Advanced search×

In cellulo DNA analysis (LMPCR footprinting).

Régen R Drouin, Nathalie N Bastien, Jean-François JF Millau, François F Vigneault, and Isabelle I Paradis

Methods Mol Biol (2009) PMID 19378174

The in cellulo analysis of DNA protein interactions and chromatin structure is very important to better understand the mechanisms involved in the regulation of gene expression. The nuclease-hypersensitive sites and sequences bound by transcription factors often correspond to genetic regulatory elements. Using the Ligation-mediated polymerase chain reaction (LMPCR) technology, it is possible to precisely analyze these DNA sequences to demonstrate the existence of DNA-protein interactions or unusual DNA structures directly in living cells. Indeed, the ideal chromatin substrate is, of course, found inside intact cells. LMPCR, a genomic-sequencing, technique that map DNA single-strand breaks at the sequence level of resolution, is the method of choice for in cellulo footprinting and DNA structure studies because it can be used to investigate any complex genomes, including human. The detailed conventional and automated LMPCR protocols are presented in this chapter.

DOI: 10.1007/978-1-60327-015-1_20
Version: za2963e q8zaf q8zbf q8zc9 q8zdd q8zed q8zf5 q8zga

Similar articles you may find interesting…

  1. The management and analysis of big data, and the SP theory of intelligence
    J Gerard Wolff

    arXiv:1306.3890 [cs.AI] 13 Jun 2013

    This article is about how the "SP theory of intelligence", and its realisation in the "SP machine", may, with advantage, be applied to the management and analysis of big data. The SP system has potential for the discovery of 'natural' structures in big data at various levels of abstraction, includi...
    View PDF
  2. Low-bandwidth and non-compute intensive remote identification of microbes from raw sequencing reads
    Laurent Gautier and Ole Lund

    arXiv:1306.1569 [q-bio.GN] 6 Jun 2013

    We propose a novel general approach to the analysis of sequencing data in Which the reference genome does not have to be specified. Using a distributed Architecture we are able to query a remote server for hints about what the Reference might be, transferring a relatively small amount of data, and t...
    View PDF
  3. Lymphatic abnormalities are associated with RASA1 gene mutations in mouse and man.
    Patricia E Burrows, Manuel L Gonzalez-Garay, and Eva M Sevick-Muraca

    Proc Natl Acad Sci U S A (2013) PMID 23650393

    We performed investigational near-infrared fluorescence lymphatic imaging and confirmatory radiographic lymphangiography in a Parkes-Weber syndrome (PKWS) patient with suspected RASA1 mutations and correlated the lymphatic abnormalities against that imaged in an inducible Rasa1 knockout mouse. Whole...