Arabidopsis histone variant H3.3 establishes a proper chromatin regulatory landscape essential for post-embryonic development [Strand-specific RNA-seq]

The acquisition of germination and post-embryonic developmental ability during seed maturation is vital for seed vigor, an important trait for plant propagation and crop production. How seed vigor is established in seeds is still poorly understood. Here, we report the crucial function of Arabidopsis histone variant H3.3 in chromatin structure regulation that endows seeds with post-embryonic developmental potentials. H3.3 is not essential for seed formation, but the loss of H3.3 results in severely impaired germination and post-embryonic development. H3.3 exhibits a seed-specific 5’ gene end distribution, which facilities chromatin opening in seeds. During germination, this H3.3-established chromatin accessibility is essential for proper gene transcriptional regulation. Moreover, H3.3 is constantly loaded at the 3’ gene end and restricts chromatin accessibility to prevent cryptic transcription and protect gene body DNA methylation. Our results suggest a fundamental role of H3.3 in initiating chromatin opening at regulatory regions in seed to license the embryonic to post-embryonic transition. Transcriptome, chromatin accessibility, H3.3 and H2A.Z enrichment, and DNA methylation were examined in Col or h3.3ko mutant

种子成熟过程中萌发能力与胚后发育能力的获得，对种子活力至关重要。种子活力是植物繁殖与作物生产的关键性状之一，目前学界对其建立机制仍知之甚少。本研究揭示了拟南芥组蛋白变体H3.3（histone variant H3.3）在染色质结构调控中的核心功能：该调控过程可赋予种子胚后发育潜能。H3.3并非种子形成所必需，但H3.3的缺失会严重损害种子萌发与胚后发育进程。H3.3呈现种子特异性的基因5'端分布模式，这有助于种子内染色质的开放。在萌发阶段，由H3.3建立的染色质可及性，对于基因的正常转录调控不可或缺。此外，H3.3持续富集于基因3'端，通过限制染色质可及性来抑制隐秘转录，并保护基因体区域的DNA甲基化。本研究结果表明，H3.3可在种子的调控区域启动染色质开放，以许可胚胎向胚后发育的转变，这一功能具有基础性意义。本研究对哥伦比亚野生型（Col）与H3.3敲除（h3.3ko）突变体开展了转录组、染色质可及性、H3.3与H2A.Z富集情况，以及DNA甲基化水平的检测分析。