A Comprehensive Analysis of the Genomic and Expressed Repertoire of the T-Cell Receptor Beta Chain in .

In this paper, we report a comprehensive and consistent annotation of the locus encoding the β-chain of the equine T-cell receptor (TRB), as inferred from recent genome assembly using bioinformatics tools. The horse TRB locus spans approximately 1 Mb, making it the largest locus among the mammalian species studied to date, with a significantly higher number of genes related to extensive duplicative events. In the region, 136 TRBV (belonging to 29 subgroups), 2 TRBD, 13 TRBJ, and 2 TRBC genes, were identified.

What Have We Learned in 30 Years of Investigations on Transposons?

Transposable elements (TEs) have been historically depicted as detrimental genetic entities that selfishly aim at perpetuating themselves, invading genomes, and destroying genes. Scientists often co-opt "special" TEs to develop new and powerful genetic tools, that will hopefully aid in changing the future of the human being. However, many TEs are gentle, rarely unleash themselves to harm the genome, and bashfully contribute to generating diversity and novelty in the genomes they have colonized, yet they offer the opportunity to develop new molecular tools.

Evidence of the Physical Interaction between Rpl22 and the Transposable Element , a Heterochromatic Transposon of .

Chromatin is a highly dynamic biological entity that allows for both the control of gene expression and the stabilization of chromosomal domains. Given the high degree of plasticity observed in model and non-model organisms, it is not surprising that new chromatin components are frequently described. In this work, we tested the hypothesis that the remnants of the transposable element, which retains a heterochromatin insertion pattern in the melanogaster species complex, can be bound by chromatin proteins, and thus be involved in the organization of heterochromatic domains.

The mitochondrial aspartate/glutamate carrier (AGC or Aralar1) isoforms in D. melanogaster: biochemical characterization, gene structure, and evolutionary analysis.

Background: In man two mitochondrial aspartate/glutamate carrier (AGC) isoforms, known as aralar and citrin, are required to accomplish several metabolic pathways. In order to fill the existing gap of knowledge in Drosophila melanogaster, we have studied aralar1 gene, orthologue of human AGC-encoding genes in this organism.

Methods: The blastp algorithm and the "reciprocal best hit" approach have been used to identify the human orthologue of AGCs in Drosophilidae and non-Drosophilidae.

"What You Need, Baby, I Got It": Transposable Elements as Suppliers of Cis-Operating Sequences in Drosophila.

Transposable elements (TEs) are constitutive components of both eukaryotic and prokaryotic genomes. The role of TEs in the evolution of genes and genomes has been widely assessed over the past years in a variety of model and non-model organisms. is undoubtedly among the most powerful model organisms used for the purpose of studying the role of transposons and their effects on the stability and evolution of genes and genomes.

On the evolution of Yeti, a Drosophila melanogaster heterochromatin gene.

Constitutive heterochromatin is a ubiquitous and still unveiled component of eukaryotic genomes, within which it comprises large portions. Although constitutive heterochromatin is generally considered to be transcriptionally silent, it contains a significant variety of sequences that are expressed, among which about 300 single-copy coding genes have been identified by genetic and genomic analyses in the last decades. Here, we report the results of the evolutionary analysis of Yeti, an essential gene of Drosophila melanogaster located in the deep pericentromeric region of chromosome 2R.

The Drosophila mojavensis Bari3 transposon: distribution and functional characterization.

Background: Bari-like transposons belong to the Tc1-mariner superfamily, and they have been identified in several genomes of the Drosophila genus. This transposon's family has been used as paradigm to investigate the complex dynamics underlying the persistence and structural evolution of transposable elements (TEs) within a genome. Three structural Bari variants have been identified so far and can be distinguished based on the organization of their terminal inverted repeats.

Yeti, an essential Drosophila melanogaster gene, encodes a protein required for chromatin organization.

The evolutionarily conserved family of Bucentaur (BCNT) proteins exhibits a widespread distribution in animal and plants, yet its biological role remains largely unknown. Using Drosophila melanogaster as a model organism, we investigated the in vivo role of the Drosophila BCNT member called YETI. We report that loss of YETI causes lethality before pupation and defects in higher-order chromatin organization, as evidenced by severe impairment in the association of histone H2A.

Genomic instability of I elements of Drosophila melanogaster in absence of dysgenic crosses.

Retrotranspostion of I factors in the female germline of Drosophila melanogaster is responsible for the so called I-R hybrid dysgenesis, a phenomenon that produces a broad spectrum of genetic abnormalities including reduced fertility, increased frequency of mutations and chromosome loss. Transposition of I factor depends on cellular conditions that are established in the oocytes of the reactive females and transmitted to their daughters. The so-called reactivity is a cellular state that may exhibit variable levels of expression and represents a permissive condition for I transposition at high levels.

The paracentric inversion In(2Rh)PL alters the centromeric organization of chromosome 2 in Drosophila melanogaster.

Centromeres are complex structures involved in an evolutionarily conserved function, the correct segregation of chromosomes and chromatids during meiosis and mitosis. The centromere is determined by epigenetic processes that result in a particular nucleosome organization (CEN chromatin) that differs from the rest of the chromatin including the heterochromatin that normally surrounds the centromere in higher organisms. Many of the current models of centromere origin and organization rely on the molecular and cytological characterization of minichromosomes and their derivatives, and on studies on the origin and maintenance of neocentromeres.

Conserved motifs and dynamic aspects of the terminal inverted repeat organization within Bari-like transposons.

In this work the structural variations of Terminal Inverted Repeats (TIR) of Bari like transposons in Drosophila species has been studied. The aim is to try and assess the relevance of different variants in the evolutionary distribution of Bari elements. Bari is a member of the widespread Tc1 superfamily of transposable elements that has colonized most species of the Drosophila genus.

Cytogenetic and molecular characterization of heterochromatin gene models in Drosophila melanogaster.

In the past decade, genome-sequencing projects have yielded a great amount of information on DNA sequences in several organisms. The release of the Drosophila melanogaster heterochromatin sequence by the Drosophila Heterochromatin Genome Project (DHGP) has greatly facilitated studies of mapping, molecular organization, and function of genes located in pericentromeric heterochromatin. Surprisingly, genome annotation has predicted at least 450 heterochromatic gene models, a figure 10-fold above that defined by genetic analysis.

Evidence for a functional interaction between the Bari1 transposable element and the cytochrome P450 cyp12a4 gene in Drosophila melanogaster.

Previous studies of the genomic distribution of the transposon Bari1 in Drosophila melanogaster have revealed an element which is fixed at division 91F in over 90 lab and natural populations. Here we report about the structural and transcriptional features of the insertion site which was studied in sublines isolated from an exceptional Drosophila line polymorphic for the presence/absence of Bari1 at 91F. The insert is located at the 3' end of the cyp12a4 gene that belongs to the cytochrome P450 family.

Organization and possible origin of the Bari-1 cluster in the heterochromatic h39 region of Drosophila melanogaster.

The molecular organization of the heterochromatic h39 region of the Drosophila melanogaster second chromosome has been investigated by studying two BAC clones identified both by Southern blotting and by FISH experiments as containing tandem arrays of Bari1, a transposable element present only in this region. Such BAC clones appear to contain different portions of the h39 region since they differ in the DNA sequences flanking the Bari1 repeats on both sides. Thus, the 80 Bari1 copies estimated to be present in the h39 region are split into at least two separated subregions.

A survey of the DNA sequences surrounding the Bari1 repeats in the pericentromeric h39 region of Drosophila melanogaster.

In Drosophila melanogaster, clustered copies of the Bari1 transposon are only present in the pericentromeric h39 region of the second chromosome, where other clusters of repetitive elements, either found organized in large tandem arrays only in the h39 region (Responder, PortoI), or both in the h39 region and in other heterochromatic regions (Hoppel), are also observed. The topological relationship among the repetitive sequences of the h39 region and the nature of the sequences separating its large repeat clusters are at present largely unknown. To get new insights on the sequence composition of the heterochromatin and on the forces governing its origin and maintenance, we have cloned and analyzed part of the DNA sequences flanking the h39 Bari1 repeats.