The LINEs and SINEs of Entamoeba histolytica: comparative analysis and genomic distribution

Exp Parasitol. 2005 Jul;110(3):207-13. doi: 10.1016/j.exppara.2005.02.009. Epub 2005 Mar 23.


Autonomous non-long terminal repeat retrotransposons are commonly referred to as long interspersed elements (LINEs). Short non-autonomous elements that borrow the LINE machinery are called SINES. The Entamoeba histolytica genome contains three classes of LINEs and SINEs. Together the EhLINEs/SINEs account for about 6% of the genome. The recognizable functional domains in all three EhLINEs included reverse transcriptase and endonuclease. A novel feature was the presence of two types of members-some with a single long ORF (less frequent) and some with two ORFs (more frequent) in both EhLINE1 and 2. The two ORFs were generated by conserved changes leading to stop codon. Computational analysis of the immediate flanking sequences for each element showed that they inserted in AT-rich sequences, with a preponderance of Ts in the upstream site. The elements were very frequently located close to protein-coding genes and other EhLINEs/SINEs. The possible influence of these elements on expression of neighboring genes needs to be determined.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Base Sequence
  • Consensus Sequence
  • Conserved Sequence
  • Entamoeba histolytica / genetics*
  • Genome, Protozoan*
  • Long Interspersed Nucleotide Elements / genetics*
  • Molecular Sequence Data
  • Open Reading Frames / genetics
  • Sequence Alignment / methods
  • Sequence Analysis, DNA / methods
  • Short Interspersed Nucleotide Elements / genetics*