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.

Babadi, Nasrin et al. (2011) International Worm Meeting "To branch or not to branch? Role of png-1 in limiting axon branching in C.elegans."

Colavita, Antonio, Arauz, Claudia, Su, Anna, Babadi, Nasrin

[International Worm Meeting, 2011]

Formation of neural networks is complex process that not only requires axon growth and guidance, but also depends on the ability of the axons to generate branches and connect with multiple targets. We use the worm's egg laying organ and the neuronal networks that control this process to study the process of axon branching. VC4, VC5 and the HSNs are the neurons that innervate the vulva muscles and regulate egg expulsion. VC4 and VC5 motor neurons project their axons laterally around the vulva, where they overlap and form branches. Our lab has showed that mutations in png-1, the sole worm orthologue of peptide N-glycanase (PNGase), cause excessive and complex ectopic branching defects in VC4 and VC5. Additionally, we also found that these png-1 branching defects are strongly enhanced when combined with mutations in sax-1/NDR kinase and sax-2/Furry. To better understand how VC neurons develop in wild-type and mutant backgrounds we are currently peforming a time-lapse analysis using an unc-4p::GFP reporter to visualize VC4 and VC5 from neuritogenesis to target innervation. We will present our findings.

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.

Leticia Sanchez-Alvarez et al. (2009) International Worm Meeting "PCP signalling polarizes C elegans motorneurons along the medial-lateral axis during organogenesis."

Leticia Sanchez-Alvarez, Anna Su, Andrea McEwan, Janice Imai, Antonio Colavita, Jiravat Visanuvimol

[International Worm Meeting, 2009]

To understand how neurons polarize in vivo we studied the morphology of two bipolar motorneurons (VC4 and VC5), which polarize medial-laterally (ML) to innervate the egg-laying system of C elegans. To identify genes responsible for the bipolar ML morphology we performed genetic screens to isolate worms with defective VC4/5 polarity. So far we have isolated mutations in prickle-1 (prickle homolog-1 LGIV, 4 alleles), vang-1 (Van Gogh homolog-1 LGX, 3 alleles) and dsh-1 (dishevelled homolog-1 LGII, 1 allele) genes that result in ectopic misdirected axons. VC4 & 5 neurons in prkl-1, vang-1 and dsh-1 mutants extend a third axon in the AP axis rendering neurons with tripolar morphology. Here we report that evolutionary conserved Planar Cell Polarity (PCP) genes prkl-1, vang-1 and dsh-1 mediate the ML orientation of VC4 and VC5 by suppressing ectopic axon outgrowth along the anterior-posterior axis. We explore the biological mechanism underlying the novel role for prkl-1, vang-1 and dsh-1 in the polarity of VC4 and VC5 by performing cell rescue experiments, loss and gain-of-function studies, examining the localization of functional translational fusions and analyzing the expression of transcriptional reporters.