Exaptation of protein coding sequences from transposable elements.

The activity of transposable elements (TEs) has had a profound impact on the evolution of eukaryotic genomes. Once thought to be purely selfish genomic entities, TEs are now recognized to occupy a continuum of relationships, ranging from parasitic to mutualistic, with their host genomes. One of the many ways that TEs contribute to the function and evolution of the genomes in which they reside is through the donation of host protein coding sequences (CDSs). In this chapter, we will describe several notable examples of eukaryotic host CDSs that are derived from TEs. Despite the existence of a number of such well-established cases, the overall extent and significance of this phenomenon remains a matter of controversy. Genome-scale computational analyses have yielded vastly different estimates for the fraction of host CDSs that are derived from TEs. We explain how these seemingly contradictory findings are the result of specific ascertainment biases introduced by the different methods used to detect TE-related sequences. In light of this problem, we propose a comprehensive and systematic framework for definitively characterizing the contribution of TEs to eukaryotic CDSs.

Chromosomal regulation by MeCP2: structural and enzymatic considerations.

The unique properties of eukaryotic DNA modified via methylation of cytosine residues are believed to result from the action of a conserved family of proteins, the MBD family. The prototype member of this family, MeCP2, was isolated independently in two laboratories. One group isolated MeCP2 as a methylated DNA-binding protein, the second as a sequence-specific DNA-binding protein. Multiple lines of evidence suggest that MeCP2 functions in assembly of specialized chromatin architecture. While initial findings pointed to an enzymatic mechanism involving histone modification for transcriptional repression mediated by MeCP2, emerging studies clearly provide exceptions to this model. In a recent study, highly compacted, unique chromatin structures were generated by stoichiometric binding of MeCP2 to model chromatin fibers. These findings support the likelihood that MeCP2 can utilize two independent, but not mutually exclusive, mechanisms to repress transcription: enzymatic and structural mechanisms.

Drosophila euchromatic LTR retrotransposons are much younger than the host species in which they reside.

The recent release of the complete euchromatic genome sequence of Drosophila melanogaster offers a unique opportunity to explore the evolutionary history of transposable elements (TEs) within the genome of a higher eukaryote. In this report, we describe the annotation and phylogenetic comparison of 178 full-length long terminal repeat (LTR) retrotransposons from the sequenced component of the D. melanogaster genome. We report the characterization of 17 LTR retrotransposon families described previously and five newly discovered element families. Phylogenetically, these families can be divided into three distinct lineages that consist of members from the canonical Copia and Gypsy groups as well as a newly discovered third group containing BEL, mazi, and roo elements. Each family consists of members with average pairwise identities > or =99% at the nucleotide level, indicating they may be the products of recent transposition events. Consistent with the recent transposition hypothesis, we found that 70% (125/178) of the elements (across all families) have identical intra-element LTRs. Using the synonymous substitution rate that has been calculated previously for Drosophila (.016 substitutions per site per million years) and the intra-element LTR divergence calculated here, the average age of the remaining 30% (53/178) of the elements was found to be 137,000 +/-89,000 yr. Collectively, these results indicate that many full-length LTR retrotransposons present in the D. melanogaster genome have transposed well after this species diverged from its closest relative Drosophila simulans, 2.3 +/-.3 million years ago.

Patient satisfaction with screening flexible sigmoidoscopy.

BACKGROUND: Screening flexible sigmoidoscopy is an underused cancer prevention procedure. Physicians often cite patient discomfort as a reason for not requesting sigmoidoscopy, but patient experiences and attitudes toward sigmoidoscopy have not been well studied. OBJECTIVE: To measure patient satisfaction and the determinants of satisfaction with screening sigmoidoscopy. METHODS: An instrument to assess satisfaction with screening sigmoidoscopy was developed. Responses were evaluated with a factor analysis, tested for reproducibility and internal consistency, and validated against an external standard. RESULTS: A total of 1221 patients (666 men and 555 women; mean age, 61.8 years) were surveyed after sigmoidoscopy. Examinations were performed by a nurse practitioner (n = 668), internist (n = 344), or gastrointestinal specialist (n= 184). More than 93% of the participants strongly agreed or agreed they would be willing to undergo another examination, and 74.9% would strongly recommend the procedure to their friends. Regarding pain and discomfort, 76.2% strongly agreed or agreed that the examination did not cause a lot of pain, 78.1% stated that it did not cause a lot of discomfort, and 68.5% thought that it was more comfortable than they expected. Fifteen percent to 25% of the patients indicated they had a lot of pain, great discomfort, or more discomfort than expected. Women were more likely to have significant pain or discomfort than men (adjusted odds ratio, 2.9; 95% confidence interval, 1.9-4.3; P<.001). CONCLUSIONS: Approximately 70% of individuals who undergo screening sigmoidoscopy are satisfied and find the procedure more comfortable than expected, whereas only 15% to 25% find the procedure unpleasant. Physicians should not project discomfort onto patients as a reason for not requesting screening sigmoidoscopy.

Genomic analysis of Caenorhabditis elegans reveals ancient families of retroviral-like elements.

Retrotransposons are the most abundant and widespread class of eukaryotic transposable elements. The recent genome sequencing of Caenorhabditis elegans has provided an unprecedented opportunity to analyze the evolutionary relationships among the entire complement of retrotransposons within a multicellular eukaryotic organism. In this article we report the results of an analysis of retroviral-like long terminal repeat retrotransposons in C. elegans that indicate that this class of elements may be even more abundant and divergent than previously expected. The unexpected presence, in C. elegans, of an element displaying a number of characteristics previously thought to be unique to vertebrate retroviruses suggests an ancient lineage for this important class of infectious agents.

LTR retrotransposons and the evolution of eukaryotic enhancers.

Since LTR retrotransposons and retroviruses are especially prone to regional duplications and recombination events, these viral-like systems may be especially conducive to the evolution of closely spaced combinatorial regulatory motifs. Using the Drosophila copia LTR retrotransposon as a model, we show that a regulatory region contained within the element's untranslated leader region (ULR) consists of multiple copies of an 8 bp motif (TTGTGAAA) with similarity to the core sequence of the SV40 enhancer. Naturally occurring variation in the number of these motifs is correlated with the enhancer strength of the ULR. Our results indicate that inter-element selection may favor the evolution of more active enhancers within permissive genetic backgrounds. We propose that LTR retroelements and perhaps other retrotransposons constitute drive mechanisms for the evolution of eukaryotic enhancers which can be subsequently distributed throughout host genomes to play a role in regulatory evolution.