Journal Article

Transposable element ‘ <i>roo</i>’ attaches to nuclear matrix of the <i>Drosophila melanogaster</i>

Anitha Mamillapalli, Rashmi U. Pathak, Hita S. Garapati and Rakesh K. Mishra

Edited by Jake Tu

in Journal of Insect Science

Volume 13, issue 1
Published online October 2013 | e-ISSN: 1536-2442 | DOI: http://dx.doi.org/10.1673/031.013.11101

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The genome of eukaryotes is organized into structural units of chromatin loops. This higher order organization is supported by a nuclear skeleton called the nuclear matrix. The genomic DNA associated with the nuclear matrix is called the matrix associated region (MAR). Only a few genome-wide screens have been attempted, although many studies have characterized locus-specific MAR DNA sequences. In this study, a MAR DNA library was prepared from the Dro-sophila melanogaster Meigen (Diptera: Drosophilidae) genome. One of the sequences identified as a MAR was from a long terminal repeat region of ‘ roo’ retrotransposon ( roo MAR). Sequence analysis of roo MAR showed its distribution across the D. melanogaster genome. roo MAR also showed high sequence similarity with a previously identified MAR in Drosophila, namely the ‘ gypsy’ retrotransposon. Analysis of the genes flanking roo MAR insertions in the Drosophila genome showed that genes were co-ordinately expressed. The results from the present study in D. melanogaster suggest this sequence plays an important role in genome organization and function. The findings point to an evolutionary role of retrotransposons in shaping the genomic architecture of eukaryotes.

Keywords: genome organization; MAR DNA; retrotransposon

Journal Article.  3980 words.  Illustrated.

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