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Large-Scale Transcriptomic Approaches for Characterization of Post-Transcriptional Control of Gene Expression

  • Laura Do Souto
  • Alfonso González-BrionesEmail author
  • Andreia J. Amaral
  • Margarida Gama-Carvalho
  • Juan F. De Paz
Conference paper
  • 708 Downloads
Part of the Advances in Intelligent Systems and Computing book series (AISC, volume 477)

Abstract

MicroRNAs are critical regulators of gene expression programs. It has been demonstrated that during the maturation of miRNAs some changes can happen leading to the production of isoforms called isomiRs. During our study, a PERL pipeline was developed to find all the miRs (miRNAs) and isomiRs in two sets of Next Generation Sequencing (NGS) of small RNA libraries derived from naïve and activated CD4+ T cells. Then, a differential expression analysis was performed using Bioconductor package DESeq. Our pipeline allowed us to find all the different types of isomiRs in both of conditions. Also, we found that the isoforms coming from changes on 3’ are more frequent that in 5’ ends. Tailing isoforms are described as the less frequent isomiRs. The use of DESeq on the read count dataset of these miRs and isomiRs identified a total of 5 miRs and 22 isomiRs which were differentially expressed. So, in addition to creating a new tool for isomiR analysis, we have been able to obtain evidence that upon activation miRs and isomiRs in T-cells are differentially expressed.

Keywords

isomirs Differentially expressed NGS 

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Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  • Laura Do Souto
    • 1
  • Alfonso González-Briones
    • 2
    Email author
  • Andreia J. Amaral
    • 3
  • Margarida Gama-Carvalho
    • 3
  • Juan F. De Paz
    • 2
  1. 1.UFR Sciences et des TechniquesUniversity of RouenMont Saint Aignan CedexFrance
  2. 2.Biomedical Research Institute of Salamanca/BISITE Research GroupUniversity of Salamanca, Edificio I+D+iSalamancaSpain
  3. 3.BioFIG-Centre for Biodiversity, Functional and Integrative Genomics, Faculty of ScienceUniversity of LisbonLisbonPortugal

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