alexa High levels of RNA-editing site conservation amongst 15 laboratory mouse strains.
Genetics & Molecular Biology

Genetics & Molecular Biology

Gene Technology

Author(s): Danecek P, Nellker C, McIntyre RE, BuendiaBuendia JE, Bumpstead S,

Abstract Share this page

Abstract BACKGROUND: Adenosine-to-inosine (A-to-I) editing is a site-selective post-transcriptional alteration of double-stranded RNA by ADAR deaminases that is crucial for homeostasis and development. Recently the Mouse Genomes Project generated genome sequences for 17 laboratory mouse strains and rich catalogues of variants. We also generated RNA-seq data from whole brain RNA from 15 of the sequenced strains. RESULTS: Here we present a computational approach that takes an initial set of transcriptome/genome mismatch sites and filters these calls taking into account systematic biases in alignment, single nucleotide variant calling, and sequencing depth to identify RNA editing sites with high accuracy. We applied this approach to our panel of mouse strain transcriptomes identifying 7,389 editing sites with an estimated false-discovery rate of between 2.9 and 10.5\%. The overwhelming majority of these edits were of the A-to-I type, with less than 2.4\% not of this class, and only three of these edits could not be explained as alignment artifacts. We validated 24 novel RNA editing sites in coding sequence, including two non-synonymous edits in the Cacna1d gene that fell into the IQ domain portion of the Cav1.2 voltage-gated calcium channel, indicating a potential role for editing in the generation of transcript diversity. CONCLUSIONS: We show that despite over two million years of evolutionary divergence, the sites edited and the level of editing at each site is remarkably consistent across the 15 strains. In the Cds2 gene we find evidence for RNA editing acting to preserve the ancestral transcript sequence despite genomic sequence divergence.
This article was published in Genome Biol and referenced in Gene Technology

Relevant Expert PPTs

Relevant Speaker PPTs

  • David Köhne
    Principles and applications of optical switching assisted imaging and structuring schemes
    PPT Version | PDF Version
  • Jeyaparvathi Somasundaram
    Identification of Serum miRNAs as prospective Bio-markers for acute and chronic pancreatitis
    PPT Version | PDF Version
  • Joachim Struck
    Pro-enkephalin (Penkid): A novel plasma biomarker to assess renal impairment
    PPT Version | PDF Version
  • Omar E Franco
    Heterogeneous Tumor Stroma and Prostate Carcinogenesis
    PPT Version | PDF Version
  • Mapitsi S Thantsha
    In vitro antagonistic effects of Listeria adhesion protein (LAP)-expressing Lactobacillus casei against Listeria monocytogenes and Salmonella Typhimurium Copenhagen
    PPT Version | PDF Version
  • Tibor Tot
    Multiparameter characterization of breast carcinoma: subgross, microscopy, proteins, and genes
    PPT Version | PDF Version
  • Saroj Velamakanni
    Multiparameter analysis using cell cycle biomarkers for breast cancer: Prognostic and predictive implications
    PPT Version | PDF Version
  • Luiza Guilherme
    Streptococcus pyogenes candidate vaccine
    PPT Version | PDF Version
  • Francis Jeshira Reynoso
    The clinical phenotype of PIGN deficiency and consequences of defective GPI biogenesis
    PPT Version | PDF Version
  • Yen-Chein Lai
    Molecular pathogenesis in granulosa cell tumor is not only due to somatic FOXL2 mutation
    PPT Version | PDF Version
  • Fathia El Sharkawi
    The effect of PTEN and TRAIL genes loaded on nanoparticles on hepatocellular carcinoma
    PPT Version | PDF Version
  • Alexandra Vatsiou
    Pathways and genes under positive selection in metabolic diseases
    PPT Version | PDF Version
  • Chia-chi Liu
    Oxidative inhibition of erythrocyte sodium pump: A functionally relevant circulating marker of oxidative stress
    PPT Version | PDF Version
  • Saurabh Chaudhary
    De novo transcriptome assembly and identification of cold and freeze responsive genes in sea buckthorn
    PPT Version | PDF Version
  • Yosef Yarden
    Classically, the 3’untranslated region (3’UTR) is that region in eukaryotic protein-coding genes from the translation termination codon to the polyA signal. It is transcribed as an integral part of the mRNA encoded by the gene. However, there exists another kind of RNA, which consists of the 3’UTR alone, without all other elements in mRNA such as 5’UTR and coding region. The importance of independent 3’UTR RNA (referred as I3’UTR) was prompted by results of artificially introducing such RNA species into malignant mammalian cells. Since 1991, we found that the middle part of the 3’UTR of the human nuclear factor for interleukin-6 (NF-IL6) or C/EBP gene exerted tumor suppression effect in vivo. Our subsequent studies showed that transfection of C/EBP 3’UTR led to down-regulation of several genes favorable for malignancy and to up-regulation of some genes favorable for phenotypic reversion. Also, it was shown that the sequences near the termini of the C/EBP 3’UTR were important for its tumor suppression activity. Then, the C/EBP 3’UTR was found to directly inhibit the phosphorylation activity of protein kinase CPKC in SMMC-7721, a hepatocarcinoma cell line. Recently, an AU-rich region in the C/EBP 3’UTR was found also to be responsible for its tumor suppression. Recently we have also found evidence that the independent C/EBP 3’UTR RNA is actually exists in human tissues, such as fetal liver and heart, pregnant uterus, senescent fibroblasts etc. Through 1990’s to 2000’s, world scientists found several 3’UTR RNAs that functioned as artificial independent RNAs in cancer cells and resulted in tumor suppression. Interestingly, majority of genes for these RNAs have promoter-like structures in their 3’UTR regions, although the existence of their transcribed products as independent 3’UTR RNAs is still to be confirmed. Our studies indicate that the independent 3’UTR RNA is a novel non-coding RNA species whose function should be the regulation not of the expression of their original mRNA, but of some essential life activities of the cell as a whole.
    PPT Version | PDF Version

Recommended Conferences

  • 2nd International Conference and Expo on Generic Drug Market and Contract Manufacturing
    September 25-26, 2017 Frankfurt, Germany
  • 6th International Conference and Exhibition on Cell and Gene Therapy
    Mar 27-28, 2017 Madrid, Spain
  • 2nd World Congress on Human Genetics & Genetic Disorders
    November 02-03, 2017 Toronto, Canada

Relevant Topics

Peer Reviewed Journals
 
Make the best use of Scientific Research and information from our 700 + peer reviewed, Open Access Journals
International Conferences 2017-18
 
Meet Inspiring Speakers and Experts at our 3000+ Global Annual Meetings

Contact Us

 
© 2008-2017 OMICS International - Open Access Publisher. Best viewed in Mozilla Firefox | Google Chrome | Above IE 7.0 version
adwords