2023,
Genome Biology.
DOI:
10.1186/s13059-023-02970-5
Genomic and epigenomic determinants of heat stress-induced transcriptional memory in Arabidopsis
Christian Kappel
, Thomas Friedrich
, Vicky Oberkofler
, Li Jiang
, Tim Crawford
, Michael Lenhard
, Isabel Bäurle
Abstract:
Abstract
Background
Transcriptional regulation is a key aspect of environmental stress responses. Heat stress induces transcriptional memory, i.e., sustained induction or enhanced re-induction of transcription, that allows plants to respond more efficiently to a recurrent HS. In light of more frequent temperature extremes due to climate change, improving heat tolerance in crop plants is an important breeding goal. However, not all heat stress-inducible genes show transcriptional memory, and it is unclear what distinguishes memory from non-memory genes. To address this issue and understand the genome and epigenome architecture of transcriptional memory after heat stress, we identify the global target genes of two key memory heat shock transcription factors, HSFA2 and HSFA3, using time course ChIP-seq.
Results
HSFA2 and HSFA3 show near identical binding patterns. In vitro and in vivo binding strength is highly correlated, indicating the importance of DNA sequence elements. In particular, genes with transcriptional memory are strongly enriched for a tripartite heat shock element, and are hallmarked by several features: low expression levels in the absence of heat stress, accessible chromatin environment, and heat stress-induced enrichment of H3K4 trimethylation. These results are confirmed by an orthogonal transcriptomic data set using both de novo clustering and an established definition of memory genes.
Conclusions
Our findings provide an integrated view of HSF-dependent transcriptional memory and shed light on its sequence and chromatin determinants, enabling the prediction and engineering of genes with transcriptional memory behavior.
Related Links:
2023-06-25 09:39:00
徐炳祥:
#paper doi:10.1186/s13059-023-02970-5 Genome Biology, 2023, Genomic and epigenomic determinants of heat stress‑induced transcriptional memory in Arabidopsis。热刺激是植物细胞经常面临的环境压力，能引起细胞内大规模转录响应。热刺激诱导的转录记忆是其中重要的调控模式，然而其形成机制尚不清楚。本文结合前后两次热刺激后的HSFA2和HSFA3结合位点、H3K4me3信号分布、ATAC-seq标记的染色质开放性和基因表达谱数据，从表观遗传层面对该问题进行了探讨。结果显示具有热刺激诱导记忆行为的基因有特征性的热刺激因子结合模式、在常温下有低表达水平但有开放的启动子区域，刺激后富集H3K4me3信号等特征。本文为刺激反应的表观遗传研究提供了一个可供借鉴的范式。