Global DNA methylation and cellular 5-methylcytosine and H4 acetylated patterns in primary and secondary dormant seeds of Capsella bursa-pastoris (L.) Medik. (shepherd’s purse)

Abstract

Despite the importance of dormancy and dormancy cycling for plants’ fitness and life cycle phenology, a comprehensive characterization of the global and cellular epigenetic patterns across space and time in different seed dormancy states is lacking. Using Capsella bursa-pastoris (L.) Medik. (shepherd’s purse) seeds with primary and secondary dormancy, we investigated the dynamics of global genomic DNA methylation and explored the spatio-temporal distribution of 5-methylcytosine (5-mC) and histone H4 acetylated (H4Ac) epigenetic marks. Seeds were imbibed at 30 °C in a light regime to maintain primary dormancy, or in darkness to induce secondary dormancy. An ELISA-based method was used to quantify DNA methylation, in relation to total genomic cytosines. Immunolocalization of 5-mC and H4Ac within whole seeds (i.e., including testa) was assessed with reference to embryo anatomy. Global DNA methylation levels were highest in prolonged (14 days) imbibed primary dormant seeds, with more 5-mC marked nuclei present only in specific parts of the seed (e.g., SAM and cotyledons). In secondary dormant seeds, global methylation levels and 5-mC signal where higher at 3 and 7 days than 1 or 14 days. With respect to acetylation, seeds had fewer H4Ac marked nuclei (e.g., SAM) in deeper dormant states, for both types of dormancy. However, the RAM still showed signal after 14 days of imbibition under dormancy-inducing conditions, suggesting a central role for the radicle/RAM in the response to perceived ambient changes and the adjustment of the seed dormancy state. Thus, we show that seed dormancy involves extensive cellular remodeling of DNA methylation and H4 acetylation.

(Epi)genetic control of secondary seed dormancy depth and germination in Capsella bursa-pastoris

“…The effect of histone deacetylase inhibitors on secondary seed dormancy induction and germination A broad range in secondary seed dormancy potential was previously observed among the nine C. bursa-pastoris ecotypes examined, with accessions -367 and -799 showing the deepest and shallowest secondary dormancy, respectively (Gomez-Cabellos et al, 2021). For the current study, we tested the effect of two HDAC inhibitors (TSA and valproic acid) on secondary seed dormancy induction and germination of the nine genotypes.…”

“…For the second aim of our study, RNA was extracted from seeds of two accessions contrasting in secondary dormancy depth (Gomez-Cabellos et al, 2021) that were imbibed in either water or valproic acid during secondary dormancy induction (Fig. 1).…”

“…The second aim of this study was to test the hypothesis that genes implicated in epigenetic regulation processes would be differentially expressed between C. bursa-pastoris accessions previously shown to contrast in secondary dormancy depth (Gomez-Cabellos et al, 2021). In particular, histone acetylases were expected to be down-regulated in a relatively deep-dormant accession compared with a non-deep dormant one.…”

Transition from Seeds to Seedlings: Hormonal and Epigenetic Aspects

“…DNA methylation patterns have a clearly dynamic character and are continuously changing during plant seed development [159][160][161][162]. Thus, the occupancy of the CHH methylation sites remarkably increases from the early to the late stages of seed development and gradually decreases later on during germination.…”

Epigenetic variation: A major player in facilitating plant fitness under changing environmental conditions

“…Three major types of epigenetic marks or signatures include DNA methylation, histone modifications, and small RNAs. During DNA methylation, the methyl groups get covalently bound to cytosine nucleotides (5 mC) ( Bartels et al, 2018 ; Gomez-Cabellos et al, 2022 ) and along with covalent modifications like methylation, acetylation, and phosphorylation in histone proteins regulate the local chromatin landscape ( Zhu et al, 2021 ; Tian et al, 2022 ). Non-coding small RNAs such as microRNAs play a significant role in post-transcriptional regulation directing DNA methylation and chromatin remodeling at their target loci ( Bossdorf et al, 2008 ; Robertson and Wolf, 2012 ; Bond and Baulcombe, 2014 ; Ariel and Manavella, 2021 ).…”