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Accueil > Départements > Biologie des Génomes > Yoshiharu YAMAICHI : Intégrité du génome et de la polarité cellulaire chez la bactérie

yamaichi y - PubMed - NCBI

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Articles syndiqués

  • WGADseq : Whole Genome Affinity Determination of Protein-DNA Binding Sites.

    27 août, par Poidevin M, Galli E, Yamaichi Y, Barre FX
    Related Articles

    WGADseq: Whole Genome Affinity Determination of Protein-DNA Binding Sites.

    Methods Mol Biol. 2017;1624:53-60

    Authors: Poidevin M, Galli E, Yamaichi Y, Barre FX

    Abstract
    We present a method through which one may monitor the relative binding affinity of a given protein to DNA motifs on the scale of a whole genome. Briefly, the protein of interest is incubated with fragmented genomic DNA and then affixed to a column. Washes with buffers containing low salt concentrations will remove nonbound DNA fragments, while stepwise washes with increasing salt concentrations will elute more specifically bound fragments. Massive sequencing is used to identify eluted DNA fragments and map them on the genome, which permits us to classify the different binding sites according to their affinity and determine corresponding consensus motifs (if any).

    PMID: 28842875 [PubMed - in process]

  • Transposon Insertion Site Sequencing for Synthetic Lethal Screening.

    27 août, par Yamaichi Y, Dörr T
    Related Articles

    Transposon Insertion Site Sequencing for Synthetic Lethal Screening.

    Methods Mol Biol. 2017;1624:39-49

    Authors: Yamaichi Y, Dörr T

    Abstract
    Transposon insertion site sequencing (TIS) permits genome-wide, quantitative fitness assessment of individual genomic loci. In addition to the identification of essential genes in given growth conditions, TIS enables the elucidation of genetic networks such as synthetic lethal or suppressor gene combinations. Therefore, TIS becomes an exceptionally powerful tool for the high-throughput determination of genotype-phenotype relationships in bacteria. Here, we describe a protocol for the generation of high-density transposon insertion libraries and subsequent preparation of DNA samples for Illumina sequencing using the Gram-negative bacterium Vibrio cholerae as an example.

    PMID: 28842874 [PubMed - in process]