RsaI repetitive DNA in Buffalo Bubalus bubalis representing retrotransposons, conserved in bovids, are part of the functional genes

Deepali Pathak,Sher Ali

doi:10.1186/1471-2164-12-338

Abstract

BackgroundRepetitive sequences are the major components of the eukaryotic genomes. Association of these repeats with transcribing sequences and their regulation in buffalo Bubalus bubalis has remained largely unresolved.ResultsWe cloned and sequenced RsaI repeat fragments pDp1, pDp2, pDp3, pDp4 of 1331, 651, 603 and 339 base pairs, respectively from the buffalo, Bubalus bubalis. Upon characterization, these fragments were found to represent retrotransposons and part of some functional genes. The resultant clones showed cross hybridization only with buffalo, cattle, goat and sheep genomic DNA. Real Time PCR, detected ~2 × 104 copies of pDp1, ~ 3000 copies of pDp2 and pDp3 and ~ 1000 of pDp4 in buffalo, cattle, goat and sheep genomes, respectively. RsaI repeats are transcriptionally active in somatic tissues and spermatozoa. Accordingly, pDp1 showed maximum expression in lung, pDp2 and pDp3 both in Kidney, and pDp4 in ovary. Fluorescence in situ hybridization showed repeats to be distributed all across the chromosomes.ConclusionsThe data suggest that RsaI repeats have been incorporated into the exonic regions of various transcribing genes, possibly contributing towards the architecture and evolution of the buffalo and related genomes. Prospects of our present work in the context of comparative and functional genomics are highlighted.

Highlights

Repetitive sequences are the major components of the eukaryotic genomes
RsaI enzyme digestion uncovers four repeat fractions Digestion of buffalo genomic DNA with RsaI enzyme, besides minor ones, showed four prominent bands ranging from 1331 base pairs, pDp1; 651, pDp2; 603, pDp3; to 339; pDp4 (Figure 1)
15-20 recombinant clones subjected to restriction digestion and slot blot hybridization screening yielded ten positive clones for each repeat

Summary

Introduction

Repetitive sequences are the major components of the eukaryotic genomes. Association of these repeats with transcribing sequences and their regulation in buffalo Bubalus bubalis has remained largely unresolved. Different families of repetitive DNA contribute towards architectural organization of the mammalian genomes [1]. They represent both, tandemly arranged and interspersed sequences [2]. The non LTR LINEs (long interspersed repeat elements) and SINEs (Short interspersed repeat elements) are widely distributed occupying a substantial fraction of the eukaryotic genomes. These elements replicate and proliferate themselves through a “copy and paste” mechanism called retrotransposition [3,4].

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Conclusion