Strand bias structure in mouse DNA gives a glimpse of how chromatin structure affects gene expression.


BACKGROUND:On a single strand of genomic DNA the number of As is usually about equal to the number of Ts (and similarly for Gs and Cs), but deviations have been noted for transcribed regions and origins of replication. RESULTS:The mouse genome is shown to have a segmented structure defined by strand bias. Transcription is known to cause a strand bias and numerous analyses are presented to show that the strand bias in question is not caused by transcription. However, these strand bias segments influence the position of genes and their unspliced length. The position of genes within the strand bias structure affects the probability that a gene is switched on and its expression level. Transcription has a highly directional flow within this structure and the peak volume of transcription is around 20 kb from the A-rich/T-rich segment boundary on the T-rich side, directed away from the boundary. The A-rich/T-rich boundaries are SATB1 binding regions, whereas the T-rich/A-rich boundary regions are not. CONCLUSION:The direct cause of the strand bias structure may be DNA replication. The strand bias segments represent a further biological feature, the chromatin structure, which in turn influences the ease of transcription.


BMC Genomics


BMC genomics


Evans KJ




Has Abstract


2008-01-14 00:00:00










  • Gene duplications in the E. coli genome: common themes among pathotypes.

    abstract:BACKGROUND:Gene duplication underlies a significant proportion of gene functional diversity and genome complexity in both eukaryotes and prokaryotes. Although several reports in the literature described the duplication of specific genes in E. coli, a detailed analysis of the extent of gene duplications in this microorg...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Bernabeu M,Sánchez-Herrero JF,Huedo P,Prieto A,Hüttener M,Rozas J,Juárez A

    更新日期:2019-04-24 00:00:00

  • Genome-wide analysis of the WRKY gene family and their positive responses to phytoplasma invasion in Chinese jujube.

    abstract:BACKGROUND:The WRKY gene family is one of the most important families in higher plants. As transcription factors, they actively respond to biotic and abiotic stress and are also involved in plant development. Chinese jujube (Ziziphus jujuba Mill.) is the largest type of dried fruit tree in China in terms of production,...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Xue C,Li H,Liu Z,Wang L,Zhao Y,Wei X,Fang H,Liu M,Zhao J

    更新日期:2019-06-07 00:00:00

  • Blood transcriptomics of drug-naïve sporadic Parkinson's disease patients.

    abstract:BACKGROUND:Parkinson's disease (PD) is a chronic progressive neurodegenerative disorder that is clinically defined in terms of motor symptoms. These are preceded by prodromal non-motor manifestations that prove the systemic nature of the disease. Identifying genes and pathways altered in living patients provide new inf...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Calligaris R,Banica M,Roncaglia P,Robotti E,Finaurini S,Vlachouli C,Antonutti L,Iorio F,Carissimo A,Cattaruzza T,Ceiner A,Lazarevic D,Cucca A,Pangher N,Marengo E,di Bernardo D,Pizzolato G,Gustincich S

    更新日期:2015-10-28 00:00:00

  • XCAVATOR: accurate detection and genotyping of copy number variants from second and third generation whole-genome sequencing experiments.

    abstract:BACKGROUND:We developed a novel software package, XCAVATOR, for the identification of genomic regions involved in copy number variants/alterations (CNVs/CNAs) from short and long reads whole-genome sequencing experiments. RESULTS:By using simulated and real datasets we showed that our tool, based on read count approac...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Magi A,Pippucci T,Sidore C

    更新日期:2017-09-21 00:00:00

  • Analysis of the SOS response of Vibrio and other bacteria with multiple chromosomes.

    abstract:BACKGROUND:The SOS response is a well-known regulatory network present in most bacteria and aimed at addressing DNA damage. It has also been linked extensively to stress-induced mutagenesis, virulence and the emergence and dissemination of antibiotic resistance determinants. Recently, the SOS response has been shown to...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Sanchez-Alberola N,Campoy S,Barbé J,Erill I

    更新日期:2012-02-03 00:00:00

  • Identification of three extra-chromosomal replicons in Leptospira pathogenic strain and development of new shuttle vectors.

    abstract:BACKGROUND:The genome of pathogenic Leptospira interrogans contains two chromosomes. Plasmids and prophages are known to play specific roles in gene transfer in bacteria and can potentially serve as efficient genetic tools in these organisms. Although plasmids and prophage remnants have recently been reported in Leptos...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Zhu W,Wang J,Zhu Y,Tang B,Zhang Y,He P,Zhang Y,Liu B,Guo X,Zhao G,Qin J

    更新日期:2015-02-15 00:00:00

  • Effect of CAR activation on selected metabolic pathways in normal and hyperlipidemic mouse livers.

    abstract:BACKGROUND:Detoxification in the liver involves activation of nuclear receptors, such as the constitutive androstane receptor (CAR), which regulate downstream genes of xenobiotic metabolism. Frequently, the metabolism of endobiotics is also modulated, resulting in potentially harmful effects. We therefore used 1,4-Bis ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Rezen T,Tamasi V,Lövgren-Sandblom A,Björkhem I,Meyer UA,Rozman D

    更新日期:2009-08-19 00:00:00

  • ArachnoServer: a database of protein toxins from spiders.

    abstract:BACKGROUND:Venomous animals incapacitate their prey using complex venoms that can contain hundreds of unique protein toxins. The realisation that many of these toxins may have pharmaceutical and insecticidal potential due to their remarkable potency and selectivity against target receptors has led to an explosion in th...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Wood DL,Miljenović T,Cai S,Raven RJ,Kaas Q,Escoubas P,Herzig V,Wilson D,King GF

    更新日期:2009-08-13 00:00:00

  • A physical map of human Alu repeats cleavage by restriction endonucleases.

    abstract:BACKGROUND:Alu repetitive elements are the abundant sequences in human genome. Diversity of DNA sequences of these elements makes difficult the construction of theoretical patterns of Alu repeats cleavage by restriction endonucleases. We have proposed a method of restriction analysis of Alu repeats sequences in silico....

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Abdurashitov MA,Tomilov VN,Chernukhin VA,Degtyarev SKh

    更新日期:2008-06-26 00:00:00

  • Introduction to the proceedings of the Avian Genomics and Gene Ontology Annotation Workshop.

    abstract::The Avian Genomics Conference and Gene Ontology Annotation Workshop brought together researchers and students from around the world to present their latest research addressing the delivery of value from the billions of base-pairs of Archosaur sequence that have become available in the last few years. This editorial de...

    journal_title:BMC genomics



    authors: Bridges SM,Burgess SC,McCarthy FM

    更新日期:2009-07-14 00:00:00

  • Markedly different genome arrangements between serotype a strains and serotypes b or c strains of Aggregatibacter actinomycetemcomitans.

    abstract:BACKGROUND:Bacterial phenotype may be profoundly affected by the physical arrangement of their genes in the genome. The Gram-negative species Aggregatibacter actinomycetemcomitans is a major etiologic agent of human periodontitis. Individual clonal types of A. actinomycetemcomitans may exhibit variable virulence and di...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Kittichotirat W,Bumgarner R,Chen C

    更新日期:2010-09-08 00:00:00

  • Genome-wide association mapping of resistance to a Brazilian isolate of Sclerotinia sclerotiorum in soybean genotypes mostly from Brazil.

    abstract:BACKGROUND:Sclerotinia Stem Rot (SSR), caused by the fungal pathogen Sclerotinia sclerotiorum, is ubiquitous in cooler climates where soybean crops are grown. Breeding for resistance to SSR remains challenging in crops like soybean, where no single gene provides strong resistance, but instead, multiple genes work toget...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Wei W,Mesquita ACO,Figueiró AA,Wu X,Manjunatha S,Wickland DP,Hudson ME,Juliatti FC,Clough SJ

    更新日期:2017-11-07 00:00:00

  • Microarray analysis of response of Salmonella during infection of HLA-B27- transfected human macrophage-like U937 cells.

    abstract:BACKGROUND:Human leukocyte antigen (HLA)-B27 is strongly associated with the development of reactive arthritis (ReA) in humans after salmonellosis. Human monocytic U937 cells transfected with HLA-B27 are less able to eliminate intracellular Salmonella enterica serovar Enteritidis than those transfected with control HLA...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Ge S,Danino V,He Q,Hinton JC,Granfors K

    更新日期:2010-07-30 00:00:00

  • Establishing an adjusted p-value threshold to control the family-wide type 1 error in genome wide association studies.

    abstract:BACKGROUND:By assaying hundreds of thousands of single nucleotide polymorphisms, genome wide association studies (GWAS) allow for a powerful, unbiased review of the entire genome to localize common genetic variants that influence health and disease. Although it is widely recognized that some correction for multiple tes...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Duggal P,Gillanders EM,Holmes TN,Bailey-Wilson JE

    更新日期:2008-10-31 00:00:00

  • A genomic perspective on the potential of Actinobacillus succinogenes for industrial succinate production.

    abstract:BACKGROUND:Succinate is produced petrochemically from maleic anhydride to satisfy a small specialty chemical market. If succinate could be produced fermentatively at a price competitive with that of maleic anhydride, though, it could replace maleic anhydride as the precursor of many bulk chemicals, transforming a multi...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: McKinlay JB,Laivenieks M,Schindler BD,McKinlay AA,Siddaramappa S,Challacombe JF,Lowry SR,Clum A,Lapidus AL,Burkhart KB,Harkins V,Vieille C

    更新日期:2010-11-30 00:00:00

  • Yes, we can use it: a formal test on the accuracy of low-pass nanopore long-read sequencing for mitophylogenomics and barcoding research using the Caribbean spiny lobster Panulirus argus.

    abstract:BACKGROUND:Whole mitogenomes or short fragments (i.e., 300-700 bp of the cox1 gene) are the markers of choice for revealing within- and among-species genealogies. Protocols for sequencing and assembling mitogenomes include 'primer walking' or 'long PCR' followed by Sanger sequencing or Illumina short-read low-coverage ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Baeza JA

    更新日期:2020-12-09 00:00:00

  • Single-cell transcriptomics using spliced leader PCR: Evidence for multiple losses of photosynthesis in polykrikoid dinoflagellates.

    abstract:BACKGROUND:Most microbial eukaryotes are uncultivated and thus poorly suited to standard genomic techniques. This is the case for Polykrikos lebouriae, a dinoflagellate with ultrastructurally aberrant plastids. It has been suggested that these plastids stem from a novel symbiosis with either a diatom or haptophyte, but...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Gavelis GS,White RA,Suttle CA,Keeling PJ,Leander BS

    更新日期:2015-07-17 00:00:00

  • Pangenome analysis of Bifidobacterium longum and site-directed mutagenesis through by-pass of restriction-modification systems.

    abstract:BACKGROUND:Bifidobacterial genome analysis has provided insights as to how these gut commensals adapt to and persist in the human GIT, while also revealing genetic diversity among members of a given bifidobacterial (sub)species. Bifidobacteria are notoriously recalcitrant to genetic modification, which prevents explora...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: O'Callaghan A,Bottacini F,O'Connell Motherway M,van Sinderen D

    更新日期:2015-10-21 00:00:00

  • Patterns of exon-intron architecture variation of genes in eukaryotic genomes.

    abstract:BACKGROUND:The origin and importance of exon-intron architecture comprises one of the remaining mysteries of gene evolution. Several studies have investigated the variations of intron length, GC content, ordinal position in a gene and divergence. However, there is little study about the structural variation of exons an...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Zhu L,Zhang Y,Zhang W,Yang S,Chen JQ,Tian D

    更新日期:2009-01-24 00:00:00

  • The complete and fully assembled genome sequence of Aeromonas salmonicida subsp. pectinolytica and its comparative analysis with other Aeromonas species: investigation of the mobilome in environmental and pathogenic strains.

    abstract:BACKGROUND:Due to the predominant usage of short-read sequencing to date, most bacterial genome sequences reported in the last years remain at the draft level. This precludes certain types of analyses, such as the in-depth analysis of genome plasticity. RESULTS:Here we report the finalized genome sequence of the envir...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Pfeiffer F,Zamora-Lagos MA,Blettinger M,Yeroslaviz A,Dahl A,Gruber S,Habermann BH

    更新日期:2018-01-05 00:00:00

  • Analysis of the genome sequence of Phomopsis longicolla: a fungal pathogen causing Phomopsis seed decay in soybean.

    abstract:BACKGROUND:Phomopsis longicolla T. W. Hobbs (syn. Diaporthe longicolla) is a seed-borne fungus causing Phomopsis seed decay in soybean. This disease is one of the most devastating diseases reducing soybean seed quality worldwide. To facilitate investigation of the genomic basis of pathogenicity and to understand the me...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Li S,Darwish O,Alkharouf NW,Musungu B,Matthews BF

    更新日期:2017-09-05 00:00:00

  • A versatile palindromic amphipathic repeat coding sequence horizontally distributed among diverse bacterial and eucaryotic microbes.

    abstract:BACKGROUND:Intragenic tandem repeats occur throughout all domains of life and impart functional and structural variability to diverse translation products. Repeat proteins confer distinctive surface phenotypes to many unicellular organisms, including those with minimal genomes such as the wall-less bacterial monoderms,...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Röske K,Foecking MF,Yooseph S,Glass JI,Calcutt MJ,Wise KS

    更新日期:2010-07-13 00:00:00

  • Identification of QTL with large effect on seed weight in a selective population of soybean with genome-wide association and fixation index analyses.

    abstract:BACKGROUND:Soybean seed weight is not only a yield component, but also a critical trait for various soybean food products such as sprouts, edamame, soy nuts, natto and miso. Linkage analysis and genome-wide association study (GWAS) are two complementary and powerful tools to connect phenotypic differences to the underl...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Yan L,Hofmann N,Li S,Ferreira ME,Song B,Jiang G,Ren S,Quigley C,Fickus E,Cregan P,Song Q

    更新日期:2017-07-12 00:00:00

  • Dual RNA-seq transcriptional analysis of wheat roots colonized by Azospirillum brasilense reveals up-regulation of nutrient acquisition and cell cycle genes.

    abstract:BACKGROUND:The rapid growth of the world's population demands an increase in food production that no longer can be reached by increasing amounts of nitrogenous fertilizers. Plant growth promoting bacteria (PGPB) might be an alternative to increase nitrogenous use efficiency (NUE) in important crops such wheat. Azospiri...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Camilios-Neto D,Bonato P,Wassem R,Tadra-Sfeir MZ,Brusamarello-Santos LC,Valdameri G,Donatti L,Faoro H,Weiss VA,Chubatsu LS,Pedrosa FO,Souza EM

    更新日期:2014-05-16 00:00:00

  • Comparative analysis of mitochondrial genomes between the hau cytoplasmic male sterility (CMS) line and its iso-nuclear maintainer line in Brassica juncea to reveal the origin of the CMS-associated gene orf288.

    abstract:BACKGROUND:Cytoplasmic male sterility (CMS) is not only important for exploiting heterosis in crop plants, but also as a model for investigating nuclear-cytoplasmic interaction. CMS may be caused by mutations, rearrangement or recombination in the mitochondrial genome. Understanding the mitochondrial genome is often th...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Heng S,Wei C,Jing B,Wan Z,Wen J,Yi B,Ma C,Tu J,Fu T,Shen J

    更新日期:2014-04-30 00:00:00

  • Overlapping genes in the human and mouse genomes.

    abstract:BACKGROUND:Increasing evidence suggests that overlapping genes are much more common in eukaryotic genomes than previously thought. In this study we identified and characterized the overlapping genes in a set of 13,484 pairs of human-mouse orthologous genes. RESULTS:About 10% of the genes under study are overlapping ge...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Sanna CR,Li WH,Zhang L

    更新日期:2008-04-14 00:00:00

  • Inferring linkage disequilibrium from non-random samples.

    abstract:BACKGROUND:Linkage disequilibrium (LD) plays a fundamental role in population genetics and in the current surge of studies to screen for subtle genetic variants affecting complex traits. Methods widely implemented in LD analyses require samples to be randomly collected, which, however, are usually ignored and thus rais...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Wang M,Jia T,Jiang N,Wang L,Hu X,Luo Z

    更新日期:2010-05-26 00:00:00

  • Transcriptome profiling in fast versus slow-growing rainbow trout across seasonal gradients.

    abstract:BACKGROUND:Circannual rhythms in vertebrates can influence a wide variety of physiological processes. Some notable examples include annual reproductive cycles and for poikilotherms, seasonal changes modulating growth. Increasing water temperature elevates growth rates in fishes, but increases in photoperiod regime can ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Danzmann RG,Kocmarek AL,Norman JD,Rexroad CE 3rd,Palti Y

    更新日期:2016-01-15 00:00:00

  • Transcriptomics of the late gestation ovine fetal brain: modeling the co-expression of immune marker genes.

    abstract:BACKGROUND:Major changes in gene expression occur in the fetal brain to modulate the function of this organ postnatally. Thus, factors can alter the genomics of the fetal brain, predisposing to neurological disorders later in life. We hypothesized that the physiological dynamics of the immune system transcriptome of th...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Rabaglino MB,Keller-Wood M,Wood CE

    更新日期:2014-11-19 00:00:00

  • Waking the sleeping dragon: gene expression profiling reveals adaptive strategies of the hibernating reptile Pogona vitticeps.

    abstract:BACKGROUND:Hibernation is a physiological state exploited by many animals exposed to prolonged adverse environmental conditions associated with winter. Large changes in metabolism and cellular function occur, with many stress response pathways modulated to tolerate physiological challenges that might otherwise be letha...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Capraro A,O'Meally D,Waters SA,Patel HR,Georges A,Waters PD

    更新日期:2019-06-06 00:00:00