Epigenetics and RNA Processing: Connections to Drought, Salt, and ABA?

Wong, Min May; Chong, Geeng Loo; Verslues, Paul E.

doi:10.1007/978-1-4939-7136-7_1

Cited by 11 publications

(11 citation statements)

References 104 publications

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“…IPT5b is also a key regulator of this trait, and DNA methylation regions found in IPT5b promoter of dwarfing rootstocks further demonstrates the complex role of IPT5b in apple rootstocks. DNA methylation status in plant is regulated by various physiological, developmental, and stress stimuli (Wong, Chong, & Verslues, ). Salt stress leads to distinct DNA methylation changes (Wibowo et al, ), suggesting that altered DNA methylation patterns might be involved in stress acclimation.…”

Section: Discussionmentioning

confidence: 99%

Natural variation in cytokinin maintenance improves salt tolerance in apple rootstocks

Feng

Liu

Zhai

et al. 2018

Plant Cell & Environment

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Plants experiencing salt-induced stress often reduce cytokinin levels during the early phases of stress-response. Interestingly, we found that the cytokinin content in the apple rootstock "robusta" was maintained at a high level under salt stress. Through screening genes involved in cytokinin biosynthesis and catabolism, we found that the high expression levels of IPT5b in robusta roots were involved in maintaining the high cytokinin content. We identified a 42 bp deletion in the promoter region of IPT5b, which elevated IPT5b expression levels, and this deletion was linked to salt tolerance in robusta×M.9 segregating population. The 42 bp deletion resulted in the deletion of a Proline Response Element (ProRE), and our results suggest that ProRE negatively regulates IPT5b expression in response to proline. Under salt stress, the robusta cultivar maintains high cytokinin levels as IPT5b expression cannot be inhibited by proline due to the deletion of ProRE, leading to improve salt tolerance.

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Section: Discussionmentioning

confidence: 99%

Natural variation in cytokinin maintenance improves salt tolerance in apple rootstocks

Feng

Liu

Zhai

et al. 2018

Plant Cell & Environment

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“…Major evidence for phytohormone-chromatin crosstalk was obtained using Arabidopsis mutants, or applying phytohormones or chemical inhibitors of chromatin modifiers in various developmental processes (Yamamuro et al, 2016; Campos-Rivero et al, 2017; Wong et al, 2017; Guo et al, 2018; Ojolo et al, 2018; Wakeel et al, 2018; Zheng et al, 2018). Only a few reports highlight potential crosstalk directly in the meristems as exemplified by PRC2 repressing particular PIN genes (auxin transporters) in the SAM of Arabidopsis clv3 mutants (Lafos et al, 2011).…”

Section: Meristems Are Central Places For Phytohormone Chromatin Crosmentioning

confidence: 99%

Phytohormone and Chromatin Crosstalk: The Missing Link For Developmental Plasticity?

et al. 2019

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“…Transcriptome analyses often center on measuring changes in mRNA abundance invoked by a stimulus, stress, or developmental process (Walley and Dehesh 2010). In particular, regulation of mRNA abundance by the epigenome (Jiang et al 2014;Wong et al 2017) and by transcription factors (Song et al 2016) has been a primary focus in elucidation of mechanisms responsible for dynamic environmental regulation of the transcriptome. Post-transcriptional regulation, including alternative polyadenylation, splicing, localization, and degradation has received less attention, but also can substantially impact mRNA abundance (Floris et al 2009;Walley and Dehesh 2010;Feng et al 2015;Kawa and Testerink 2017;Wong et al 2017;Gu et al 2018;Sorenson et al 2018).…”

Section: Introductionmentioning

confidence: 99%

“…In particular, regulation of mRNA abundance by the epigenome (Jiang et al 2014;Wong et al 2017) and by transcription factors (Song et al 2016) has been a primary focus in elucidation of mechanisms responsible for dynamic environmental regulation of the transcriptome. Post-transcriptional regulation, including alternative polyadenylation, splicing, localization, and degradation has received less attention, but also can substantially impact mRNA abundance (Floris et al 2009;Walley and Dehesh 2010;Feng et al 2015;Kawa and Testerink 2017;Wong et al 2017;Gu et al 2018;Sorenson et al 2018). Changes in mRNA secondary and tertiary structures influence post-transcriptional processes (Bevilacqua et al 2016), as revealed by many examples based on in depth analysis of specific transcripts (Zaug and Cech 1995;Hull et al 2016).…”

Section: Introductionmentioning

confidence: 99%

Tissue-specific changes in the RNA structurome mediate salinity response in Arabidopsis

Tack

et al. 2020

RNA

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Little is known concerning the effects of abiotic factors on in vivo RNA structures. We applied Structure-seq to assess the in vivo mRNA structuromes of Arabidopsis thaliana under salinity stress, which negatively impacts agriculture. Structure-seq utilizes dimethyl sulfate reactivity to identify As and Cs that lack base pairing or protection. Salt stress refolded transcripts differentially in root vs. shoot, evincing tissue-specificity of the structurome. Both tissues exhibited an inverse correlation between salt stress-induced changes in transcript reactivity and changes in abundance, with stressrelated mRNAs showing particular structural dynamism. This inverse correlation is more pronounced in mRNAs wherein the mean reactivity of the 5'UTR, CDS and 3'UTR concertedly change under salinity stress, suggesting increased susceptibility to abundance control mechanisms in transcripts exhibiting this phenomenon, which we name "concordancy". Concordant salinity-induced increases in reactivity were notably observed in photosynthesis genes, thereby implicating mRNA structural loss in the well-known depression of photosynthesis by salt stress. Overall, changes in secondary structure appear to impact mRNA abundance, molding the functional specificity of the transcriptome under stress.

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Epigenetics and RNA Processing: Connections to Drought, Salt, and ABA?

Cited by 11 publications

References 104 publications

Natural variation in cytokinin maintenance improves salt tolerance in apple rootstocks

Natural variation in cytokinin maintenance improves salt tolerance in apple rootstocks

Phytohormone and Chromatin Crosstalk: The Missing Link For Developmental Plasticity?

Tissue-specific changes in the RNA structurome mediate salinity response in Arabidopsis

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