Learning a weighted sequence model of the nucleosome core and linker yields more accurate predictions in Saccharomyces cerevisiae and Homo sapiens.

PLoS Computational Biology
Sheila M ReynoldsWilliam Stafford Noble

Abstract

DNA in eukaryotes is packaged into a chromatin complex, the most basic element of which is the nucleosome. The precise positioning of the nucleosome cores allows for selective access to the DNA, and the mechanisms that control this positioning are important pieces of the gene expression puzzle. We describe a large-scale nucleosome pattern that jointly characterizes the nucleosome core and the adjacent linkers and is predominantly characterized by long-range oscillations in the mono, di- and tri-nucleotide content of the DNA sequence, and we show that this pattern can be used to predict nucleosome positions in both Homo sapiens and Saccharomyces cerevisiae more accurately than previously published methods. Surprisingly, in both H. sapiens and S. cerevisiae, the most informative individual features are the mono-nucleotide patterns, although the inclusion of di- and tri-nucleotide features results in improved performance. Our approach combines a much longer pattern than has been previously used to predict nucleosome positioning from sequence-301 base pairs, centered at the position to be scored-with a novel discriminative classification approach that selectively weights the contributions from each of the input features. The result...Continue Reading

References

Oct 20, 1986·Journal of Molecular Biology·S C SatchwellA A Travers
Jul 1, 1980·Proceedings of the National Academy of Sciences of the United States of America·E N Trifonov, J L Sussman
Apr 28, 1995·The Journal of Biological Chemistry·E W Englander, B H Howard
Sep 20, 1996·Journal of Molecular Biology·I IoshikhesE N Trifonov
Nov 5, 1999·The Journal of Biological Chemistry·H R WidlundM Kubista
Feb 13, 2002·Quarterly Reviews of Biophysics·J Widom
Jun 25, 2002·Journal of Molecular Biology·Curt A DaveyTimothy J Richmond
Mar 26, 2003·Nucleic Acids Research·Alexander E Vinogradov
Nov 25, 2003·Nature Structural Biology·Helen BermanHaruki Nakamura
Apr 22, 2004·Proceedings of the National Academy of Sciences of the United States of America·Rajeswari S EdayathumangalamKarolin Luger
Aug 12, 2005·Cytogenetic and Genome Research·J JurkaJ Walichiewicz
Sep 2, 2005·Genetica·Deepak GroverMitali Mukerji
Dec 13, 2005·Nucleic Acids Research·Ji-Ping Z Wang, Jonathan Widom
Apr 18, 2006·Proceedings of the National Academy of Sciences of the United States of America·Philip J J RobinsonDaniela Rhodes
Jul 25, 2006·Nature·Eran SegalJonathan Widom
Sep 12, 2006·Nature Genetics·Ilya P IoshikhesB Franklin Pugh
Jul 11, 2007·Genome Research·Heather E PeckhamZhiping Weng
Aug 31, 2007·BMC Bioinformatics·Aleksey Porollo, Jaroslaw Meller
Sep 18, 2007·Nature Genetics·William LeeCorey Nislow
Oct 19, 2007·Nucleic Acids Research·Hiroyuki WakaguriKenta Nakai
Jan 30, 2008·PLoS Computational Biology·Guo-Cheng Yuan, Jun S Liu
Feb 1, 2008·Journal of Molecular Biology·Rodolfo Ghirlando, Gary Felsenfeld
Mar 11, 2008·Cell·Dustin E SchonesKeji Zhao
Apr 22, 2008·Biophysical Journal·Thomas C Bishop
Jun 7, 2008·Journal of Biomolecular Structure & Dynamics·F SalihE N Trifonov
Jun 28, 2008·Proceedings of the National Academy of Sciences of the United States of America·Andrew RouthDaniela Rhodes
Aug 30, 2008·Genome Research·Peter V KharchenkoPeter J Park
Aug 30, 2008·PLoS Computational Biology·Shobhit GuptaWilliam Stafford Noble
Nov 8, 2008·PLoS Computational Biology·Yair FieldEran Segal
Dec 19, 2008·Nature·Noam KaplanEran Segal
Feb 12, 2009·Current Opinion in Structural Biology·Eran Segal, Jonathan Widom
Feb 28, 2009·Genome Research·Michael Y TolstorukovPeter J Park
Jul 22, 2009·Nature Structural & Molecular Biology·Yong ZhangKevin Struhl
Jul 30, 2009·Nature Genetics·Steven Henikoff
Aug 5, 2010·Nature Structural & Molecular Biology·Noam KaplanEran Segal

❮ Previous
Next ❯

Citations

Aug 1, 2014·PLoS Computational Biology·Sergey Hosid, Ilya Ioshikhes
Sep 10, 2011·Genome Research·James G D Prendergast, Colin A M Semple
Feb 26, 2013·Chromosome Research : an International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology·Yong-qiang XingLu Cai
Sep 25, 2015·Nucleic Acids Research·Hope A ColeDavid J Clark
Jul 31, 2016·BMC Genomics·Guénola DrillonAlain Arneodo
Nov 16, 2010·Epigenetics & Chromatin·Christoforos NikolaouRoderic Guigó
Jan 28, 2020·PLoS Computational Biology·Erinija PranckevicieneIlya Ioshikhes
Jan 8, 2015·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Vladimir B TeifKarsten Rippe

❮ Previous
Next ❯

Methods Mentioned

BETA
immunoprecipitation
ChIP-seq
ChIP

Software Mentioned

Solexa
PolyView
- 3D
NPS ( Nucleosome Position from Sequencing )
NPS
PyMol
RepeatMasker

Related Concepts

Related Feeds

Ataxia telangiectasia (MDS)

Ataxia telangiectasia is a rare neurodegenerative diseases caused by defects in the ATM gene, which is involved in DNA damage recognition and repair pathways. Here is the latest research on this autosomal recessive disease.