Cold-dependent alternative splicing of a Jumonji C domain-containing gene MtJMJC5 in Medicago truncatula

Shen, Yingfang; Wu, Xiaopei; Liu, Demei; Song, Shengjing; Liu, Dengcai; Wang, Haiqing

doi:10.1016/j.bbrc.2016.04.062

Cited by 40 publications

(39 citation statements)

References 42 publications

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“…The phylogenetic relationships of AtJMJ30, OsJMJ717 , and MtJMJC5 (Mtr4g066020) in PKDM12 are consistent with a recent report (Shen et al, 2016). Shen et al showed that MtJMJC5 is involved in regulating circadian rhythm (Shen et al, 2016).…”

Section: Resultssupporting

confidence: 91%

“…Shen et al showed that MtJMJC5 is involved in regulating circadian rhythm (Shen et al, 2016). And recently, Li et al also reported that JMJ524, consistent with its counterparts AtJMJ30, is also involved in a circadian clock response in tomato (Li et al, 2015).…”

Section: Resultsmentioning

confidence: 99%

“…In tomato, a similar role is played by JMJ524 , which standardizes the circadian clock and also alters GA response to regulate stem elongation (Li et al, 2015). In Medicago truncatula, MtJMJC5 (Medtr4g066020), an ortholog of AtJMJ30/JMJD5 , may play a role in epigenetic regulation of the link between the circadian clock and cold signaling (Shen et al, 2016). In rice, OsJMJ705 is a biotic stress-responsive H3K27me2/3 demethylase that may remove H3K27me3 from marked defense-related genes and increase their basal and induced expression during pathogen infection (Li et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

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Genome-Wide Analysis of Soybean JmjC Domain-Containing Proteins Suggests Evolutionary Conservation Following Whole-Genome Duplication

Han

Cheng

et al. 2016

Front. Plant Sci.

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Histone modifications, such as methylation and demethylation, play an important role in regulating chromatin structure and gene expression. The JmjC domain-containing proteins, an important family of histone lysine demethylases (KDMs), play a key role in maintaining homeostasis of histone methylation in vivo. In this study, we performed a comprehensive analysis of the jumonji C (JmjC) gene family in the soybean genome and identified 48 JmjC genes (GmJMJs) distributed unevenly across 18 chromosomes. Phylogenetic analysis showed that these JmjC domain-containing genes can be divided into eight groups. GmJMJs within the same phylogenetic group share similar exon/intron organization and domain composition. In addition, 16 duplicated gene pairs were formed by a Glycine-specific whole-genome duplication (WGD) event approximately 13 million years ago (Mya). By investigating the expression profiles of these gene pairs in various tissues, we showed that the expression pattern is conserved in the polyploidy-derived JmjC duplicates, demonstrating that the majority of GmJMJs were preferentially retained after the most recent WGD event and suggesting important roles for demethylase duplications in soybean evolution. These results shed light on the evolutionary history of this family in soybean and provide insights into the JmjCs which will be helpful to reveal their functions in controlling soybean development.

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Section: Resultssupporting

confidence: 91%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Genome-Wide Analysis of Soybean JmjC Domain-Containing Proteins Suggests Evolutionary Conservation Following Whole-Genome Duplication

Han

Cheng

et al. 2016

Front. Plant Sci.

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“…In Medicago truncatula, an orthologue of arabidopsis JMJD5 has been shown to undergo cold‐dependent alternative splicing (Shen et al., ). Because JMJD5 is a component of the circadian clock (Jones et al., ; Shen et al., ; Yan et al., ), it has been suggested that cold‐dependent alternative splicing in some species might provide a link for epigenetic regulation in response to changes in circadian rhythms induced by shifts in temperature.…”

Section: Discussionmentioning

confidence: 99%

Expression of FLOWERING LOCUS C and a frameshift mutation of this gene on chromosome 20 differentiate a summer and winter annual biotype of Camelina sativa

et al. 2018

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The nature of the vegetative to reproductive transition in the shoot apical meristem of Camelina sativa summer annual cultivar CO46 and winter annual cultivar Joelle was confirmed by treating seedlings with or without 8 weeks of vernalization. True to their life cycle classification, Joelle required a vernalization treatment to induce bolting and flowering, whereas CO46 did not. In this study, whole genome sequence, RNAseq, and resequencing of PCR‐amplified transcripts for a key floral repressor were used to better understand factors involved in the flowering habit of summer and winter biotypes at the molecular level. Analysis of transcriptome data indicated that abundance for one of the three genes encoding the floral repressor FLOWERING LOCUS C (FLC; Csa20 g015400) was 16‐fold greater in Joelle compared to CO46 prior to vernalization. Abundance of this transcript decreased only slightly in CO46 postvernalization, compared to a substantial decrease in Joelle. The results observed in the winter annual biotype Joelle are consistent with repression of FLC by vernalization. Further characterization of FLC at both the genome and transcriptome levels identified a one base deletion in the 5th exon coding for a keratin‐binding domain in chromosome 20 of CO46 and Joelle. The one base deletion detected in chromosome 20 FLC is predicted to result in a frameshift that would produce a nonfunctional protein. Analysis of whole genome sequence indicated that the one base deletion in chromosome 20 FLC occurred at a greater ratio in the summer biotype CO46 (2:1) compared to the winter biotype Joelle (1:4); similar trends were also observed for RNAseq and cDNA transcripts mapping to chromosome 20 FLC of CO46 and Joelle.

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“…AtJMJ11/ELF6 and AtJMJ12/REF6 interacted with BES1, which is a key transcription factor in the Brassinosteroid (BR) signaling pathway, and participated in the regulation of BR‐mediated stress responses (Yu et al ., ). In Medicago truncatula , MtJMJC5 undergoes cold specifically induced alternative splicing and might play a role in epigenetic regulation of cold acclimation and freezing tolerance (Shen et al ., ). However, whether JmjC family histone demethylases are involved in the regulation of anthocyanin biosynthesis in plants response to environmental cues remains unclear.…”

Section: Introductionmentioning

confidence: 97%

Histone H3K9 demethylase JMJ25 epigenetically modulates anthocyanin biosynthesis in poplar

et al. 2018

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Anthocyanins are involved in several aspects of development and defence in poplar (Populus spp.). Although, over the past decades, significant progress has been made in uncovering these anthocyanin biosynthetic and regulatory mechanisms, the fundamental understanding of the epigenetic regulation in this pathway is still largely unclear. Here, we isolated a histone H3K9 demethylase gene JMJ25 from Populus and characterized its role in anthocyanin biosynthesis by genetic and biochemical approaches. JMJ25 was induced by continuous dark treatment. Overexpression of JMJ25 led to downregulated expression of anthocyanin biosynthetic genes in transgenic poplar, resulting in a significant reduction in anthocyanin content. ChIP-qPCR assays showed that JMJ25 could directly associate with MYB182 chromatin and dynamically demethylate at H3K9me2. Furthermore, JMJ25 also affected the DNA methylation levels of MYB182. By contrast, knockout of JMJ25 by CRISPR/Cas9 resulted in ectopic anthocyanin accumulation under dark condition and increased expression of anthocyanin biosynthetic genes. Our results support a model in which JMJ25 directly affects MYB182 expression by altering the histone methylation status of its chromatin and DNA methylation, resulting in repression of anthocyanin accumulation. This study uncovered an epigenetic mechanism that modulates anthocyanin biosynthesis in poplar.

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Cold-dependent alternative splicing of a Jumonji C domain-containing gene MtJMJC5 in Medicago truncatula

Cited by 40 publications

References 42 publications

Genome-Wide Analysis of Soybean JmjC Domain-Containing Proteins Suggests Evolutionary Conservation Following Whole-Genome Duplication

Genome-Wide Analysis of Soybean JmjC Domain-Containing Proteins Suggests Evolutionary Conservation Following Whole-Genome Duplication

Expression of FLOWERING LOCUS C and a frameshift mutation of this gene on chromosome 20 differentiate a summer and winter annual biotype of Camelina sativa

Histone H3K9 demethylase JMJ25 epigenetically modulates anthocyanin biosynthesis in poplar

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