An Annotated Catalog of Inverted Repeats of Caenorhabditis elegans Chromosomes III and X, with Observations Concerning Odd/Even Biases and Conserved Motifs

Abstract

We have taken a computational approach to the problem of discovering and deciphering the grammar and syntax of gene regulation in eukaryotes. A logical first step is to produce an annotated catalog of all regulatory sites in a given genome. Likely candidates for such sites are direct and indirect repeats, including three subcategories of indirect repeats: inverted (palindromic), everted, and mirror-image repeats. To that end we have produced a searchable database of inverted repeats of chromosomes III and X of Caenorhabditis elegans, the first completely sequenced multicellular eukaryote. Initial results from the use of this catalog are observations concerning odd/even biases in perfect IRs. The potential usefulness of the catalog as a discovery tool for promoters was shown for some of the genes involved with G-protein functions and for heat shock protein 104 (hsp104).

A new way to visualize DNA’s base succession: the Caenorhabditis elegans chromosome landscapes

“…And each scalogram represents one thousand base pairs. We are interested here with a variety of tandem repeats of particular biology [7,8,14,16,24,38,40]. We illustrate the representation of repeats of various lengths and periodicities.…”

Evidence for Active Maintenance of Inverted Repeat Structures Identified by a Comparative Genomic Approach

“…Although inverted repeats have been the focus of several studies [14]–[17], this is the first time that inverted repeat structures involving paralogous gene pairs have been described. The presence of divergently/convergently oriented paralogs flanking the intergenic inverted repeat suggests that the inverted repeat was introduced during an intra-strand gene duplication in the common ancestor of the nematodes.…”

Discovery and characterization of 91 novel transcripts expressed in cattle placenta

“…Five of the putative ncRNAs are preferentially expressed in tissues that comprise the brain-immune-endocrine axis; placentome, thymus, thalamus, cerebrum or cerebellum. Seven contain inverted repeats that may be involved in internal base-pairing and gene regulation [31]. These putative ncRNAs may thus represent spliced, single-exon, primary snoRNA or microRNA transcripts [6].…”