Literature DB >> 20476799

Single-base resolution nucleosome mapping on DNA sequences.

I Gabdank1, D Barash, E N Trifonov.   

Abstract

Nucleosome DNA bendability pattern extracted from large nucleosome DNA database of C. elegans is used for construction of full length (116 dinucleotide positions) nucleosome DNA bendability matrix. The matrix can be used for sequence-directed mapping of the nucleosomes on the sequences. Several alternative positions for a given nucleosome are typically predicted, separated by multiples of nucleosome DNA period. The corresponding computer program is successfully tested on best known experimental examples of accurately positioned nucleosomes. The uncertainty of the computational mapping is +/-1 base. The procedure is placed on publicly accessible server and can be applied to any DNA sequence of interest.

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Year:  2010        PMID： 20476799     DOI： 10.1080/07391102.2010.10507347

Source DB:  PubMed          Journal:  J Biomol Struct Dyn        ISSN： 0739-1102


  10 in total

1.  Calculation of nucleosomal DNA deformation energy: its implication for nucleosome positioning.

Authors:  Jian-Ying Wang; Jingyan Wang; Guoqing Liu
Journal:  Chromosome Res       Date:  2012-12-05       Impact factor: 5.239

2.  Sequence determinants of histone-DNA binding preferences: comment on "Cracking the chromatin code: precise rule of nucleosome positioning" by Edward N. Trifonov.

Authors:  Alexandre V Morozov
Journal:  Phys Life Rev       Date:  2011-02-02       Impact factor: 11.025

3.  Nucleosome DNA sequence structure of isochores.

Authors:  Zakharia M Frenkel; Thomas Bettecken; Edward N Trifonov
Journal:  BMC Genomics       Date:  2011-04-21       Impact factor: 3.969

4.  Human nucleosomes: special role of CG dinucleotides and Alu-nucleosomes.

Authors:  Thomas Bettecken; Zakharia M Frenkel; Edward N Trifonov
Journal:  BMC Genomics       Date:  2011-05-31       Impact factor: 3.969

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

Authors:  Yanglan Gan; Jihong Guan; Shuigeng Zhou; Weixiong Zhang
Journal:  BMC Bioinformatics       Date:  2012-03-26       Impact factor: 3.169

6.  A deformation energy-based model for predicting nucleosome dyads and occupancy.

Authors:  Guoqing Liu; Yongqiang Xing; Hongyu Zhao; Jianying Wang; Yu Shang; Lu Cai
Journal:  Sci Rep       Date:  2016-04-07       Impact factor: 4.379

Review 7.  Thirty years of multiple sequence codes.

Authors:  Edward N Trifonov
Journal:  Genomics Proteomics Bioinformatics       Date:  2011-04       Impact factor: 7.691

8.  A deformation energy model reveals sequence-dependent property of nucleosome positioning.

Authors:  Guoqing Liu; Hongyu Zhao; Hu Meng; Yongqiang Xing; Lu Cai
Journal:  Chromosoma       Date:  2021-01-16       Impact factor: 4.316

9.  Apoptotic lymphocytes of H. sapiens lose nucleosomes in GC-rich promoters.

Authors:  Sergey Hosid; Ilya Ioshikhes
Journal:  PLoS Comput Biol       Date:  2014-07-31       Impact factor: 4.475

10.  The implication of DNA bending energy for nucleosome positioning and sliding.

Authors:  Guoqing Liu; Yongqiang Xing; Hongyu Zhao; Lu Cai; Jianying Wang
Journal:  Sci Rep       Date:  2018-06-11       Impact factor: 4.379
  10 in total

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