Development of primer sets that can verify the enrichment of histone modifications, and their application to examining vernalization-mediated chromatin changes in &lt;i&gt;Brassica rapa&lt;/i&gt; L.

Kawanabe, Takahiro; Osabe, Kenji; Itabashi, Etsuko; Okazaki, Keiichi; Dennis, Elizabeth S.; Fujimoto, Ryo

doi:10.1266/ggs.15-00058

Cited by 27 publications

(34 citation statements)

References 49 publications

(59 reference statements)

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“…Characterization of histone modifications has also been initiated in other Brassica species (e.g., Chinese cabbage, Kawanabe et al, 2016). To the best of our knowledge, however, ChIP experiments have not hitherto been performed on field samples through different seasons, and nothing is known about how histone modifications may change in the field.…”

Section: Discussionmentioning

confidence: 99%

From the laboratory to the field: assaying histone methylation at FLOWERING LOCUS C in naturally growing Arabidopsis halleri

et al. 2016

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Gene regulatory mechanisms are often defined in studies performed in the laboratory but are seldom validated for natural habitat conditions, i.e., in natura. Vernalization, the promotion of flowering by winter cold, is a prominent naturally occurring phenomenon, so far best characterized using artificial warm and cold treatments. The floral inhibitor FLOWERING LOCUS C (FLC) gene of Arabidopsis thaliana has been identified as the central regulator of vernalization. FLC shows an idiosyncratic pattern of histone modification at different stages of cold exposure, believed to regulate transcriptional responses of FLC. Chromatin modifications, including H3K4me3 and H3K27me3, are routinely quantified using chromatin immunoprecipitation (ChIP), standardized for laboratory samples. In this report, we modified a ChIP protocol to make it suitable for analysis of field samples. We first validated candidate normalization control genes at two stages of cold exposure in the laboratory and two seasons in the field, also taking into account nucleosome density. We further describe experimental conditions for performing sampling and sample preservation in the field and demonstrate that these conditions give robust results, comparable with those from laboratory samples. The ChIP protocol incorporating these modifications, "Field ChIP", was used to initiate in natura chromatin analysis of AhgFLC, an FLC orthologue in A. halleri, of which a natural population is already under investigation. Here, we report results on levels of H3K4me3 and H3K27me3 at three representative regions of AhgFLC in controlled cold and field samples, before and during cold exposure. We directly compared the results in the field with those from laboratory samples. These data revealed largely similar trends in histone modification dynamics between laboratory and field samples at AhgFLC, but also identified some possible differences. The Field ChIP method described here will facilitate comprehensive chromatin analysis of AhgFLC in the future to contribute to our understanding of gene regulation in fluctuating natural environments.

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Section: Discussionmentioning

confidence: 99%

From the laboratory to the field: assaying histone methylation at FLOWERING LOCUS C in naturally growing Arabidopsis halleri

et al. 2016

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“…Before cold treatment, only BrFLC1 showed accumulation of both H3K4me3 and H3K36me3 modifications, while three of the BrFLC paralogs (BrFLC2, BrFLC3, and BrFLC5) had only H3K4me3. After 4 weeks of cold treatment, the accumulation of H3K27me3 was observed in BrFLC1, BrFLC2, and BrFLC3, and H3K27me3 was maintained after returning to a warm temperature [85]. These results indicate that, like A. thaliana, the repression of BrFLC expression by prolonged cold treatment was associated with the states of histone modification.…”

Section: Regulation Of Flcs By Vernalization In the Genus Brassicamentioning

confidence: 73%

“…In B. rapa, it has been shown that there is a difference in the expression levels of the FLC paralogs [85]. The coding sequences for the FLC paralogs are relatively conserved between Brassica species, but the alignment of the upstream sequences or introns are more divergent [57].…”

Section: Regulation Of Flcs By Vernalization In the Genus Brassicamentioning

confidence: 99%

Genetic and Epigenetic Regulation of Vernalization in Brassicaceae

Akter¹,

Nishida²,

Takada³

et al. 2018

Brassica Germplasm - Characterization, Breeding and Utilization

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A wide variation of morphological traits exists in Brassica rapa L. and Brassica oleracea L., and cultivated vegetable varieties of these species are consumed worldwide. Flowering time is an important agronomic trait in these species and varies among varieties or cultivars. Especially, leafy vegetable species need a high bolting resistance. Isolation of FLOWERING LOCUS C (FLC), one of the key genes involved in vernalization, has now provided an insight into the molecular mechanism involved in the regulation of flowering time, including the role of histone modification. In the model plant Arabidopsis thaliana, FLC plays an important role in modulating flowering time. The response to vernalization causes an increase in histone H3 lysine 27 tri-methylation (H3K27me3) that leads to reduced expression of the FLC gene. B. rapa and B. oleracea both contain several paralogs of FLC at syntenic regions identified as major flowering time and vernalization response quantitative trait loci (QTL). We introduce the recent research, not only in A. thaliana, but also in the genus Brassica from a genetic and epigenetic view point.

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“…In Chinese cabbage, the reduced transcription of FLC could be an important factor in premature bolting (Itabashi et al, 2018;Shea et al, 2018;Su et al, 2018;Takada et al, 2019). There are four FLC paralogs in B. rapa and at least three of them act as floral repressors (Kawanabe et al, 2016;Kim et al, 2007;Schranz et al, 2002;Takada et al, 2019). All FLC paralogs were downregulated by prolonged cold treatment, and an increased level of H3K27me3 was observed around the first exon in all FLC paralogs in Chinese cabbage (Akter et al, 2019;Kawanabe et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

“…There are four FLC paralogs in B. rapa and at least three of them act as floral repressors (Kawanabe et al, 2016;Kim et al, 2007;Schranz et al, 2002;Takada et al, 2019). All FLC paralogs were downregulated by prolonged cold treatment, and an increased level of H3K27me3 was observed around the first exon in all FLC paralogs in Chinese cabbage (Akter et al, 2019;Kawanabe et al, 2016). Following a return to normal temperature growth conditions, H3K27me3 spreads along all four BrFLC paralogs providing stable repression of the gene (Akter et al, 2019;Takada et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

Gene Expression Analysis in Response to Vernalization in Chinese Cabbage (Brassica rapa L.)

et al. 2020

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Chinese cabbage (Brassica rapa L. var. pekinensis) is an economically and agriculturally significant leafy vegetable that is extensively cultivated throughout the world. Vernalization is exposure to prolonged cold that alters gene expression and accelerates a transition from the vegetative to reproductive phase. Premature bolting caused by exposure to cold inhibits head production and reduces the yield of Chinese cabbage, and developing a late bolting line is important for breeding. Therefore, it is critical to identify the genes showing differential expression patterns during cold treatment in Chinese cabbage. However, there are few studies on the transcriptome profiling of different durations of cold treatments in Chinese cabbage. Here, we analyzed the gene expression profiles in a Chinese cabbage inbred line, RJKB-T24, given different durations of cold treatments using RNA sequencing. Differentially expressed genes (DEGs) between non-vernalized and vernalized samples tended to be downregulated, and some genes involved in the flowering pathway (including BrFLC and BrMAF genes) were downregulated following cold treatment. Functional enrichment analysis indicated that some DEGs were involved in the stress response and hormone signaling pathways. For genes involved in the FRI-containing complex, a known activator of FLC in Arabidopsis thaliana, only BrFRL1 showed changes in expression. In contrast to A. thaliana, BrVIP and BrVRN genes showed different expression patterns between paralogs during cold treatment, suggesting that Chinese cabbage's flowering pathway is somehow different and more complex than in A. thaliana. These outcomes provide significant insights into the genetic control of bolting and flowering that occur during the vernalization of Chinese cabbage.

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Development of primer sets that can verify the enrichment of histone modifications, and their application to examining vernalization-mediated chromatin changes in <i>Brassica rapa</i> L.

Cited by 27 publications

References 49 publications

From the laboratory to the field: assaying histone methylation at <i>FLOWERING LOCUS C</i> in naturally growing <i>Arabidopsis halleri</i>

From the laboratory to the field: assaying histone methylation at <i>FLOWERING LOCUS C</i> in naturally growing <i>Arabidopsis halleri</i>

Genetic and Epigenetic Regulation of Vernalization in Brassicaceae

Gene Expression Analysis in Response to Vernalization in Chinese Cabbage (<i>Brassica rapa</i> L.)

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