title: Identification of Scaffold/Matrix Attachment (S/MAR) like DNA element from the gastrointestinal protozoan parasite Giardia lamblia.
abstract: BACKGROUND
  Chromatin in the nucleus of all eukaryotes is organized into a system of loops and domains. These loops remain fastened at their bases to the fundamental framework of the nucleus, the matrix or the scaffold. The DNA sequences which anchor the bases of the chromatin loops to the matrix are known as Scaffold/Matrix Attachment Regions or S/MARs. Though S/MARs have been studied in yeast and higher eukaryotes and they have been found to be associated with gene organization and regulation of gene expression, they have not been reported in protists like Giardia. Several tools have been discovered and formulated to predict S/MARs from a genome of a higher eukaryote which take into account a number of features. However, the lack of a definitive consensus sequence in S/MARs and the randomness of the protozoan genome in general, make it a challenge to predict and identify such sequences from protists.
  
  
  RESULTS
  Here, we have analysed the Giardia genome for the probable S/MARs predicted by the available computational tools; and then shown these sequences to be physically associated with the nuclear matrix. Our study also reflects that while no single computational tool is competent to predict such complex elements from protist genomes, a combination of tools followed by experimental verification is the only way to confirm the presence of these elements from these organisms.
  
  
  CONCLUSIONS
  This is the first report of S/MAR elements from the protozoan parasite Giardia lamblia. This initial work is expected to lay a framework for future studies relating to genome organization as well as gene regulatory elements in this parasite.
authors.affiliation: Division of Life Sciences, AU-KBC Research Center, MIT Campus, Chromepet, Chennai, Tamilnadu, India.
authors.forename: Sushma S
authors.initials: SS
authors.lastname: Padmaja
authors.forename: Jagannathan
authors.initials: J
authors.lastname: Lakshmanan
authors.forename: Ravi
authors.initials: R
authors.lastname: Gupta
authors.forename: Santanu
authors.initials: S
authors.lastname: Banerjee
authors.forename: Pennathur
authors.initials: P
authors.lastname: Gautam
authors.forename: Sulagna
authors.initials: S
authors.lastname: Banerjee
mesh_terms: D000818:Animals; D026501:Blotting, Southwestern; D002417:Cattle; D016054:DNA, Protozoan / Q000235:genetics*; D041981:Gastrointestinal Tract / Q000469:parasitology*; D018503:Genome, Protozoan / Q000235:genetics; D023281:Genomics; D016829:Giardia lamblia / Q000235:genetics*; D007753:Laboratories; D013058:Mass Spectrometry; D045170:Matrix Attachment Regions / Q000235:genetics*; D015530:Nuclear Matrix / Q000378:metabolism; D034521:Nuclear Matrix-Associated Proteins / Q000235:genetics / Q000378:metabolism; D016133:Polymerase Chain Reaction
chemical_list: D016054:DNA, Protozoan; D034521:Nuclear Matrix-Associated Proteins