title: Differential distribution of a SINE element in the Entamoeba histolytica and Entamoeba dispar genomes: role of the LINE-encoded endonuclease.
abstract: BACKGROUND
  Entamoeba histolytica and Entamoeba dispar are closely related protistan parasites but while E. histolytica can be invasive, E. dispar is completely non pathogenic. Transposable elements constitute a significant portion of the genome in these species; there being three families of LINEs and SINEs. These elements can profoundly influence the expression of neighboring genes. Thus their genomic location can have important phenotypic consequences. A genome-wide comparison of the location of these elements in the E. histolytica and E. dispar genomes has not been carried out. It is also not known whether the retrotransposition machinery works similarly in both species. The present study was undertaken to address these issues.
  
  
  RESULTS
  Here we extracted all genomic occurrences of full-length copies of EhSINE1 in the E. histolytica genome and matched them with the homologous regions in E. dispar, and vice versa, wherever it was possible to establish synteny. We found that only about 20% of syntenic sites were occupied by SINE1 in both species. We checked whether the different genomic location in the two species was due to differences in the activity of the LINE-encoded endonuclease which is required for nicking the target site. We found that the endonucleases of both species were essentially very similar, both in their kinetic properties and in their substrate sequence specificity. Hence the differential distribution of SINEs in these species is not likely to be influenced by the endonuclease. Further we found that the physical properties of the DNA sequences adjoining the insertion sites were similar in both species.
  
  
  CONCLUSIONS
  Our data shows that the basic retrotransposition machinery is conserved in these sibling species. SINEs may indeed have occupied all of the insertion sites in the genome of the common ancestor of E. histolytica and E. dispar but these may have been subsequently lost from some locations. Alternatively, SINE expansion took place after the divergence of the two species. The absence of SINE1 in 80% of syntenic loci could affect the phenotype of the two species, including their pathogenic properties, which needs to be explored.
authors: School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
authors: Vandana
authors: V
authors: Kumari
authors: Rahul
authors: R
authors: Sharma
authors: Vijay P
authors: VP
authors: Yadav
authors: Abhishek K
authors: AK
authors: Gupta
authors: Alok
authors: A
authors: Bhattacharya
authors: Sudha
authors: S
authors: Bhattacharya
references: BMC Bioinformatics. 2005 Jan 17;6:9
references: 15655071
references: Cell Cycle. 2009 Sep 15;8(18):2895-900
references: 19736519
references: Cell. 1993 Feb 26;72(4):595-605
references: 7679954
references: Exp Parasitol. 2005 Jul;110(3):207-13
references: 15955314
references: J Eukaryot Microbiol. 1993 May-Jun;40(3):340-4
references: 8508172
references: PLoS Negl Trop Dis. 2010 Jun 15;4(6):e716
references: 20559563
references: Eukaryot Cell. 2004 Feb;3(1):170-9
references: 14871947
references: Infect Immun. 2002 Dec;70(12):6798-804
references: 12438355
references: Mol Biochem Parasitol. 2007 Mar;152(1):47-52
references: 17178164
references: Science. 2003 May 23;300(5623):1288-91
references: 12764196
references: Cell. 2010 Jun 11;141(6):956-69
references: 20550932
references: Funct Integr Genomics. 2010 Aug;10(3):307-19
references: 20393868
references: Methods Mol Biol. 1993;16:107-200
references: 19082972
references: Mol Biochem Parasitol. 2001 Aug;116(1):45-53
references: 11463465
references: Gene. 2002 Sep 4;297(1-2):229-39
references: 12384304
references: Annu Rev Genomics Hum Genet. 2007;8:241-59
references: 17506661
references: Nucleic Acids Res. 2006;34(20):5752-63
references: 17040894
references: Mol Biol Evol. 1999 Dec;16(12):1740-51
references: 10605115
references: Genome Res. 2008 Mar;18(3):343-58
references: 18256243
references: BMC Genomics. 2010 May 24;11:321
references: 20497534
references: Annu Rev Genet. 2001;35:501-38
references: 11700292
references: FEBS J. 2009 Dec;276(23):7070-82
references: 19878305
references: Gene. 2002 Sep 18;298(1):101-8
references: 12406580
references: BMC Genomics. 2008 Dec 10;9:595
references: 19077187
references: Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W20-5
references: 15215342
references: Chromosome Res. 2008;16(1):203-15
references: 18293113