1,721,232 research outputs found
A tandemly repeated DNA family originated from SINE-related elements in the European plethodontid salamanders (Amphibia, Urodela).
No full textWe have characterized a highly repetitive family, named Hy/Pol III, in the genome of the European salamanders Hydromantes (Plethodontidae). This family consists of short, tandemly repeated sequences organized in clusters, scattered through the genome as shown both by in situ hybridization to chromosomes and by Southern blot hybridization. The repeat unit is about 200 bp in length and it is a composite element since it contains a SINE-like retroposon with a tRNA structure, flanked by two short direct repeats. The whole element itself is bordered by two other direct repeats. The sequence data suggest that two elements, presumably derived from polymerase III transcripts, have been inserted one into the other, giving rise to the observed composite structure. During evolution the Hy/Pol III family was then amplified by tandem duplication at the DNA level. The inferred relationships between Hy/Pol III members from three representative species of the European Hydromantes suggests that a subfamily structure characterizes the evolutionary history of this family
Using Weeder for the discovery of conserved transcription factor binding sites
No full textOne of the greatest challenges facing modern molecular biology is the understanding of the complex mechanisms regulating gene expression. A fundamental step in this process requires the characterization of motifs involved in the regulation of gene expression at transcriptional and post-transcriptional levels. In particular, transcription is modulated by the interaction of transcription factors with their corresponding binding sites. Weeder is a software package freely available for non commercial users as a stand-alone or Web-based application for the automatic discovery of conserved motifs in a set of related DNA sequences from coregulated genes. The motifs found are likely to represent instances of binding sites for some common transcription factor regulating the genes of the set. The program has been designed to make its usage as simple as possible and to require very little prior knowledge about the length and conservation of the motifs to be found
Gypsy-Ty3 like elements in the genome of the terrestrial salamander Hydromantes (Amphibia: Urodela)
No full textWe have studied a family of long repetitive DNA sequences (Hsr1) interspersed in the large genome of the European plethodontid salamander Hydromantes. The sequence analysis of a 5-kb fragment (Hsr1A) of one member has revealed significant similarities with aminoacidic domains of retroviruses and retrotransposons. The similarity of the reverse transcriptase domain and the gene organization identifies Hsr1A as a member of the gypsy/Ty3 class of retrotransposons. We hypothesize that Hsr1 sequences are vestiges of an invasion of the Hydromantes genome that occurred early in the evolutionary history of these European plethodontids. About 10(6) Hsr1 sequences are present in the large Hydromantes genome. This is the highest number of copies so far discovered for retrotransposon-like elements in eukaryote organisms
Systematic and evolutionary studies in mammals: The contribution of the mitochondrial genome
No full textMolecular data represent an important source of information for systematic and evolutionary studies; ideally this information should be evaluated together with data coming from other approaches (e.g., paleontological and morphological), since the molecular approach is limited by the availability of suitable homologous sequences, and these may be taxonomically informative only if they derive from speciation events (i.e., orthologous) and not from gene duplications (i.e., paralogous). This study focuses on the availability of sequences from the vertebrate class of Mammalia. The results show a strong bias in databases as, for some orders, little or no sequences are stored. For nuclear genes it is often difficult to discriminate between orthologous and paralogous ones. Therefore we advise the use in comparative studies of entire mitochondrial genomes which are easy to sequence and only contain orthologous genes. We report here the genetic organization of the mitochondrial DNA in mammals. In addition a phylogenetic tree of mammals, obtained by using the complete mitochondrial genomes of 23 species, is reported here
Detection of a-to-i rna editing in sars-cov-2
Full text linkADAR1-mediated deamination of adenosines in long double-stranded RNAs plays an important role in modulating the innate immune response. However, recent investigations based on metatranscriptomic samples of COVID-19 patients and SARS-COV-2-infected Vero cells have recovered contrasting findings. Using RNAseq data from time course experiments of infected human cell lines and transcriptome data from Vero cells and clinical samples, we prove that A-to-G changes observed in SARS-COV-2 genomes represent genuine RNA editing events, likely mediated by ADAR1. While the A-to-I editing rate is generally low, changes are distributed along the entire viral genome, are overrepresented in exonic regions, and are (in the majority of cases) nonsynonymous. The impact of RNA editing on virus–host interactions could be relevant to identify potential targets for therapeutic interventions
Molecular evolution: From past to future
No full textNucleic acids, the molecules responsible for the storage and transmission of genetic information, can reveal the beguiling history of the evolution of life on earth. In this paper, the molecular mechanisms underlying the evolutionary processes are illustrated together with the methods for the reconstruction of their history. The new technologies and the development of genetic engineering suggest future scenarios for the evolutionary process in relation to environmental phenomena
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