Literature DB >> 20232930

Nucleosome positioning by sequence, state of the art and apparent finale.

Edward N Trifonov1.   

Abstract

All major suggestions about the nucleosome positioning sequence pattern(s) are overviewed. Two basic binary periodical patterns are well established: in purine/pyrimidine alphabet - YRRRRRYYYYYR and in strong/weak alphabet -SWWWWWSSSSSW. Their merger in four-letter alphabet sequence coincides with first ever complete matrix of nucleosome DNA bendability derived from very large database of nucleosome DNA sequences. Its simplified linear form is CGGAAATTTCCG. Several independent ways of derivation of the same pattern are described. It appears that the pattern represents an ultimate solution of long-standing problem of nucleosome positioning, and provides simple means for nucleosome mapping on sequences with single-base resolution.

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Year:  2010        PMID： 20232930     DOI： 10.1080/073911010010524944

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


  8 in total

1.  A lattice model for transcription factor access to nucleosomal DNA.

Authors:  Vladimir B Teif; Ramona Ettig; Karsten Rippe
Journal:  Biophys J       Date:  2010-10-20       Impact factor: 4.033

2.  Variety of genomic DNA patterns for nucleosome positioning.

Authors:  Ilya Ioshikhes; Sergey Hosid; B Franklin Pugh
Journal:  Genome Res       Date:  2011-07-12       Impact factor: 9.043

3.  Impact of methylation on the physical properties of DNA.

Authors:  Alberto Pérez; Chiara Lara Castellazzi; Federica Battistini; Kathryn Collinet; Oscar Flores; Ozgen Deniz; Maria Luz Ruiz; David Torrents; Ramon Eritja; Montserrat Soler-López; Modesto Orozco
Journal:  Biophys J       Date:  2012-05-02       Impact factor: 4.033

4.  Galaxy Dnpatterntools for Computational Analysis of Nucleosome Positioning Sequence Patterns.

Authors:  Erinija Pranckeviciene; Sergey Hosid; Indiras Maziukas; Ilya Ioshikhes
Journal:  Int J Mol Sci       Date:  2022-04-28       Impact factor: 6.208

5.  The influence of DNA sequence on epigenome-induced pathologies.

Authors:  Richard B Meagher; Kristofer J Müssar
Journal:  Epigenetics Chromatin       Date:  2012-07-20       Impact factor: 4.954

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

Authors:  Ozgen Deniz; Oscar Flores; Federica Battistini; Alberto Pérez; Montserrat Soler-López; Modesto Orozco
Journal:  BMC Genomics       Date:  2011-10-07       Impact factor: 3.969

Review 7.  Thirty years of multiple sequence codes.

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

8.  Periodic distribution of a putative nucleosome positioning motif in human, nonhuman primates, and archaea: mutual information analysis.

Authors:  Daniela Sosa; Pedro Miramontes; Wentian Li; Víctor Mireles; Juan R Bobadilla; Marco V José
Journal:  Int J Genomics       Date:  2013-06-10       Impact factor: 2.326
  8 in total

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