Genome-wide Analysis of Alternative Splicing in An Inbred Cabbage (Brassica oleracea L.) Line 'HO' in Response to Heat Stress

Current Genomics
Sang Sook LeeHye Sun Cho

Abstract

High-throughput RNA sequencing (RNA-Seq) studies demonstrate that Alter-native Splicing (AS) is a widespread mechanism that enhances transcriptome diversity, particularly in plants exposed to environmental stress. In an attempt to determine the transcriptome and AS patterns of cabbage inbred line "HO" under Heat Stress (HS), RNA-Seq was carried out using HS-treated and con-trol samples. Genome-wide analysis indicated that AS is differentially regulated in response to HS. The number of AS events markedly increased in HS-treated samples compared to the control. We identified 1,864 genes, including Heat shock transcription factor (Hsf) and heat shock protein (Hsp) genes, that exhibited >4-fold changes in expression upon exposure to HS. The enriched Gene Ontology (GO) terms of the 1,864 genes included 'response to stress/abiotic stimulus/chemical stimulus', among, which the genes most highly induced by HS encode small Hsps and Hsf proteins. The heat-induced genes also showed an increased number of AS events under HS conditions. In addi-tion, the distribution of AS types was altered under HS conditions, as the level of Intron Retention (IR) decreased, whereas other types of AS increased, under these conditions. Severe HS-induced AS ...Continue Reading

Citations

Nov 17, 2019·International Journal of Molecular Sciences·Saeed Ul HaqZhen-Hui Gong

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Methods Mentioned

BETA
environmental stress
Reverse Transcription-PCR
PCR
electrophoresis
RNA-Seq
environmental stresses
protein folding

Software Mentioned

Agro GO tool
TopHat
SOLEXA QA
Agro
TopHatII
house Perl scripts
Cluster
in

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