Zhao G et al. (2007) PLoS One "Evidence for active maintenance of inverted repeat structures identified by a comparative genomic approach."

Varley K, Stormo GD, Chang KY, Zhao G

[PLoS One, 2007]

Inverted repeats have been found to occur in both prokaryotic and eukaryotic genomes. Usually they are short and some have important functions in various biological processes. However, long inverted repeats are rare and can cause genome instability. Analyses of C. elegans genome identified long, nearly-perfect inverted repeat sequences involving both divergently and convergently oriented homologous gene pairs and complete intergenic sequences. Comparisons with the orthologous regions from the genomes of C. briggsae and C. remanei show that the inverted repeat structures are often far more conserved than the sequences. This observation implies that there is an active mechanism for maintaining the inverted repeat nature of the sequences.

Hegsted A et al. (2017) Cytoskeleton (Hoboken) "Inverted formins: A subfamily of atypical formins."

Hegsted A, Pruyne D, Yingling CV

[Cytoskeleton (Hoboken), 2017]

Formins are a family of regulators of actin and microtubule dynamics that are present in almost all eukaryotes. These proteins are involved in many cellular processes, including cytokinesis, stress fiber formation, and cell polarization. Here we review one subfamily of formins, the inverted formins. Inverted formins as a group break several formin stereotypes, having atypical biochemical properties and domain organization, and they have been linked to kidney disease and neuropathy in humans. In this review, we will explore recent research on members of the inverted formin sub-family in mammals, zebrafish, fruit flies, and worms.

Colloms SD et al. (1994) Nucleic Acids Res "DNA binding activities of the Caenorhabditis elegans Tc3 transposase."

Colloms SD, Plasterk RHA, van Luenen HGAM

[Nucleic Acids Res, 1994]

Tc3 is a member of the Tc1/mariner family of transposable elements. All these elements have terminal inverted repeats, encode related transposases and insert exclusively into TA dinucleotides. We have studied the DNA binding properties of Tc3 transposase and found that an N-terminal domain of 65 amino acids binds specifically to two regions within the 462 bp Tc3 inverted repeat; one region is located at the end of the inverted repeat, the other is located about 180 bp from the end. Methylation interference experiments indicate that this N-terminal DNA binding domain of the Tc3 transposase interacts with nucleotides on one face of the DNA helix over adjacent

Felsenstein KM et al. (1987) J Mol Evol "Structure and evolution of a family of interspersed repetitive DNA sequences in Caenorhabditis elegans."

Felsenstein KM, Emmons SW

[J Mol Evol, 1987]

The structure of three members of a repetitive DNA family from the genome of the nematode Caenorhabditis elegans has been studied. The three repetitive elements have a similar unitary structure consisting of two 451-bp sequences in inverted orientation separated by 491 bp, 1.5 kb, and 2.5 kb, respectively. The 491-bp sequence separating the inverted 451-bp sequences of the shortest element is found adjacent to one of the repeats in the other two elements as well. The combination of the three sequences we define as the basic repetitive unit. Comparison of the nucleotide sequences of the three elements has allowed the identification of the one most closely resembling the primordial repetitive element. Additionally, a process of co- evolution is evident that results in the introduction of identical sequence changes into both copies of the inverted sequence within a single unit. Possible mechanisms are discussed for the homogenization of these sequences. A direct test of one possible homogenization mechanism, namely homologous recombination between the inverted sequences accompanied by gene conversion, shows that recombination between the inverted repeats does not occur at high frequency.

Oosumi T et al. (1996) J Mol Evol "Identification of putative nonautonomous transposable elements associated with several transposon families in Caenorhabditis elegans."

Belknap WR, Garlick B, Oosumi T

[J Mol Evol, 1996]

Putative nonautonomous transposable elements related to the autonomous transposons Tc1, Tc2, Tc5, and mariner were identified in the C. elegans database by computational analysis. These elements are found throughout the C. elegans genome and are defined by terminal inverted repeats with regions of sequence similarity, or identity, to the autonomous transposons. Similarity between loci containing related nonautonomous elements ends at, or near, the boundaries of the terminal inverted repeats. In most cases the terminal inverted repeats of the putative nonautonomous transposable elements are flanked by potential target-site duplications consistent with the associated autonomous elements. The nonautonomous elements identified vary considerably in size (from 100 bp to 1.5 kb in length) and copy number in the available database and are localized to introns and flanking regions of a wide variety of C. elegans genes.

Harvey SC et al. (2009) BMC Evol Biol "Correction: Quantitative genetic analysis of life-history traits of Caenorhabditis elegans in stressful environments."

Shorto A, Viney ME, Harvey SC

[BMC Evol Biol, 2009]

ABSTRACT: In Figure 1 of Harvey et al (Evolutionary Biology 2008, 8:15) the plotted data were inverted. The correct Figure is shown below. The text and statistical analyses in Harvey et al (Evolutionary Biology 2008, 8:15) are correct.

Ruvolo VR et al. (1992) DNA Cell Biol "The Tc2 transposon of Caenorhabditis elegans has the structure of a self-regulated element."

Ruvolo VR, Hill JE, Levitt A

[DNA Cell Biol, 1992]

We have analyzed the sequence of the Tc2 transposon of the nematode Caenorhabditis elegans. The Tc2 element is 2,074 bp in length and has perfect inverted terminal repeats of 24 bp. The structure of this element suggests that it may have the capacity to code for a transposase protein and/or for regulatory functions. Three large reading frames on one strand exhibit nonrandom codon usage and may represent exons. The first open coding region is preceded by a potential CAAT box, TATA box, and consensus heat shock sequence. In addition to its inverted terminal repeats, Tc2 has an unusual structural feature: subterminal degenerate direct repeats that are arranged in an irregular overlapping pattern. We have also examined the insertion sites of two Tc2 elements previously identified as the cause of restriction fragment length polymorphisms. Both insertions generated a target site duplication of 2 bp. One element had inserted inside the inverted terminal repeat of another transposon, splitting it into two unequal parts.

Emmons SW et al. (1980) J Mol Biol "Arrangement of repeated sequences in the DNA of the nematode Caenorhabditis elegans."

Emmons SW, Hirsh DI, Rosenzweig WD

[J Mol Biol, 1980]

The arrangement of repeated sequences in the DNA of the nematode Caenorhabditis elegans has been studied by electron microscopy and reassociation kinetics. Inverted repeats observed in the electron microscope are mostly less than 1000 base-pairs in length and are distributed randomly with an average separation of 33,000 bases. Comparison of the number and distribution of these inverted repeats with the amount of DNA in the foldback fraction isolated by hydroxyapatite chromatography suggests that much of the material in the foldback fraction contains a sequence distinct from the class of inverted repeats observed in the electron microscope. Cot analysis of DNA fragments several thousand nucleotides in length shows that moderately repetitive sequences are interspersed with unique sequences. Most of these interspersed, repeated sequences are a few hundred nucleotides in length, as determined from electron micrographs. DNA sequence arrangement in C. elegans is therefore similar to the arrangement found in most other eukaryotes.

Nadine L Vastenhouw et al. (2001) International C. elegans Meeting "Pulling the Trigger of Transposon Silencing"

Ronald H A Plasterk, Titia Sijen, Nadine L Vastenhouw

[International C. elegans Meeting, 2001]

Transposons are mobile genetic elements that are widespread among prokaryotes and eukaryotes. C. elegans contains different types of transposons among which are Tc1, Tc3 and Tc5. These elements belong to the Tc1/mariner family. Members of this family encode a transposase that is flanked by terminal inverted repeats. The transposase binds near the inverted repeats mediating the ability to jump from one position in the genome to another through a 'cut-and-paste' mechanism. In C. elegans , the activity of these intragenomic parasites is highly regulated by the mechanism of RNA interference (RNAi), e.g. in the laboratory strain Bristol N2, transposition activity is only detectable in somatic tissue and not in the germline. The mechanism of RNAi involves the silencing of gene expression in response to double stranded RNA (dsRNA). There are at least two possible ways by which transposons can produce dsRNA. First, readthrough transcription from flanking promoters in the genome may yield both sense and antisense transcripts that can basepair and form dsRNA. Alternatively, either a sense or an antisense transcript of one transposon could snap back by basepairing between the two terminal inverted repeats, thus forming dsRNA. Here, we use Tc5 of which only four copies are present in N2. Preliminary results show that all four copies are transcribed in both the soma and germline. In addition, dsRNA of the terminal inverted repeats of Tc5 was detected in soma and germline. We are currently generating strains that contain only one element each in order to determine the origin of the dsRNA that triggers transposon silencing.

Shaham S et al. (1992) Worm Breeder's Gazette "Three Classes of Repeats in the C. elegans Genome: Clues About IntronEvolution?"

Horvitz HR, Shaham S, Hengartner MO

[Worm Breeder's Gazette, 1992]

While determining the sequence of the genomic regions of ced-3 ,ced-9 and unc-50 ,several classes of inverted repeats were discovered in non-coding regions both upstream of the ced-3 start site and within some of the introns (see article this issue by Shaham and Horvitz). We searched the GenBank database for similar sequences using the "Blast" program and identified three sequences similar to other regions of the C. elegans genome. The sequence comparisons of these various repeats are shown below. Repeats a and c [See Figres 1 & 2] are found as inverted repeats, thus, we have compared each arm (forward) to its partner (reverse) and to the other sequences. Repeat d [See Figure 3] was found as a single (as opposed to inverted) repeat in both ced-3 and lin-12 .The four largest introns of ced-3 contain repetitive elements, suggesting that large introns (>200 bp) in C. elegans might be a consequence of the presence of defective transposons, which might not affect the function of the gene. We are interested in obtaining more information concerning these or other repeats in other regions of the genome.