Literature DB >> 12855475

Skew in CG content near the transcription start site in Arabidopsis thaliana.

Tatiana Tatarinova1, Vyacheslav Brover, Maxim Troukhan, Nickolai Alexandrov.   

Abstract

We have discovered a novel statistical feature of Arabidopsis thaliana genome that remarkably correlates with a position of transcription start site--CG skew peak. We hypothesize that the phenomenon can be explained by the higher mutability of unprotected cytosines.

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Year:  2003        PMID： 12855475     DOI： 10.1093/bioinformatics/btg1043

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  20 in total

1.  Looking for organization patterns of highly expressed genes: purine-pyrimidine composition of precursor mRNAs.

Authors:  A Paz; D Mester; E Nevo; A Korol
Journal:  J Mol Evol       Date:  2007-01-08       Impact factor: 2.395

2.  Synonymous codon usage, GC(3), and evolutionary patterns across plastomes of three pooid model species: emerging grass genome models for monocots.

Authors:  Gaurav Sablok; Kinshuk Chandra Nayak; Franck Vazquez; Tatiana V Tatarinova
Journal:  Mol Biotechnol       Date:  2011-10       Impact factor: 2.695

3.  Seqping: gene prediction pipeline for plant genomes using self-training gene models and transcriptomic data.

Authors:  Kuang-Lim Chan; Rozana Rosli; Tatiana V Tatarinova; Michael Hogan; Mohd Firdaus-Raih; Eng-Ti Leslie Low
Journal:  BMC Bioinformatics       Date:  2017-01-27       Impact factor: 3.169

4.  Agrobacterium T-DNA integration in Arabidopsis is correlated with DNA sequence compositions that occur frequently in gene promoter regions.

Authors:  Richard G Schneeberger; Ke Zhang; Tatiana Tatarinova; Max Troukhan; Shing F Kwok; Josh Drais; Kevin Klinger; Francis Orejudos; Kimberly Macy; Amit Bhakta; James Burns; Gopal Subramanian; Jonathan Donson; Richard Flavell; Kenneth A Feldmann
Journal:  Funct Integr Genomics       Date:  2005-03-03       Impact factor: 3.410

5.  GC3 biology in corn, rice, sorghum and other grasses.

Authors:  Tatiana V Tatarinova; Nickolai N Alexandrov; John B Bouck; Kenneth A Feldmann
Journal:  BMC Genomics       Date:  2010-05-16       Impact factor: 3.969

6.  A general model of codon bias due to GC mutational bias.

Authors:  Gareth A Palidwor; Theodore J Perkins; Xuhua Xia
Journal:  PLoS One       Date:  2010-10-27       Impact factor: 3.240

7.  Insights into corn genes derived from large-scale cDNA sequencing.

Authors:  Nickolai N Alexandrov; Vyacheslav V Brover; Stanislav Freidin; Maxim E Troukhan; Tatiana V Tatarinova; Hongyu Zhang; Timothy J Swaller; Yu-Ping Lu; John Bouck; Richard B Flavell; Kenneth A Feldmann
Journal:  Plant Mol Biol       Date:  2008-10-21       Impact factor: 4.076

8.  Opposite GC skews at the 5' and 3' ends of genes in unicellular fungi.

Authors:  Malcolm A McLean; Itay Tirosh
Journal:  BMC Genomics       Date:  2011-12-30       Impact factor: 3.969

9.  Eukaryotic genomes may exhibit up to 10 generic classes of gene promoters.

Authors:  Paul Gagniuc; Constantin Ionescu-Tirgoviste
Journal:  BMC Genomics       Date:  2012-09-28       Impact factor: 3.969

10.  Incidence of genome structure, DNA asymmetry, and cell physiology on T-DNA integration in chromosomes of the phytopathogenic fungus Leptosphaeria maculans.

Authors:  Salim Bourras; Michel Meyer; Jonathan Grandaubert; Nicolas Lapalu; Isabelle Fudal; Juliette Linglin; Benedicte Ollivier; Françoise Blaise; Marie-Hélène Balesdent; Thierry Rouxel
Journal:  G3 (Bethesda)       Date:  2012-08-01       Impact factor: 3.154
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