Colleges of Life Science, and Teafood Science and Technology, Anhui Agricultural University, Hefei 230030, China.
J Biosci. 2012 Mar;37(1):19-24. doi: 10.1007/s12038-012-9182-x.
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.
侧翼调节长末端重复序列（LTRs）是人类内源性逆转录病毒（HERV）中的一种典型 DNA 重复序列，广泛存在于人类基因组中。目前，已经开发了许多算法来检测广泛的 DNA 重复序列的潜在周期性。然而，对于 HERV LTRs，尚未进行此类尝试。本研究专注于调查 HERV LTRs 中可能存在的序列周期性模式及其调节机制。我们使用设计的矩阵模拟算法计算了 HERV 中的 5'、3'和组合 LTR 的序列周期。有趣的是，5'和 3'LTR 具有相同的 7 个周期，而组合 LTR 具有 9 个周期。这些结果表明 HERV LTRs 具有主要的周期性模式。基于获得的序列周期性，我们构建了 5'、3'和组合 LTR 的周期性一致序列。对于具有相同周期-7 的 5'和 3'LTR，我们手动扫描其周期性一致序列中相应位置的核苷酸碱基，发现一些位置的核苷酸碱基保持不变，例如第 1、5 和 7 位。这些保守核苷酸碱基位置代表调节 LTR 的关键结合位点，可能表明 LTR 参与的调节网络中存在保守的调节机制。
