Genome-wide analysis of alternative splicing events in Hordeum vulgare: Highlighting retention of intron-based splicing and its possible function through network analysis

Bahman Panahi, Seyed Mohammadi, Reyhaneh Khaksefidi, Jalil Mehrabadi, Esmaeil Ebrahimie

    Research output: Contribution to journalArticle

    22 Citations (Scopus)

    Abstract

    In this study, using homology mapping of assembled expressed sequence tags against the genomic data, we identified alternative splicing events in barley. Results demonstrated that intron retention is frequently associated with specific abiotic stresses. Network analysis resulted in discovery of some specific sub-networks between miRNAs and transcription factors in genes with high number of alternative splicing, such as cross talk between SPL2, SPL10 and SPL11 regulated by miR156 and miR157 families. To confirm the alternative splicing events, elongation factor protein (MLOC-3412) was selected followed by experimental verification of the predicted splice variants by Semi quantitative Reverse Transcription PCR (qRT-PCR). Our novel integrative approach opens a new avenue for functional annotation of alternative splicing through regulatory-based network discovery.

    Original languageEnglish
    Pages (from-to)3564-3575
    Number of pages12
    JournalFEBS Letters
    Volume589
    Issue number23
    DOIs
    Publication statusPublished - 2015

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