The characteristics of the porcine (Sus scrofa) liver miRNAome with the use of next generation sequencing View Full Text


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Article Info

DATE

2014-09-18

AUTHORS

Klaudia Pawlina, Artur Gurgul, Maria Oczkowicz, Monika Bugno-Poniewierska

ABSTRACT

MicroRNAs (miRNAs) are a class of small, noncoding RNAs, which play a vital role in the regulation of gene expression by binding to the 3′ untranslated region (3′UTR) of a target mRNA. Despite a significant improvement in the identification of miRNAs in a variety of species, the coverage of the porcine miRNAome is still scarce. To identify porcine miRNAs potentially regulating processes taking place in the liver, we applied next generation sequencing. As a result, we detected 206 distinct miRNAs, of which 68 represented potential novel miRNAs. Among these new miRNAs, there were miRNAs deriving from the opposite arm of a hairpin precursor of already known miRNAs. Moreover, we observed 3′ and 5′ length and sequence variants, probably constituting so called isomiRs, as well as differentially mapped precursor loci, alternative precursor sequences and clustering of miRNA encoding genes. On the basis of expression levels, reflected by the number of sequence reads, we identified the most abundant miRNAs followed by gene target prediction and pathway analysis. The enriched pathways were connected with cellular and metabolic processes, growth factors as well as enzymatic activity. The obtained results are the first ones to concern the porcine liver miRNAome. Consequently, they will increase the number of known porcine miRNAs and facilitate further research on gene regulation mechanisms as well as biological processes associated with the liver functioning in pigs. More... »

PAGES

239-252

References to SciGraph publications

  • 2004-09-15. Mechanisms of gene silencing by double-stranded RNA in NATURE
  • 2010-05-07. Analysis of microRNA transcriptome by deep sequencing of small RNA libraries of peripheral blood in BMC GENOMICS
  • 2006-04-04. RNA editing of human microRNAs in GENOME BIOLOGY
  • 2004-09-29. A custom microarray platform for analysis of microRNA gene expression in NATURE METHODS
  • 2006-05-30. microRNA target predictions in animals in NATURE GENETICS
  • 2003-09. The nuclear RNase III Drosha initiates microRNA processing in NATURE
  • 2013-06-13. A genome-wide integrative study of microRNAs in human liver in BMC GENOMICS
  • 2008-06-12. Identification and characterization of new microRNAs from pig in MAMMALIAN GENOME
  • 2007-09-26. Tumour invasion and metastasis initiated by microRNA-10b in breast cancer in NATURE
  • 2010-04-30. Deciphering the porcine intestinal microRNA transcriptome in BMC GENOMICS
  • 2004-07. MicroRNAs: small RNAs with a big role in gene regulation in NATURE REVIEWS GENETICS
  • 2005-02-16. Identification of microRNAs of the herpesvirus family in NATURE METHODS
  • 2010-02-24. Cloning and characterization of microRNAs from porcine skeletal muscle and adipose tissue in MOLECULAR BIOLOGY REPORTS
  • 2005-12-20. A single-molecule method for the quantitation of microRNA gene expression in NATURE METHODS
  • 2004-02-16. Expression profiling of mammalian microRNAs uncovers a subset of brain-expressed microRNAs with possible roles in murine and human neuronal differentiation in GENOME BIOLOGY
  • 2000-03. An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells in NATURE
  • 2005-04-03. Combinatorial microRNA target predictions in NATURE GENETICS
  • 2012-07-22. Fibroblast growth factor (Fgf) signaling pathway regulates liver homeostasis in zebrafish in TRANSGENIC RESEARCH
  • 2008-01. Endogenous human microRNAs that suppress breast cancer metastasis in NATURE
  • 2008-10-03. A truth serum for cancer — microRNAs have major potential as cancer biomarkers in CELL RESEARCH
  • 2009-07-28. Role of miRNAs in the progression of malignant melanoma in BRITISH JOURNAL OF CANCER
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1007/s13353-014-0245-6

    DOI

    http://dx.doi.org/10.1007/s13353-014-0245-6

    DIMENSIONS

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    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/25230983


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