Diversity of vertebrate splicing factor U2AF35 : identification of alternatively spliced U2AF1 mRNAS

© 2004 ASBMB. Currently published by Elsevier Inc; originally published by American Society for Biochemistry and Molecular Biology. This is an Open Access article under the CC BY license.U2 small nuclear ribonucleoprotein auxiliary factor small subunit (U2AF(35)) is encoded by a conserved gene designated U2AF1. Here we provide evidence for the existence of alternative vertebrate transcripts encoding different U2AF(35) isoforms. Three mRNA isoforms (termed U2AF(35)a-c) were produced by alternative splicing of the human U2AF1 gene. U2AF(35)c contains a premature stop codon that targets the resulting mRNA to nonsense-mediated mRNA decay. U2AF(35)b differs from the previously described U2AF(35)a isoform in 7 amino acids located at the atypical RNA Recognition Motif involved in dimerization with U2AF(65). Biochemical experiments indicate that isoform U2AF(35)b, which has been highly conserved from fish to man, maintains the ability to interact with U2AF(65), stimulates U2AF(65) binding to a pre-mRNA, and promotes U2AF splicing activity in vitro. Real time, quantitative PCR analysis indicates that U2AF(35)a is the most abundant isoform expressed in murine tissues, although the ratio between U2AF(35)a and U2AF(35)b varies from 10-fold in the brain to 20-fold in skeletal muscle. We propose that post-transcriptional regulation of U2AF1 gene expression may provide a mechanism by which the relative cellular concentration and availability of U2AF(35) protein isoforms are modulated, thus contributing to the finely tuned control of splicing events in different tissues.This work was supported in part by Grant POCTI/MGI/36547/2000 from Fundação para a Ciência e Tecnologia, Portugal, and by Grant RG0300/2000-M from the Human Frontier Science Program Organization. Supported by Fundação para a Ciência e Tecnologia Fellowship PRAXIS XXI/BD/18044/98. Supported by Fundação para a Ciência e Tecnologia Fellowship POCTI SFRH/BPD/9388/2002. Supported by Fundação para a Ciência e Tecnologia Fellowship PRAXIS XXI SFRH/BD/2914/2000.info:eu-repo/semantics/publishedVersio

Conferencia "Secuencing technology for the Human Genome"

Conferencia divulgativa organizada por la Sociedad de Amigos del Museo Nacional de Ciencias Naturales y celebrada en enero de 1991.N

Next-generation DNA sequencing techniques

Next-generation high-throughput DNA sequencing techniques are opening fascinating opportunities in the life sciences. Novel fields and applications in biology and medicine are becoming a reality, beyond the genomic sequencing which was original development goal and application. Serving as examples are: personal genomics with detailed analysis of individual genome stretches; precise analysis of RNA transcripts for gene expression, surpassing and replacing in several respects analysis by various microarray platforms, for instance in reliable and precise quantification of transcripts and as a tool for identification and analysis of DNA regions interacting with regulatory proteins in functional regulation of gene expression. The next-generation sequencing technologies offer novel and rapid ways for genome-wide characterisation and profiling of mRNAs, small RNAs, transcription factor regions, structure of chromatin and DNA methylation patterns, microbiology and metagenomics. In this article, development of commercial sequencing devices is reviewed and some European contributions to the field are mentioned. Presently commercially available very high-throughput DNA sequencing platforms, as well as techniques under development, are described and their applications in bio-medical fields discussed

Transcriptomics and Proteomics - Application to Ecotoxicology

The Joint Research Center (JRC) of the European Commission hosted a workshop, DNA microarray and Proteomics. Application to Ecotoxicology;, in Ispra, Italy, on May 19-20th 2005. Researchers from Europe and the USA met to discuss how to integrate gene and protein expression analyses with bioinformatics tools in the field of ecotoxicology and how this new approach could be translated in improved risk assessment procedures. The measurements of gene and/or protein expression levels, upon exposure to a chemical or a stressor, can be used to develop robust molecular biomarkers that will allow the early detection of environmental stress, study long-term exposure and infer the mechanism of action. These molecular biomarkers should be linked to traditional end points of exposure such as adverse effects in growth and reproduction in single organisms and populations. At the low concentrations of chemicals found in real environments there could be “non standard” dose-response curves and this possibility should be taken into account in the experimental design and in the analyses of the data. The application of gene and protein expression profiling in ecotoxicology will have a significant impact on the ecotoxicology field in the near future and international collaborations will play an important role in accelerating the application of those techniques.JRC.H.5-Rural, water and ecosystem resource

Expression of coiled-coil protein 1, a novel gene downstream of FGF2, in the developing brain

Fibroblast growth factor 2 (FGF2) plays an important role in cortical development. However, the genes downstream of FGF2 that mediate its effect are largely unknown. We have performed a microarray screening of genes regulated by FGF2 using primary cortical neuron culture derived from embryonic day 14.5 (E14.5) mouse forebrains. In this study, we have analysed a previously uncharacterised gene encoding a 180-amino acid protein, hereby named ‘coiled-coil protein 1 (ccp1)’, that showed a modest up-regulation upon FGF2 stimulation. Northern blots and RT-PCR showed specific expression of ccp1 in multiple tissues including adult and embryonic brains. In situ hybridizations revealed that ccp1 was expressed in the cortical plate between Reelin and Tbr1-positive layers in the dorsal cortex at E15.5. Furthermore, the expression pattern of ccp1 at E13.5–E14.5 reflected some of the aspects of tangential migration of cortical progenitors during the early phase. We observed that the expressed ccp1 protein was localised to endo/lysosomal compartment in the cell body as well as to vesicles present in the processes of primary cortical neurons and oligodendrocyte cell line