NDLI: Toward a unified physical model of nucleosome patterns flanking transcription start sites

Content Provider	PubMed Central
Author	Möbius, Wolfram Osberg, Brendan Tsankov, Alexander M. Rando, Oliver J. Gerland, Ulrich
Abstract	Recent genome-wide maps of nucleosome positions in different eukaryotes revealed patterns around transcription start sites featuring a nucleosome-free region flanked by a periodic modulation of the nucleosome density. For Saccharomyces cerevisiae, the average in vivo pattern was previously shown to be quantitatively described by a “nucleosome gas” model based on the statistical positioning mechanism. However, this simple physical description is challenged by the fact that the pattern differs quantitatively between species and by recent experiments that appear incompatible with statistical positioning, indicating important roles for chromatin remodelers. We undertake a data-driven search for a unified physical model to describe the nucleosome patterns of 12 yeast species and also consider an extension of the model to capture remodeling effects. We are led to a nucleosome gas that takes into account nucleosome breathing, i.e., transient unwrapping of nucleosomal DNA segments. This known biophysical property of nucleosomes rationalizes a “pressure”-induced dependence of the effective nucleosome size that is suggested by the data. By fitting this model to the data, we find an average energy cost for DNA unwrapping consistent with previous biophysical experiments. Although the available data are not sufficient to reconstruct chromatin remodeling mechanisms, a minimal model extension by one mechanism yields an “active nucleosome gas” that can rationalize the behavior of systems with reduced histone–DNA ratio and remodeler knockouts. We therefore establish a basis for a physical description of nucleosome patterns that can serve as a null model for sequence-specific effects at individual genes and in models of transcription regulation.
Related Links	http://dx.doi.org/10.1073/pnas.1214048110
Ending Page	5724
Page Count	6
Starting Page	5719
File Format	PDF
ISSN	00278424
e-ISSN	10916490
Journal	Proceedings of the National Academy of Sciences of the United States of America
Issue Number	14
Volume Number	110
Language	English
Publisher	National Academy of Sciences
Publisher Date	2013-04-02
Access Restriction	Open
Rights Holder	National Academy of Sciences
Subject Keyword	General Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Multidisciplinary

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Toward a unified physical model of nucleosome patterns flanking transcription start sites.

DNA Methylation Patterns Facilitate the Identification of MicroRNA Transcription Start Sites: A Brain-Specific Study

Physical properties of naked DNA influence nucleosome positioning and correlate with transcription start and termination sites in yeast

ARGONAUTE2 cooperates with SWI/SNF complex to determine nucleosome occupancy at human Transcription Start Sites

Histone H3.5 forms an unstable nucleosome and accumulates around transcription start sites in human testis

Prediction of Nucleosome Positioning Based on Transcription Factor Binding Sites

Exploration of nucleosome positioning patterns in transcription factor function

Distinct localization of histone H3 acetylation and H3-K4 methylation to the transcription start sites in the human genome

Nucleosome-mediated cooperativity between transcription factors

Toward a unified physical model of nucleosome patterns flanking transcription start sites

Similar Documents

Toward a unified physical model of nucleosome patterns flanking transcription start sites.

DNA Methylation Patterns Facilitate the Identification of MicroRNA Transcription Start Sites: A Brain-Specific Study

Physical properties of naked DNA influence nucleosome positioning and correlate with transcription start and termination sites in yeast

ARGONAUTE2 cooperates with SWI/SNF complex to determine nucleosome occupancy at human Transcription Start Sites

Histone H3.5 forms an unstable nucleosome and accumulates around transcription start sites in human testis

Prediction of Nucleosome Positioning Based on Transcription Factor Binding Sites

Exploration of nucleosome positioning patterns in transcription factor function

Distinct localization of histone H3 acetylation and H3-K4 methylation to the transcription start sites in the human genome

Nucleosome-mediated cooperativity between transcription factors

Toward a unified physical model of nucleosome patterns flanking transcription start sites