Harris LJ et al. (1988) Nucleic Acids Res "Sequence identity between an inverted repeat family of transposable elements in Drosophila and Caenorhabditis."

Baillie DL, Rose AM, Harris LJ

[Nucleic Acids Res, 1988]

The Tc1-like transposable elements, originally described in Caenorhabditis elegans, have a much wider phylogenetic distribution than previously thought. In this paper, we demonstrate that Tc1 shares sequence identity in its open reading frame and terminal repeats with a new transposable element Barney (also known as TCb1- Transposon Caenorhabditis briggsae 1). Barney was detected and isolated by Tc1 hybridization from the closely related nematode species, Caenorhabditis briggsae. The conserved open reading frames of Tc1 and Barney share identity with a structurally similar family of elements named HB found in Drosophila melanogaster, after the introduction of 3 small centrally located deletions in HB1. These reading frames would code for proteins with 30% amino acid identity (42% when conservative changes are included). Tc1, Barney and HB1 contain highly conserved blocks of amino acids which are likely to be in the functional domains of the putative transposase.

Harris LJ et al. (1988) Worm Breeder's Gazette "sequence identity between Caenorhabditis and Drosophila transposable elements."

Harris LJ, Rose AM, Baillie DL

[Worm Breeder's Gazette, 1988]

Transposable elements, like Tc1, have a much wider phylogenetic distribution than previously thought. Tc1 and TCb1 (also known as Barney) share sequence identity with the open reading frame (ORF) of the HB elements found in Drosophila melanogaster. The ORFs of Tc1 and Barney can be aligned with HB1 after the introduction of 3 centrally located deletions in HB1. These reading frames would code for proteins with 30% amino acid identity (42% when conservative changes are included). Tc1, Barney and HB1 contain highly conserved blocks of amino acids which are likely to be in the functional domains of the putative transposase. It is unfortunate that the HB elements in Drosophila are defective and can't reveal secrets of mobility. Within the class of inverted repeat elements, a subclass of closely related elements exists. This subclass includes Tc1 and Barney in the Nematoda and HB in Arthropoda. Since these phyla are evolutionarily quite distant it is reasonable to suppose that Tc1-like elements will have a wide distribution within the eukaryotes. Their presence in these two phyla could have resulted from the existence of the element in a common ancestor prior to the time of divergence (>500 million years) or might have resulted from more recent horizontal transfer. The sequence comparisons of Tc1, Barney and HB1 are to be published in Nucleic Acids Research.

Elder, Corrina et al. (2021) International Worm Meeting "Tissue-Specific Roles of microRNA Argonaute Proteins in Aging"

Pasquinelli, Amy, Nicastro, Ian, Elder, Corrina, Barney, Nathan, Chipman, Laura

[International Worm Meeting, 2021]

MicroRNAs (miRNAs) are short, non-coding RNA molecules that negatively regulate gene expression post-transcriptionally. When bound with Argonautes (AGOs) and other companion proteins, miRNAs can target mRNAs for degradation or translational repression. The miRNA pathway is conserved through many organisms and is involved in development, longevity, and stress responses. Two integral Caenorhabditis elegans AGOs (ALG-1 and ALG-2) are 81% identical at the amino acid level and have similar spatiotemporal expression patterns in developing C. elegans, but recent work shows that these developmentally redundant AGOs take on opposing roles in adults. There is a global reduction of ALG-1 expression in adults, while ALG-2 levels remain constant. Loss of function (LOF) alg-1 mutants have shortened lifespans, whereas LOF alg-2 mutants live longer than wildtype organisms. Through transcriptional profiling of these mutants, we've identified unique sets of misregulated miRNAs and protein-coding genes. Interestingly, there is an enrichment of up-regulated neuronal-specific genes in the alg-1 adult mutant, and previous work has shown that individual tissues play pivotal roles in regulating longevity. We have begun to test well-characterized aging phenotypes at the tissue level, which reveal that ALG-1 is important in the maintenance of pharyngeal, muscular, and intestinal integrity in adulthood. Additionally, we have generated tissue-specific ALG-1- or ALG-2-depleted strains to begin testing the hypothesis that ALG-1 and ALG-2 regulate miRNA targets in a tissue-specific manner, leading to opposing roles in the lifespan of C. elegans.

Harris LJ et al. (1986) Worm Breeder's Gazette "Barney - a repetitive element in C Briggsae with Tc1 homology."

Harris LJ, Rose AM

[Worm Breeder's Gazette, 1986]

A repetitive element which is homologous to the transposable element Tc1 from C. elegans resides in C. briggsae. When an EcoRV-cut Tc1 probe is hybridized with moderate stringency to C. briggsae EcoRI- digested genomic DNA, numerous bands can be visualized at a weaker signal than those seen in C. elegans. This Tc1 probe was used to screen a C. briggsae var. G16 Charon 4 library (constructed by T. Snutch). A single EcoRI fragment in each of 13 phage contained Tc1 homology and these have been subcloned. These plasmids are being compared with respect to their restriction map and homologous regions. The restriction sites found in Tc1 are not present in these subclones. The Tc1 homology appears to extend over the entirety of the Tc1 element. The size of the C. briggsae repetitive element is not known. A SalI/EcoRI fragment with Tc1 homology from one of the C. briggsae plasmids was hybridized against DNA from two C. briggsae strains, G16 and Zuckerman. The repetitive element is at low copy number ( approximately fifteen bands in G16) in both strains, but there are at least six banding differences between these strains. The repetitive element has been named Barney.

Harris LJ et al. (1990) J Mol Evol "Isolation and sequence analysis of Caenorhabditis briggsae repetitive elements related to the Caenorhabditis elegans transposon Tc1."

Rose AM, Harris LJ, Prasad SS

[J Mol Evol, 1990]

We have identified two repetitive element families in the genome of the nematode Caenorhabditis briggsae with extensive sequence identity to the Caenorhabditis elegans transposable element Tc1. Five members each of the TCb1 (previously known as Barney) and TCb2 families were isolated by hybridization to a Tc1 probe. Tc1-hybridizing repetitive elements were grouped into either the TCb1 or TCb2 family based on cross-hybridization intensities among the C. briggsae elements. The genomic copy number of the TCb1 family is 15 and the TCb2 family copy number is 33 in the C. briggsae strain G16. The two transposable element families show numerous genomic hybridization pattern differences between two C. briggsae strains, suggestive of transpositional activity. Two members of the TCb1 family, TCb1#5 and TCb1#10, were sequenced. Each of these two elements had suffered an independent single large deletion. TCb1#5 had a 627-bp internal deletion and TCb1#10 had lost 316 bp of one end. The two sequenced TCb1 elements were highly conserved over the sequences they shared. A 1616-bp composite TCb1 element was constructed from TCb1#5 and TCb1#10. The composite TCb1 element has 80-bp terminal inverted repeats with three nucleotide mismatches and two open reading frames (ORFs) on opposite strands. TCb1 and the 1610-bp Tc1 share 58% overall nucleotide sequence identity, and the greatest similarity occurs in their ORF1 and inverted repeat termini.