title: Cold-dependent alternative splicing of a Jumonji C domain-containing gene MtJMJC5 in Medicago truncatula.
abstract: Histone methylation is an epigenetic modification mechanism that regulates gene expression in eukaryotic cells. Jumonji C domain-containing demethylases are involved in removal of methyl groups at lysine or arginine residues. The JmjC domain-only member, JMJ30/JMJD5 of Arabidopsis, is a component of the plant circadian clock. Although some plant circadian clock genes undergo alternative splicing in response to external cues, there is no evidence that JMJ30/JMJD5 is regulated by alternative splicing. In this study, the expression of an Arabidopsis JMJ30/JMJD5 ortholog in Medicago truncatula, MtJMJC5, in response to circadian clock and abiotic stresses were characterized. The results showed that MtJMJC5 oscillates with a circadian rhythm, and undergoes cold specifically induced alternative splicing. The cold-induced alternative splicing could be reversed after ambient temperature returning to the normal. Sequencing results revealed four alternative splicing RNA isoforms including a full-length authentic protein encoding variant, and three premature termination condon-containing variants due to alternative 3' splice sites at the first and second intron. Under cold treatment, the variants that share a common 3' alternative splicing site at the second intron were intensively up-regulated while the authentic protein encoding variant and the premature termination condon-containing variant only undergoing a 3' alternative splicing at the first intron were down regulated. Although all the premature termination condon-harboring alternative splicing variants were sensitive to nonsense-mediated decay, the premature termination codon-harboring alternative splicing variants sharing the 3' alternative splicing site at the second intron showed less sensitivity than the one only containing the 3' alternative slicing site at the first intron under cold treatment. These results suggest that the cold-dependent alternative splicing of MtJMJC5 is likely a species or genus-specific mechanism of gene expression regulation on RNA levels, and might play a role in epigenetic regulation of the link between the circadian clock and ambient temperature fluctuation in Medicago.
authors.affiliation: Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810001, People's Republic of China; Graduate University of the Chinese Academy of Sciences, Beijing 100081, People's Republic of China.
authors.forename: Yingfang
authors.initials: Y
authors.lastname: Shen
authors.affiliation: Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810001, People's Republic of China; Graduate University of the Chinese Academy of Sciences, Beijing 100081, People's Republic of China.
authors.forename: Xiaopei
authors.initials: X
authors.lastname: Wu
authors.affiliation: Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810001, People's Republic of China.
authors.forename: Demei
authors.initials: D
authors.lastname: Liu
authors.affiliation: College of Life Sciences, Northwest University, Xi'an 710069, People's Republic of China.
authors.forename: Shengjing
authors.initials: S
authors.lastname: Song
authors.affiliation: Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810001, People's Republic of China.
authors.forename: Dengcai
authors.initials: D
authors.lastname: Liu
authors.affiliation: Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810001, People's Republic of China. Electronic address: wanghq@nwipb.cas.cn.
authors.forename: Haiqing
authors.initials: H
authors.lastname: Wang
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics; D017398:Alternative Splicing / Q000235:genetics*; D057906:Circadian Clocks / Q000235:genetics*; D003080:Cold Temperature; D058639:Cold-Shock Response / Q000235:genetics*; D018506:Gene Expression Regulation, Plant / Q000235:genetics; D056484:Jumonji Domain-Containing Histone Demethylases / Q000235:genetics*; D046913:Medicago truncatula / Q000502:physiology*; D000072417:Protein Domains / Q000235:genetics
chemical_list: D056484:Jumonji Domain-Containing Histone Demethylases
keywords: Alternative splicing; Cold stress; JMJ30/JMJD5 ortholog; JmjC domain-containing protein; Medicago truncatula