Chromatin dynamics associated with seed desiccation tolerance/sensitivity at early germination in Medicago truncatula

Abstract

Desiccation tolerance (DT) has contributed greatly to the adaptation of land plants to severe water-deficient conditions. DT is mostly observed in reproductive parts in flowering plants such as seeds. The seed DT is lost at early post germination stage but is temporally re-inducible in 1 mm radicles during the so-called DT window following a PEG treatment before being permanently silenced in 5 mm radicles of germinating seeds. The molecular mechanisms that activate/reactivate/silence DT in developing and germinating seeds have not yet been elucidated. Here, we analyzed chromatin dynamics related to re-inducibility of DT before and after the DT window at early germination in Medicago truncatula radicles to determine if DT-associated genes were transcriptionally regulated at the chromatin levels. Comparative transcriptome analysis of these radicles identified 948 genes as DT re-induction-related genes, positively correlated with DT re-induction. ATAC-Seq analyses revealed that the chromatin state of genomic regions containing these genes was clearly modulated by PEG treatment and affected by growth stages with opened chromatin in 1 mm radicles with PEG (R1P); intermediate openness in 1 mm radicles without PEG (R1); and condensed chromatin in 5 mm radicles without PEG (R5). In contrast, we also showed that the 103 genes negatively correlated with the re-induction of DT did not show any transcriptional regulation at the chromatin level. Additionally, ChIP-Seq analyses for repressive marks H2AK119ub and H3K27me3 detected a prominent signal of H3K27me3 on the DT re-induction-related gene sequences at R5 but not in R1 and R1P. Moreover, no clear H2AK119ub marks was observed on the DT re-induction-related gene sequences at both developmental radicle stages, suggesting that silencing of DT process after germination will be mainly due to H3K27me3 marks by the action of the PRC2 complex, without involvement of PRC1 complex. The dynamic of chromatin changes associated with H3K27me3 were also confirmed on seed-specific genes encoding potential DT-related proteins such as LEAs, oleosins and transcriptional factors. However, several transcriptional factors did not show a clear link between their decrease of chromatin openness and H3K27me3 levels, suggesting that their accessibility may also be regulated by additional factors, such as other histone modifications. Finally, in order to make these comprehensive genome-wide analyses of transcript and chromatin dynamics useful to the scientific community working on early germination and DT, we generated a dedicated genome browser containing all these data and publicly available at https://iris.angers.inrae.fr/mtseedepiatlas/jbrowse/?data=Mtruncatula.

The re-establishment of desiccation tolerance in germinated tomato (Solanum lycopersicum) seeds

“…Organ-/tissue-specific differences in DT during the postgermination process have been reported in several plant species, including Medicago (Faria et al, 2005;Sano et al, 2022), Arabidopsis (Maia et al, 2011), mung bean (Tian et al, 2019), C. korshinskii (Peng et al, 2017) and pea (Wang et al, 2021). The common characteristic is that the ability to re-acquire DT is lost at younger stages in roots of post-germination compared to cotyledon and hypocotyl, and/or the lost root-DT is hardly re-established by PEG treatment compared to cotyledons and hypocotyl.…”

“…After the DT assay in Medicago without PEG treatment, germinating seeds often demonstrated cotyledon growth, albeit resuming less radicle growth (Faria et al, 2005). This tendency is more prominent in the PEG-treated DT assay, where root growth re-initiation was only observed at the early post-germination phase, whereas a high proportion of healthy cotyledons were developed from all the tested post-germination stages (Sano et al, 2022), consistent with previous findings that a greater proportion of seeds treated by PEG succeed in re-inducing DT to cotyledons than to roots for a longer time frame of postgermination in Arabidopsis (Maia et al, 2011). Moreover, levels of osmotic potential, temperature and treatment time are known to be factors that influence the degree of re-establishment of seed-DT, and the optimal conditions vary among the reported plant species (Peng et al, 2022).…”

Seed longevity and genome damage

“…Re-acquisition of desiccation tolerance in M. truncatula was preceded by a transcriptional programme with similarities to seed maturation and repression of metabolism and cell cycle activity [ 19 ]. Changes in gene expression associated with the re-acquisition of desiccation tolerance were reflected in chromatin accessibility and histone modifications [ 20 ]. Protein levels of cell cycle and glycolysis enzymes (e.g.…”

“…9-CIS-EPOXYCAROTENOID DIOXYGENASE (NCED6), a key enzyme in ABA biosynthesis, is progressively silenced at the transcriptional and chromatin level during germination, potentially correlating with loss of desiccation tolerance [ 100 ]. Changes in chromatin dynamics of several genes were associated with the re-imposition of desiccation tolerance in Medicago [ 20 ]. Epigenetic modification modulates chromatin structure and compaction, thereby controlling accessibility of DNA repair, DNA replication and transcriptional machinery [ 101 ].…”