Determination of the entire sequence of turtle CR1: the first open reading frame of the turtle CR1 element encodes a protein with a novel zinc finger motif

Abstract

CR1 elements are a family of retroposons. They are classified as long interspersed elements (LINEs) or non-long-terminal-repeat (non-LTR) retrotransposons, and they have been found in the genomes of many vertebrates. However, they have been only partially characterized, and only a 2-kb region of the 3' end of chicken CR1 has been sequenced. In the present study, we determined the entire consensus sequence of CR1 elements in the turtle genome, designated PsCR1. The first open reading frame (ORF1) of PsCR1 has two unusual arrangements of Cys residues. One of them includes a zinc finger motif, CX2CX14CX2C. The putative zinc finger has cysteine residues with identical spacing and a similar amino acid composition to those found in the species-specific transcription initiation factors SL1 and TIF-IB. The 5' untranslated region (5' UTR) of PsCR1 contains a sequence similar to part of the human L1 promoter, L1 site A, and several cis elements of the type found in eukaryotic genes. Within a region of about 500 bp, there are nine "E boxes," cis elements that are recognized by the basic helix-loop-helix (bHLH) family of proteins. This observation raises the possibility that cellular transcription factors that bind to these sequences might act in concert to regulate the expression of PsCR1. The extent of the sequence divergence of the 3' UTR of CR1 between species was found to be lower than the rate of nonsynonymous substitutions per site in ORF2, suggesting that a strict functional constraint must exist for this region. This result strongly suggests that the conserved 3'-end sequence of CR1 is the recognition site for the reverse transcriptase of CR1. A discussion is presented of a possible mechanism for the integration of CR1 elements and also of the intriguing possible recruitment of the reverse transcriptase for the retroposition of SINEs.

Extension, single-locus conversion and physical mapping of sex chromosome sequences identify the Z microchromosome and pseudo-autosomal region in a dragon lizard, Pogona vitticeps

“…The CR1-like repetitive element belongs to the non-long terminal repeat class of retrotransposons. CR1-like elements seem to be ubiquitous in vertebrates (Vandergon and Reitman, 1994;Kajikawa et al, 1997;Poulter et al, 1999;Jurka, 2000) and they are also present in invertebrates (Drew and Brindley, 1997). It is possible that the amplified 3-kb probe, which contained the sequences for the 188-bp CR1-like element, hybridized preferentially to CR1-like elements on the Z and W chromosomes.…”

LINE-1 ORF1 protein enhances Alu SINE retrotransposition

“…LINE-1 is present throughout mammalian genomes. However, bird genomes contain only a very distantly-related family of non-LTR retroelement termed CR-1 (Burch et al, 1993;Haas et al, 1997;Kajikawa et al, 1997). Furthermore, analysis of the chicken genome reveals a paucity of new SINEs or retropseudogenes, strongly indicating that CR1 proteins may not efficiently mobilize in trans other "A-tail" containing transcripts ie.…”

Phylogenetics of modern birds in the era of genomics

“…Sequencing of songbird cosmid clones have already yielded CR1 and L1 elements that may prove to be phylogenetically useful (Hess et al 2000;Gasper et al 2001). Likewise, subfamilies of retroposons such those in the Pol-III family of SINEs previously characterized in turtles may also provide useful systematic information for bird evolutionary studies (Kajikawa et al 1997;Sasaki et al 2004b). Moreover, novel families of SINEs not detected thus far in chickens have already been isolated in penguins and lizards by conventional genomic library screening and are providing useful phylogenetic information for each of these groups (N. Okada, unpublished data).…”