title: Matrix attachment regions and structural colinearity in the genomes of two grass species.
abstract: In order to gain insights into the relationship between spatial organization of the genome and genome function we have initiated studies of the co-linear Sh2/A1- homologous regions of rice (30 kb) and sorghum (50 kb). We have identified the locations of matrix attachment regions (MARs) in these homologous chromosome segments, which could serve as anchors for individual structural units or loops. Despite the fact that the nucleotide sequences serving as MARs were not detectably conserved, the general organizational patterns of MARs relative to the neighboring genes were preserved. All identified genes were placed in individual loops that were of comparable size for homologous genes. Hence, gene composition, gene orientation, gene order and the placement of genes into structural units has been evolutionarily conserved in this region. Our analysis demonstrated that the occurrence of various 'MAR motifs' is not indicative of MAR location. However, most of the MARs discovered in the two genomic regions were found to co-localize with miniature inverted repeat transposable elements (MITEs), suggesting that MITEs preferentially insert near MARs and/or that they can serve as MARs.
authors.affiliation: Department of Biological Sciences and Purdue Genetics Program, Purdue University, West Lafayette, IN 47907, USA. zavramov@bilbo.bio.purdue.edu
authors.forename: Z
authors.initials: Z
authors.lastname: Avramova
authors.forename: A
authors.initials: A
authors.lastname: Tikhonov
authors.forename: M
authors.initials: M
authors.lastname: Chen
authors.forename: J L
authors.initials: JL
authors.lastname: Bennetzen
mesh_terms: D001482:Base Composition; D001483:Base Sequence; D002874:Chromosome Mapping; D003001:Cloning, Molecular; D017124:Conserved Sequence / Q000235:genetics; D004251:DNA Transposable Elements / Q000235:genetics; D018744:DNA, Plant / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D017343:Genes, Plant / Q000235:genetics; D018745:Genome, Plant; D015530:Nuclear Matrix / Q000378:metabolism*; D012275:Oryza / Q000235:genetics*; D006109:Poaceae / Q000235:genetics*; D012689:Sequence Homology, Nucleic Acid
chemical_list: D004251:DNA Transposable Elements; D018744:DNA, Plant