Limited information is available on abiotic stress-mediated alterations of chromatin conformation influencing gene expression in plants. In order to characterize the effect of abiotic stresses on changes in chromatin conformation, we employed FAIRE-seq (formaldehyde-assisted isolation of regulatory element sequencing) and DNase-seq to isolate accessible regions of chromatin from Arabidopsis thaliana seedlings exposed to either heat, cold, salt, or drought stress. Approximately 25% of regions in the Arabidopsis genome were captured as open chromatin, the majority of which included promoters and exons. A large proportion of chromatin regions apparently did not change their conformation in response to any of the four stresses. Digital footprints present within these regions had differential enrichment of motifs for binding of 43 different transcription factors. Further, in contrast to drought and salt stress, both high and low temperature treatments resulted in increased accessibility of the chromatin. Also, pseudogenes attained increased chromatin accessibility in response to cold and drought stresses. The highly accessible and inaccessible chromatin regions of seedlings exposed to drought stress correlated with the Ser/Thr protein kinases (MLK1 and MLK2)-mediated reduction and increase in H3 phosphorylation (H3T3Ph), respectively. The presented results provide a deeper understanding of abiotic stress-mediated chromatin modulation in plants.

中文翻译：

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非生物胁迫介导的拟南芥染色质景观的调控。

关于影响植物中基因表达的非生物胁迫介导的染色质构象变化的信息有限。为了表征非生物胁迫对染色质构象变化的影响，我们使用了FAIRE-seq（甲醛辅助分离的调控元件测序）和DNase-seq从拟南芥中分离出染色质的可及区域幼苗处于高温，寒冷，盐碱或干旱胁迫下。拟南芥基因组中约25％的区域被捕获为开放染色质，其中大部分包括启动子和外显子。很大一部分染色质区域显然不响应于四个应力中的任何一个而改变其构象。这些区域内存在的数字足迹具有差异丰富的基序，可以结合43种不同的转录因子。此外，与干旱和盐胁迫相反，高温和低温处理均导致染色质的可及性增加。另外，响应寒冷和干旱胁迫，假基因获得了较高的染色质可及性。暴露于干旱胁迫下的幼苗的高度可及和不可及的染色质区域分别与Ser / Thr蛋白激酶（MLK1和MLK2）介导的H3磷酸化（H3T3Ph）的减少和增加相关。提出的结果提供了对植物中非生物胁迫介导的染色质调节的更深入了解。