title: LINEs and SINE-like elements of the protist Entamoeba histolytica.
abstract: A survey of whole genome shotgun sequences of the protozoan parasite Entamoeba histolytica revealed three families of non-long terminal repeat (LTR) retrotransposons or long interspersed elements (LINEs) (called EhLINEs in this report). The 4.8 kb EhLINEs each had a single open reading frame with a putative nucleic acid binding motif (CCHC) and restriction enzyme-like endonuclease domain located downstream of the reverse transcriptase (RT) domain. Phylogenetic analysis of the RT domain placed the EhLINEs in the R4 clade of non-LTR elements, a mixed clade of non-LTR elements that includes members from nematodes, insects, and vertebrates. EhLINE1 (which was previously identified as HMc and EhRLE) shared a common 3' end with a highly transcribed 0.55 kb short interspersed element (SINE)-like element previously identified as IE or ehapt2 and called EhLSINE1 in this report. Similarly, EhLINE2 shared a common 3' end with a highly transcribed 0.65 kb SINE-like element called EhLSINE2 in this report. The shared 3' end sequences of the EhLINEs and EhLSINEs suggested that EhLINEs are involved in the retrotransposition of the EhLSINEs. EhLSINEs were flanked by target site duplications and contained conserved 5' sequences, which likely regulate their transcription. The EhLSINEs are the first protist SINE-like elements identified that share a common 3' sequence with LINEs, and the first SINE-like elements that have been associated with the R4 clade of non-LTR elements.
authors.affiliation: Department of Immunology and Infectious Diseases, Harvard School of Public Health, 665 Huntington Avenue, Boston, MA 02115, USA.
authors.forename: Katrina
authors.initials: K
authors.lastname: Van Dellen
authors.forename: Jessica
authors.initials: J
authors.lastname: Field
authors.forename: Zheng
authors.initials: Z
authors.lastname: Wang
authors.forename: Brendan
authors.initials: B
authors.lastname: Loftus
authors.forename: John
authors.initials: J
authors.lastname: Samuelson
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D004748:Entamoeba histolytica / Q000235:genetics*; D018628:Gene Dosage; D018503:Genome, Protozoan; D007313:Insecta / Q000235:genetics; D020084:Long Interspersed Nucleotide Elements / Q000235:genetics*; D008969:Molecular Sequence Data; D009348:Nematoda / Q000235:genetics; D010802:Phylogeny; D012194:RNA-Directed DNA Polymerase / Q000235:genetics; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D012689:Sequence Homology, Nucleic Acid; D020086:Short Interspersed Nucleotide Elements / Q000235:genetics*; D014714:Vertebrates / Q000235:genetics
chemical_list: D012194:RNA-Directed DNA Polymerase