. Molecular modeling and analysis of Pol II-nucleosome intermediates by DNase I footprinting suggest that efficient Ø-loop formation and nucleosome survival are mediated by electrostatic interactions between the largest subunit of Pol II and core histones.

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