Arabidopsis histone deacetylase HD2A and HD2B regulate seed dormancy by repressing DELAY OF GERMINATION 1

Abstract

Seed dormancy is a crucial developmental transition that affects the adaption and survival of plants. Arabidopsis DELAY OF GERMINATION 1 (DOG1) is known as a master regulator of seed dormancy. However, although several upstream factors of DOG1 have been reported, the exact regulation of DOG1 is not fully understood. Histone acetylation is an important regulatory layer, controlled by histone acetyltransferases and histone deacetylases. Histone acetylation strongly correlates with transcriptionally active chromatin, whereas heterochromatin is generally characterized by hypoacetylated histones. Here we describe that loss of function of two plant-specific histone deacetylases, HD2A and HD2B, resulted in enhanced seed dormancy in Arabidopsis. Interestingly, the silencing of HD2A and HD2B caused hyperacetylation of the DOG1 locus and promoted the expression of DOG1 during seed maturation and imbibition. Knockout of DOG1 could rescue the seed dormancy and partly rescue the disturbed development phenotype of hd2ahd2b. Transcriptomic analysis of the hd2ahd2b line shows that many genes involved in seed development were impaired. Moreover, we demonstrated that HSI2 and HSL1 interact with HD2A and HD2B. In sum, these results suggest that HSI2 and HSL1 might recruit HD2A and HD2B to DOG1 to negatively regulate DOG1 expression and to reduce seed dormancy, consequently, affecting seed development during seed maturation and promoting seed germination during imbibition.

Histone Deacetylases HD2A and HD2B Undergo Feedback Regulation by ABA and Modulate Drought Tolerance via Mediating ABA-Induced Transcriptional Repression

“…Therefore, we performed an RNA-sequencing (RNA-seq) analysis of ten days old WT and hd2ahd2b seedlings treated with or without 100 μM ABA for 6 h. Differentially expressed genes were defined based on a threshold of at least 2-fold change ( p -value < 0.05). Compared to the WT control sample, 3920 differential expressed genes (DEGs) (including 2258 up-regulated genes and 1662 down-regulated genes) were identified in WT seedlings treated with ABA, whereas 2492 DEGs (including 1720 up-regulated genes and 772 down-regulated genes) were identified in hd2ahd2b seedlings without ABA treatment ( Supplemental data set S1 [ 55 ]). Since ABA down-regulating the expression of HD2A and HD2B, we expected a similar expression pattern between “WT/ABA vs. WT/control” and “ hd2ahd2b /control vs. WT/control”.…”

“…Although HD2A and HD2B have been recognized as HDACs, their exact biochemical function in Arabidopsis is still unknown [ 56 , 57 ]. We found that the loss of HD2A and reduced function of HD2B caused a 45% reduction in total HDAC activity compared to the WT [ 55 ], highlighting the crucial role of both proteins in HDAC activity. To further examine the histone deacetylating functions of HD2A and HD2B, global acetylation levels of H4, H4K5, and H3K9 in 4 weeks old rosette leaves of WT and hd2ahd2b mutant were quantified by immunoblotting.…”

“…And all these phenotypes are reminiscent of the phenotype of a ribosome-biogenesis deficient phenotype [ 69 , 70 ]. Additionally, HD2A, HD2B, and HD2C could form homo-oligomer and be involved in plant development by affecting ribosomal RNA (rRNA) and snoRNA processing and methylation [ 52 , 55 , 71 ], A former colleague found that the NOP56 and FIB2 (the core members of box C/D snoRNA-associated proteins complex which multifunction in snoRNA processing, 2′-O-methylation of rRNA, and snoRNA transport to the nucleolus [ 72 ]) are putative interaction partner proteins of HD2C by Co-IP, which was confirmed by BIFC ( Supplement Figure S2 ). That indicates that HD2A and HD2B may also work as part of this protein complex.…”

“…Interestingly, hd2ahd2b plants display a typical ribosomal mutant phenotype ( Figure 8 ), which was already in part reported previously and quite similar to the phenotype of apum23 (slow growth and pointed leaves) [ 52 , 69 , 70 , 98 ]. The transcriptome analysis revealed that the expression of ribosome biogenesis proteins both in hd2ahd2b and apum23 mutant is affected [ 55 , 98 ]. Additionally, the previous study attributes the pleiotropic phenotype of the hd2ahd2b line to a result of the deregulation of ribosome biogenesis as well as other nucleolar functions [ 52 ], while the interaction of HD2A/HD2B with FIB2 and NOP56 ( Figure 9 ), two core proteins of Arabidopsis C/D box snoRNP complex involved in RNA methylation, suggest that HD2A/HD2B may play a critical role in coordinating stress responses and plant development by dynamically regulating HDACs-mediated rRNA post-transcriptional modification, which broadens and deepen the understanding of HD2A and HD2B in ribosome biogenesis, but the molecular mechanisms still need to be further studied.…”