TY - JOUR
T1 - Genome-wide analysis of alternative splicing events in Hordeum vulgare: Highlighting retention of intron-based splicing and its possible function through network analysis
AU - Panahi, Bahman
AU - Mohammadi, Seyed
AU - Khaksefidi, Reyhaneh
AU - Mehrabadi, Jalil
AU - Ebrahimie, Esmaeil
PY - 2015/11/30
Y1 - 2015/11/30
N2 - 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.
AB - 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.
KW - Alternative splicing
KW - Functional diversity
KW - Hordeum vulgare
KW - Network discovery
KW - Semi quantitative Reverse Transcription PCR
UR - http://www.scopus.com/inward/record.url?scp=84947087870&partnerID=8YFLogxK
U2 - 10.1016/j.febslet.2015.09.023
DO - 10.1016/j.febslet.2015.09.023
M3 - Article
SN - 0014-5793
VL - 589
SP - 3564
EP - 3575
JO - FEBS Letters
JF - FEBS Letters
IS - 23
ER -