Journal of Biosciences

, Volume 37, Issue 1, pp 19–24 | Cite as

Sequence periodic pattern of HERV LTRs: A matrix simulation algorithm

Brief communication
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Abstract

Flanking regulatory long terminal repeats (LTRs) in Human endogenous retrovirus (HERV) is a kind of typical DNA repeat that is widespread in the human genome. Currently, many algorithms have been developed to detect the latent periodicity of a wide range of DNA repeats. However, no such attempt was made for HERV LTRs. The present study focused on the investigation of the possible sequence periodic patterns in the HERV LTRs and their regulatory mechanisms. We calculated the sequence periods of 5′, 3′ and combined LTRs in HERVs with our devised matrix simulation algorithm. It is interesting that 5′ and 3′ LTRs have the same period of 7, and combined LTRs have a period of 9. These results indicated that HERV LTRs have predominant periodic patterns. Based on the obtained sequence periodicity, we constructed periodic consensus sequences of 5′, 3′ and combined LTRs. As to 5′ and 3′ LTRs with the same period – 7, we manually scanned the nucleotide bases in the corresponding positions of their periodic consensus sequences, and found some positions have the nucleotide base unchanged, such as the 1st, 5th and 7th positions. These conservative nucleotide base positions represent critical binding sites of regulatory LTRs, and may be indicative of conserved regulatory mechanisms in LRT-participating regulatory networks.

Keywords

DNA repeats HERV periodicity periodic consensus sequence 
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Notes

Acknowledgements

This work was supported the Natural Science Foundation of Heilongjiang Province (Grant Nos. ZJG0501 and GB03C602-4).

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Copyright information

© Indian Academy of Sciences 2012

Authors and Affiliations

  1. 1.Colleges of Life Science, and Teafood Science and TechnologyAnhui Agricultural UniversityHefeiChina

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