Albany 2009: Conversation 16
June 16-20 2009
© Adenine Press (2008)
A Spring 2010 Issue
Current Perspectives on Nucleosome Positioning
Journal of Biomolecular Structure & Dynamics, Volume 27, Issue #6, June 2010
As Editor-in-Chief, I am delighted that in the Spring of 2010 we will be coming out with a regular issue of JBSD dealing exclusively with the diverse thoughts and perspectives on the hot topic of nucleosome positioning. The positioning of nucleosomes on DNA controls the ability of the cellular machinery to access genetic messages. Generally, the messages become silent when and where the DNA wraps around the histones to form stable nucleosomes, and active when nucleosomes reposition by dynamically and reversibly sliding over the DNA. It is thought that enzymes and cofactors are recruited to regulate gene expression by modifying the DNA and histones via nucleosome repositioning. Correctly predicting the positioning of the nucleosome is accordingly linked to the 'activity' of the cell. Nucleosome positioning is driven primarily by sequence-dependent physicochemical properties of DNA (deformable versus 'rigid' sequences) and electrostatic interactions between the negatively charged DNA and the positively charged histone proteins (differences in charge build-up on AT-rich versus GC-rich sequences). The details of this sequence dependence are not known with any certainity, and leading laboratories in the world significantly disagree how genetic message is accessed and silenced.
In the twelve articles in this issue of JBSD, to be released in the spring of 2010, the scientists working in the area present their perspectives on the subject. Below are the title of the articles, their authors and affiliation.
Ramaswamy H. Sarma
Interested in obtaining a copy of this issue of JBSD devoted to Perspectives in Nucleosome Positioning?
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The DNA Sequence-Dependence of Nucleosome Positioning in vivo and in vitro
Andrew Travers, Edwige Hiriart, Mark Churcher, Micaela Caserta and Ernesto di Mauro
MRC Lab. of Molecular Biology, Cambridge UK; Fondation Pierre-Gilles de Gennes, Cachan, France; Univ. La Sapienza, Rome, Italy.
DNA Architecture, Deformability, and Nucleosome Positioning
Fei Xu and Wilma K. Olson
Rutgers, the State University of New Jersey, Piscataway NJ.
Nucleosome Positioning by Sequence, State of the Art and Apparent Finale
University of Haifa, Haifa, Israel.
Prediction of Nucleosome Positioning in Genomes: Limits and Perspectives of Physical and Bioinformatic Approaches
Pasquale De Santis, Stefano Morosetti and Anita Scipioni
University of Rome 'La Sapienza', Rome, Italy.
The Molecular Evolution of Nucleosome Positioning Through Sequence-Dependent Deformation of the DNA Polymer
Gregory A. Babbitt, Michael Y. Tolstorukov, and Yuseob Kim
Arizona State University; Tempe AZ; Harvard Medical School, Boston MA; Brigham and Women's Hospital, Boston MA.
Nucleosome Positioning, Nucleosome Spacing and the Nucleosome Code
David J. Clark
National Institutes of Health, Bethesda MD.
Painting a Perspective on the Landscape of Nucleosome Positioning
Steven M. Johnson
Brigham Young University, Provo, UT.
A Structural Perspective on Where, How, What, and Why of Nucleosome Positioning
Gaurav Arya Arijit Maitra, and Sergei Grigoryev
University of California at San Diego, La Jolla CA; Penn State University School of Medicine, Hershey, PA.
Structure-based Analysis of DNA Sequence Patterns Guiding Nucleosome Positioning in vitro
Feng Cui and Victor B. Zhurkin
National Institutes of Health, Bethesda MD.
Sequence-dependent ‘Kink-and-Slide’ Deformations of Nucleosomal DNA Facilitated by Histone Arginines Bound in the Minor Groove
Difei Wang, Nikolai B. Ulyanov and Victor B. Zhurkin
National Institutes of Health, Bethesda MD; University of California at San Francisco,CA.
Electrostatic Interactions between Arginines and the Minor Groove in the Nucleosome
Sean M. West, Remo Rohs , Richard S. Mann, and Barry Honig
Columbia University, 1130 St. Nicholas Avenue, New York NY.
Evaluation of Elastic Rod Models with Long Range Interactions for Predicting Nucleosome Stability
Yuriy Sereda and Thomas C Bishop
Tulane University, New Orleans LA.
This issue is part of the subscription to the Journal. However hardcopies can be purchased for institutional use, personal use or by authors and co-authors by paying the appropriate cost listed in the Online Order Form. The senior author of an article will receive a complimentary copy and additional copies can be purchased at the highly discounted price shown in the Online Order Form .
The book is expected to be ready to be shipped by early April 2010.