Rte-1, a retrotransposon-like element in Caenorhabditis elegans

AbstractWe have characterized a retrotransposon-like element (Rte-1) in C. elegans. It was identified while we were sequencing the pim related kinase-1 (prk-1) gene. The element is 3,298 bp long and flanked by a 200 bp direct repeat. 95 bp of the direct repeat are present in the coding region of prk-1. Rte-1 contains an open reading frame, in the opposite orientation of prk-1, potentially encoding 625 amino acids, with similarity to reverse transcriptases. The element is most similar to members of the non-LTR group of retrotransposable elements. There is weak homology of the predicted amino acid sequence of Rte-1 to several reverse transcriptase-like genes identified by the C. elegans genome sequencing consortium, suggesting that there may be a large family of these elements. Southern blots indicate that there are approximately 10–15 additional Rte-1 elements in the C. elegans Bristol N2 genome and a similar number is found in the genomes of two other geographically distinct strains. The insertion pattern of Rte-1 is polymorphic between these strains

mut-7 of C. elegans, Required for Transposon Silencing and RNA Interference, Is a Homolog of Werner Syndrome Helicase and RNaseD

AbstractWhile all known natural isolates of C. elegans contain multiple copies of the Tc1 transposon, which are active in the soma, Tc1 transposition is fully silenced in the germline of many strains. We mutagenized one such silenced strain and isolated mutants in which Tc1 had been activated in the germline (“mutators”). Interestingly, many other transposons of unrelated sequence had also become active. Most of these mutants are resistant to RNA interference (RNAi). We found one of the mutated genes, mut-7, to encode a protein with homology to RNaseD. This provides support for the notion that RNAi works by dsRNA-directed, enzymatic RNA degradation. We propose a model in which MUT-7, guided by transposon-derived dsRNA, represses transposition by degrading transposon-specific messengers, thus preventing transposase production and transposition

The protein that binds to DNA base J in trypanosomatids has features of a thymidine hydroxylase

© 2007 The Author et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in Nucleic Acids Research 35 (2007): 2107-2115, doi:10.1093/nar/gkm049.Trypanosomatids contain an unusual DNA base J (ß-D-glucosylhydroxymethyluracil), which replaces a fraction of thymine in telomeric and other DNA repeats. To determine the function of base J, we have searched for enzymes that catalyze J biosynthesis. We present evidence that a protein that binds to J in DNA, the J-binding protein 1 (JBP1), may also catalyze the first step in J biosynthesis, the conversion of thymine in DNA into hydroxymethyluracil. We show that JBP1 belongs to the family of Fe2+ and 2-oxoglutarate-dependent dioxygenases and that replacement of conserved residues putatively involved in Fe2+ and 2-oxoglutarate-binding inactivates the ability of JBP1 to contribute to J synthesis without affecting its ability to bind to J-DNA. We propose that JBP1 is a thymidine hydroxylase responsible for the local amplification of J inserted by JBP2, another putative thymidine hydroxylase.This work was funded by a grant from the Netherlands Organization for Scientific Research and Chemical Sciences (NWO-CW) to P.B., NIH grant A1063523 to R.S. and NIH grant GM063584 to R.P.H

Benchmarking biology research organizations using a new, dedicated tool

International competition forces fundamental research organizations to assess their relative performance. We present a benchmark tool for scientific research organizations where, contrary to existing models, the group leader is placed in a central position within the organization. We used it in a pilot benchmark study involving six research institutions. Our study shows that data collection and data comparison based on this new tool can be achieved. It proved possible to compare relative performance and organizational characteristics and to generate suggestions for improvement for most participants. However, strict definitions of the parameters used for the benchmark and a thorough insight into the organization of each of the benchmark partners is required to produce comparable data and draw firm conclusions

DNA binding activities of the Caenorhabditis elegans Tc3 transposase

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-termlnal 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 ∼ 180 bp from the end. Methylatlon interference experiments indicate that this N-termlnal DNA binding domain of the Tc3 transposase Interacts with nucleotides on one face of the DNA helix over adjacent major and minor grooves

The mechanism of transposition of Tc3 in C. elegans

The Tc3 transposon of C. elegans belongs to a family of inverted repeat DNA transposons, found in many different phyla. We studied the mechanism of Tc3 transposition by expression of Tc3 transposase from a heat-shock promoter in transgenic nematodes. Transposition is accompanied by the appearance of linear extrachromosomal Tc3 DNA. Analysis of the ends of this presumed transposition intermediate shows that the transposon is excised incompletely: the 5′ ends of the transposon lack two nucleotides. The 3′ ends coincide with the last nucleotide of the integrated element and carry 3′ hydroxyls. The nucleotides that are not coexcised with the transposon remain at the donor site and result in a characteristic footprint. A model is derived for the mechanism of Tc3 jumping that probably applies to the entire family of Tc1/mariner transposable elements

Southern blot and J-immunoblot of genomic DNA of various kinetoplastid parasites digested with frequently cutting restriction enzymes

<p><b>Copyright information:</b></p><p>Taken from "Telomeric localization of the modified DNA base J in the genome of the protozoan parasite "</p><p></p><p>Nucleic Acids Research 2007;35(7):2116-2124.</p><p>Published online 28 Feb 2007</p><p>PMCID:PMC1874636.</p><p>© 2007 The Author(s)</p> DNA was digested with the restriction enzymes AluI, AvaII, CfoI, HinfI, RsaI, SspI, size-fractionated and blotted as described in . The left panel shows the result after incubation with the J-antiserum (α-J). The right panel shows the result of the hybridization with the telomeric probe (telo)