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Structural features based genome-wide characterization and prediction of nucleosome organization

Yanglan Gan, Jihong Guan, Shuigeng Zhou, Weixiong Zhang
2012 BMC Bioinformatics  
The results indicated that our proposed methods are effective in predicting nucleosome occupancy and positions and that these structural features are highly predictive of nucleosome organization.  ...  Here, taking a structural perspective, we systematically explored nucleosome formation potential of genomic sequences and the effect on chromatin organization and gene expression in S. cerevisiae.  ...  To determine the predictive power of different structural features, we validated our predicted nucleosome locations against the genome-wide nucleosome position map from Lee et al.  ... 
doi:10.1186/1471-2105-13-49 pmid:22449207 pmcid:PMC3378464 fatcat:h3gymb26vzdtnp7xmm5s567avi

Predicting nucleosome positioning in genomes: Physical and bioinformatic approaches

Anita Scipioni, Pasquale De Santis
2011 Biophysical Chemistry  
nucleosome organization.  ...  In this review we describe and compare bioinformatic and physical approaches adopted to predict nucleosome occupancy along genomes.  ...  from yeast and used these sequences in a new computational approach to construct and validate experimentally a nucleosome-DNA interaction model, and to predict the genome-wide organization of nucleosomes  ... 
doi:10.1016/j.bpc.2011.03.006 pmid:21482020 fatcat:ab3ph4xxzradjml2e6n3n6qj3a

Predicting Nucleosome Positioning Based on Geometrically Transformed Tsallis Entropy

Jing Wu, Yusen Zhang, Zengchao Mu, Junwen Wang
2014 PLoS ONE  
In this paper, based on the geometrically transformed Tsallis entropy and two index-vectors, a valid nucleosome positioning information model is developed to describe the distribution of A/T-riched and  ...  As the fundamental unit of eukaryotic chromatin structure, nucleosome plays critical roles in gene expression and regulation by controlling physical access to transcription factors.  ...  Acknowledgments The authors thank the anonymous referees and editor for their corrections and valuable comments.  ... 
doi:10.1371/journal.pone.0109395 pmid:25380134 pmcid:PMC4224380 fatcat:ruaxph7jcbbidjswalz56omkre

NUCOME: A comprehensive database of nucleosome organization referenced landscapes in mammalian genomes

Xiaolan Chen, Hui Yang, Guifen Liu, Yong Zhang
2021 BMC Bioinformatics  
The NUCOME database provides standardized, qualified data source and informative nucleosome organization features at a whole-genome scale and on the level of individual loci.  ...  However, studies integrating nucleosome organization in mammalian genomes are very limited mainly due to the lack of comprehensive data quality control (QC) assessment and uneven data quality of public  ...  Acknowledgements We thank Ji Liao for his contribution in the early stage of this project.  ... 
doi:10.1186/s12859-021-04239-9 pmid:34120586 fatcat:fxxuu4nq7bh7nbwg4mkepuveiq

Genome-Wide Prediction of Nucleosome Occupancy in Maize Reveals Plant Chromatin Structural Features at Genes and Other Elements at Multiple Scales

J. A. Fincher, D. L. Vera, D. D. Hughes, K. M. McGinnis, J. H. Dennis, H. W. Bass
2013 Plant Physiology  
The nucleosome is a fundamental structural and functional chromatin unit that affects nearly all DNA-templated events in eukaryotic genomes.  ...  To predict the nucleosome landscape of a model plant genome, we used a support vector machine computational algorithm trained on human chromatin to predict the nucleosome occupancy likelihood (NOL) across  ...  ACKNOWLEDGMENTS We thank Anne Thistle and members of the H.W. Bass, J.H. Dennis, and K.M. McGinnis laboratories for critique of the manuscript.  ... 
doi:10.1104/pp.113.216432 pmid:23572549 pmcid:PMC3668044 fatcat:vzgmvlcc4bb45ikprcy4ax6qty

Prediction of Nucleosome Positioning Based on Support Vector Machine

Jihua Feng, Jianping Xiao, Ying Lu, Qiufu Shan
2013 International Journal of Bioscience Biochemistry and Bioinformatics  
This widespread local rates heterogeneity represents an evolutionary footprint of nucleosome positions and reveals that nucleosome organization is a genomic feature conserved over evolutionary timescales  ...  potential of any given sequence of DNA, we observed that chromatin structure has an impact on the evolution of genomic DNA molecules.  ...  The authors are with Yunnan University of Nationalities, China (e-mail: fengjihua@21cn.com, 275939685@qq.com).  ... 
doi:10.7763/ijbbb.2013.v3.253 fatcat:wkganm7arzdedmvpr2b6phkvji

The effects of chromatin organization on variation in mutation rates in the genome

Kateryna D. Makova, Ross C. Hardison
2015 Nature reviews genetics  
Deciphering the molecular determinants of this variation will be aided by resolving distinct types of mutation, since they differ in regional preferences and in associations with genomic features.  ...  In both germ-line mutations and somatic mutations, base substitutions are more abundant in regions of closed chromatin, perhaps reflecting error accumulation late in replication.  ...  Of particular interest are topics on regional variation in mutation rates, mitochondrial mutations, microsatellites and genome stability, and mutations at sex chromosomes. Ross Hardison is the T.  ... 
doi:10.1038/nrg3890 pmid:25732611 pmcid:PMC4500049 fatcat:c5dxtkn2orh23e7mlyaecndoce

A genomic code for nucleosome positioning

Eran Segal, Yvonne Fondufe-Mittendorf, Lingyi Chen, AnnChristine Thåström, Yair Field, Irene K. Moore, Ji-Ping Z. Wang, Jonathan Widom
2006 Nature  
model, and to predict the genome-wide organization of nucleosomes.  ...  Our results demonstrate that genomes encode an intrinsic nucleosome organization and that this intrinsic organization can explain ,50% of the in vivo nucleosome positions.  ...  model, and to predict the genome-wide organization of nucleosomes.  ... 
doi:10.1038/nature04979 pmid:16862119 pmcid:PMC2623244 fatcat:coolobluerd5dftlwb2i4stdnu

Remodelers Organize Cellular Chromatin by Counteracting Intrinsic Histone-DNA Sequence Preferences in a Class-Specific Manner

Y. M. Moshkin, G. E. Chalkley, T. W. Kan, B. A. Reddy, Z. Ozgur, W. F. J. van Ijcken, D. H. W. Dekkers, J. A. Demmers, A. A. Travers, C. P. Verrijzer
2011 Molecular and Cellular Biology  
Remodelers influence nucleosome organization genome-wide, reflecting their high genomic density and the propagation of nucleosome redistribution beyond remodeler binding sites.  ...  Each remodeler has a unique set of genomic targets and generates distinct chromatin signatures. Remodeler loci have characteristic DNA sequence features, predicted to influence nucleosome formation.  ...  (B and C) Heatmaps of the correlations between experimentally determined chromatin structure and DNA sequence-derived predictions genome-wide.  ... 
doi:10.1128/mcb.06365-11 pmid:22124157 pmcid:PMC3266603 fatcat:udepbhfnnvalval5j6h4mceb4m

Protein–DNA binding in high-resolution

Shaun Mahony, B. Franklin Pugh
2015 Critical reviews in biochemistry and molecular biology  
In this review, we survey current experimental and computational methods that yield genome-wide protein-DNA occupancy profiles at single base-pair resolution.  ...  Recent advances in experimental and computational methodologies are enabling ultra-high resolution genome-wide profiles of protein-DNA binding events.  ...  With the advent of high-throughput sequencing technologies, MNase and DNase I have been used to profile genome-wide distributions of nucleosomes and nucleosome-depleted regions, respectively.  ... 
doi:10.3109/10409238.2015.1051505 pmid:26038153 pmcid:PMC4580520 fatcat:qygnojyg55ekfnej2nxsfvnkni

Contributions of Sequence to the Higher-Order Structures of DNA

Stefjord Todolli, Pamela J. Perez, Nicolas Clauvelin, Wilma K. Olson
2017 Biophysical Journal  
These features also determine the positions of nucleosomes on DNA and the lengths of the interspersed DNA linkers.  ...  The local sequence-dependent features of DNA found in high-resolution structures introduce irregularities in the disposition of adjacent residues that facilitate the specific binding of proteins and modulate  ...  ACKNOWLEDGMENTS We thank Pablo Dans Puiggròs and Modesto Orozco for sharing their statistical data, and Victor Zhurkin for valuable discussions.  ... 
doi:10.1016/j.bpj.2016.11.017 pmid:27955889 pmcid:PMC5300782 fatcat:p7544r7j7je33b7q3kzhaflfam

NUCOME: A Comprehensive Database of Nucleosome Organizations in Mammalian Genomes [article]

Xiaolan Chen, Hui Yang, Yong Zhang
2018 bioRxiv   pre-print
However, studies integrating nucleosome organizations in mammalian genomes are very limited mainly due to the lack of comprehensive data management.  ...  The NUCOME provides standard, qualified and informative nucleosome organization data at the genome scale and at any genomic regions for users' downstream analyses.  ...  The nucleosome organization maps focus on genome-wide nucleosome occupancy and the location of nucleosome arrays.  ... 
doi:10.1101/414094 fatcat:7oxdt4n7cngqvdxbmxtv7vsnze

CpGIMethPred: computational model for predicting methylation status of CpG islands in human genome

Hao Zheng, Hongwei Wu, Jinping Li, Shi-Wen Jiang
2013 BMC Medical Genomics  
Computational prediction of the DNA methylation status can be employed to speed up the genome-wide methylation profiling, and to identify the key features that are correlated with various methylation patterns  ...  Here, we develop CpGIMethPred, the support vector machine-based models to predict the methylation status of the CpG islands in the human genome under normal conditions.  ...  Nucleosome positioning propensities of the CpG islands are estimated based on the genome-wide prediction of the nucleosome organization map [27] .  ... 
doi:10.1186/1755-8794-6-s1-s13 pmid:23369266 pmcid:PMC3552668 fatcat:roidualckbdnlohpx6ojiqnzjy

DNA shape, genetic codes, and evolution

Stephen CJ Parker, Thomas D Tullius
2011 Current Opinion in Structural Biology  
Recent advances include the discovery of shape-dependent recognition of DNA that depends on minor groove width and electrostatics, the existence of overlapping codes in protein-coding regions of the genome  ...  , and evolutionary selection for compensatory changes in nucleotide composition that facilitate nucleosome occupancy.  ...  This work was supported by a grant to TDT from the National Human Genome Research Institute of the National Institutes of Health (R01 HG003541).  ... 
doi:10.1016/j.sbi.2011.03.002 pmid:21439813 pmcid:PMC3112471 fatcat:h3jzq4bqkjh2ldxxxjynvbtcra

DNA-Encoded Chromatin Structural Intron Boundary Signals Identify Conserved Genes with Common Function

Justin A. Fincher, Gary S. Tyson, Jonathan H. Dennis
2015 International Journal of Genomics  
We found that (i) NOL scores reveal a sequence-based feature at the introns on both sides of the intron-exon boundary; (ii) this feature is not part of any recognizable consensus sequence; (iii) this feature  ...  different genomic characteristics; (vi)in vivonucleosome positioning data confirm ontological enrichment at this feature; and (vii) genes with this feature exhibit unique dinucleotide distributions at  ...  We used predictions of nucleosome occupancy to characterize intron/ exon boundaries in five metazoan species and identified a cryptic sequence-based DNA property that is specific to a subset of fundamental  ... 
doi:10.1155/2015/167578 pmid:25861617 pmcid:PMC4377520 fatcat:pirqqxdy6rhl7j72nzey5e5rde
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