Genome-wide analysis of transcription in dek3 mutants and DEK3-over expressors [8 time points]

The decision of whether to grow and proliferate or to restrict growth and develop resilience to stress is a key biological trade-off. Multiple tumour suppressors have roles in suppressing growth and proliferation when conditions are unfavourable, and aggressive tumours show re-wiring of the metabolic pathways and removal of these restraints on growth. In plants, constitutive growth results in increased sensitivity to environmental stress. However, the underlying mechanisms controlling this decision are not well understood. We used temperature as a cue to discover regulators of this process in plants, as it both enhances growth and development rates within a specific range, and is also a stress at extremes. We find the conserved chromatin protein DEK plays a central role in balancing the response between growth and arrest in Arabidopsis, and it does this via H2A.Z-nucleosomes. DEK target genes show two distinct categories of chromatin architecture, and these predict induction or repression by DEK. We show that these chromatin signatures of DEK target genes might be conserved in human cells, suggesting that DEK may act through a fundamental evolutionarily conserved mechanism to control the balance between growth and arrest in plants and animals. RNA-seq were generated for seedlings grown at 27C harvested in 8 different time points. ZT0 time point just before the lights are on (End of the night); ZT8-just before the light are off(end of the day)

细胞在增殖生长与抑制生长以增强应激抗性之间做出选择，这是一类核心的生物学权衡策略。多种肿瘤抑制因子可在环境条件不利时抑制细胞生长与增殖，而侵袭性肿瘤则会重编程代谢通路，解除这类生长抑制约束。在植物中，组成型生长会提升其对环境胁迫的敏感性，但调控这一生长-胁迫权衡的潜在分子机制目前仍未被充分阐明。我们以温度作为调控信号开展研究，旨在发掘植物中参与该过程的调控因子：温度在特定区间内可促进植物生长发育速率，但极端温度则会成为胁迫因子。我们发现，保守染色质蛋白DEK（DEK）在拟南芥（Arabidopsis）的生长与生长停滞平衡响应中发挥核心调控作用，其调控依赖于H2A.Z核小体（H2A.Z-nucleosomes）。DEK的靶基因可分为两类截然不同的染色质结构类型，且该分类可预测DEK对靶基因的诱导或抑制效应。我们进一步发现，DEK靶基因的这类染色质特征在人类细胞中同样保守，这表明DEK可能通过一套进化上保守的核心机制，调控动植物的生长与生长停滞平衡。本研究针对27℃下培养的拟南芥幼苗生成了RNA测序（RNA-seq）数据，样本采集自8个不同时间节点：ZT0为光照开启前即刻（夜间结束时）；ZT8为光照关闭前即刻（日间结束时）。