@article {49639, title = {The Trypanosoma cruzi L1Tc and NARTc non-LTR retrotransposons show relative site specificity for insertion.}, journal = {Mol Biol Evol}, volume = {23}, year = {2006}, month = {2006 Feb}, pages = {411-20}, abstract = {

The trypanosomatid protozoan Trypanosoma cruzi contains long autonomous (L1Tc) and short nonautonomous (NARTc) non-long terminal repeat retrotransposons. NARTc (0.25 kb) probably derived from L1Tc (4.9 kb) by 3{\textquoteright}-deletion. It has been proposed that their apparent random distribution in the genome is related to the L1Tc-encoded apurinic/apyrimidinic endonuclease (APE) activity, which repairs modified residues. To address this question we used the T. cruzi (CL-Brener strain) genome data to analyze the distribution of all the L1Tc/NARTc elements present in contigs larger than 10 kb. This data set, which represents 0.91x sequence coverage of the haploid nuclear genome ( approximately 55 Mb), contains 419 elements, including 112 full-length L1Tc elements (14 of which are potentially functional) and 84 full-length NARTc. Approximately half of the full-length elements are flanked by a target site duplication, most of them (87\%) are 12 bp long. Statistical analyses of sequences flanking the full-length elements show the same highly conserved pattern upstream of both the L1Tc and NARTc retrotransposons. The two most conserved residues are a guanine and an adenine, which flank the site where first-strand cleavage is performed by the element-encoded endonuclease activity. This analysis clearly indicates that the L1Tc and NARTc elements display relative site specificity for insertion, which suggests that the APE activity is not responsible for first-strand cleavage of the target site.

}, keywords = {Animals, DNA, Protozoan, DNA-(Apurinic or Apyrimidinic Site) Lyase, Mutagenesis, Insertional, Retroelements, Sequence Deletion, Trypanosoma cruzi}, issn = {0737-4038}, doi = {10.1093/molbev/msj046}, author = {Bringaud, Frederic and Bartholomeu, Daniella C and Blandin, Ga{\"e}lle and Delcher, Arthur and Baltz, Th{\'e}o and el-Sayed, Najib M A and Ghedin, Elodie} } @article {49696, title = {Genetic enhancement of RNA-processing defects by a dominant mutation in B52, the Drosophila gene for an SR protein splicing factor.}, journal = {Mol Cell Biol}, volume = {15}, year = {1995}, month = {1995 Nov}, pages = {6273-82}, abstract = {

SR proteins are essential for pre-mRNA splicing in vitro, act early in the splicing pathway, and can influence alternative splice site choice. Here we describe the isolation of both dominant and loss-of-function alleles of B52, the gene for a Drosophila SR protein. The allele B52ED was identified as a dominant second-site enhancer of white-apricot (wa), a retrotransposon insertion in the second intron of the eye pigmentation gene white with a complex RNA-processing defect. B52ED also exaggerates the mutant phenotype of a distinct white allele carrying a 5{\textquoteright} splice site mutation (wDR18), and alters the pattern of sex-specific splicing at doublesex under sensitized conditions, so that the male-specific splice is favored. In addition to being a dominant enhancer of these RNA-processing defects, B52ED is a recessive lethal allele that fails to complement other lethal alleles of B52. Comparison of B52ED with the B52+ allele from which it was derived revealed a single change in a conserved amino acid in the beta 4 strand of the first RNA-binding domain of B52, which suggests that altered RNA binding is responsible for the dominant phenotype. Reversion of the B52ED dominant allele with X rays led to the isolation of a B52 null allele. Together, these results indicate a critical role for the SR protein B52 in pre-mRNA splicing in vivo.

}, keywords = {Alleles, Amino Acid Sequence, Animals, Base Sequence, DNA Primers, Drosophila melanogaster, Drosophila Proteins, Frameshift Mutation, Genes, Dominant, Genes, Insect, Molecular Sequence Data, Nuclear Proteins, Phosphoproteins, Point Mutation, Protein Structure, Tertiary, Proteins, RNA Splicing, RNA-Binding Proteins, Sequence Deletion, Sex Determination Analysis}, issn = {0270-7306}, author = {Peng, X and Mount, S M} } @article {49699, title = {P element-mediated in vivo deletion analysis of white-apricot: deletions between direct repeats are strongly favored.}, journal = {Genetics}, volume = {136}, year = {1994}, month = {1994 Mar}, pages = {1001-11}, abstract = {

We have isolated and characterized deletions arising within a P transposon, P[hswa], in the presence of P transposase. P[hswa] carries white-apricot (wa) sequences, including a complete copia element, under the control of an hsp70 promoter, and resembles the original wa allele in eye color phenotype. In the presence of P transposase, P[hswa] shows a high overall rate (approximately 3\%) of germline mutations that result in increased eye pigmentation. Of 234 derivatives of P[hswa] with greatly increased eye pigmentation, at least 205 carried deletions within copia. Of these, 201 were precise deletions between the directly repeated 276-nucleotide copia long terminal repeats (LTRs), and four were unique deletions. High rates of transposase-induced precise deletion were observed within another P transposon carrying unrelated 599 nucleotide repeats (yeast 2 mu FLP; recombinase target sites) separated by 5.7 kb. Our observation that P element-mediated deletion formation occurs preferentially between direct repeats suggests general methods for controlling deletion formation.

}, keywords = {Alleles, Animals, Animals, Genetically Modified, Base Sequence, Crosses, Genetic, DNA, DNA Transposable Elements, Drosophila, Eye Color, Female, Genes, Insect, Male, Molecular Sequence Data, Nucleotidyltransferases, PHENOTYPE, Recombination, Genetic, Repetitive Sequences, Nucleic Acid, Sequence Deletion, Transformation, Genetic, Transposases}, issn = {0016-6731}, author = {Kurkulos, M and Weinberg, J M and Roy, D and Mount, S M} }