转录组谱分析揭示了组蛋白乙酰化调控的拟南芥体细胞胚胎发生相关基因。

Transcriptomic profiling reveals histone acetylation-regulated genes involved in somatic embryogenesis in Arabidopsis thaliana.

机构信息

Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland.

Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, Bialystok, Poland.

出版信息

BMC Genomics. 2024 Aug 15;25(1):788. doi: 10.1186/s12864-024-10623-5.

DOI:10.1186/s12864-024-10623-5

PMID:39148037

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11325840/

Abstract

BACKGROUND

Somatic embryogenesis (SE) exemplifies the unique developmental plasticity of plant cells. The regulatory processes, including epigenetic modifications controlling embryogenic reprogramming of cell transcriptome, have just started to be revealed.

RESULTS

To identify the genes of histone acetylation-regulated expression in SE, we analyzed global transcriptomes of Arabidopsis explants undergoing embryogenic induction in response to treatment with histone deacetylase inhibitor, trichostatin A (TSA). The TSA-induced and auxin (2,4-dichlorophenoxyacetic acid; 2,4-D)-induced transcriptomes were compared. RNA-seq results revealed the similarities of the TSA- and auxin-induced transcriptomic responses that involve extensive deregulation, mostly repression, of the majority of genes. Within the differentially expressed genes (DEGs), we identified the master regulators (transcription factors - TFs) of SE, genes involved in biosynthesis, signaling, and polar transport of auxin and NITRILASE-encoding genes of the function in indole-3-acetic acid (IAA) biosynthesis. TSA-upregulated TF genes of essential functions in auxin-induced SE, included LEC1/LEC2, FUS3, AGL15, MYB118, PHB, PHV, PLTs, and WUS/WOXs. The TSA-induced transcriptome revealed also extensive upregulation of stress-related genes, including those related to stress hormone biosynthesis. In line with transcriptomic data, TSA-induced explants accumulated salicylic acid (SA) and abscisic acid (ABA), suggesting the role of histone acetylation (Hac) in regulating stress hormone-related responses during SE induction. Since mostly the adaxial side of cotyledon explant contributes to SE induction, we also identified organ polarity-related genes responding to TSA treatment, including AIL7/PLT7, RGE1, LBD18, 40, HB32, CBF1, and ULT2. Analysis of the relevant mutants supported the role of polarity-related genes in SE induction.

CONCLUSION

The study results provide a step forward in deciphering the epigenetic network controlling embryogenic transition in somatic cells of plants.

摘要

背景

体细胞胚胎发生（SE）是植物细胞独特发育可塑性的典范。调控过程，包括控制细胞转录组胚胎发生重编程的表观遗传修饰，才刚刚开始被揭示。

结果

为了鉴定 SE 中组蛋白乙酰化调控表达的基因，我们分析了拟南芥外植体在受到组蛋白去乙酰化酶抑制剂曲古抑菌素 A（TSA）处理时进行胚胎发生诱导的全转录组。比较了 TSA 诱导和生长素（2,4-二氯苯氧乙酸；2,4-D）诱导的转录组。RNA-seq 结果显示，TSA 和生长素诱导的转录组反应具有相似性，涉及大多数基因的广泛去调控，主要是抑制。在差异表达基因（DEGs）中，我们鉴定了 SE 的主调控因子（转录因子-TFs）、参与生长素生物合成、信号转导和极性运输的基因以及在吲哚-3-乙酸（IAA）生物合成中起作用的 nitrilase 编码基因。在生长素诱导的 SE 中，TSA 上调的必需功能 TF 基因包括 LEC1/LEC2、FUS3、AGL15、MYB118、PHB、PHV、PLTs 和 WUS/WOXs。TSA 诱导的转录组还揭示了大量与应激相关基因的上调，包括与应激激素生物合成相关的基因。与转录组数据一致，TSA 诱导的外植体积累了水杨酸（SA）和脱落酸（ABA），表明组蛋白乙酰化（Hac）在调控 SE 诱导过程中与应激激素相关反应的作用。由于子叶外植体的近轴侧主要有助于 SE 诱导，我们还鉴定了对 TSA 处理有反应的器官极性相关基因，包括 AIL7/PLT7、RGE1、LBD18、40、HB32、CBF1 和 ULT2。相关突变体的分析支持了极性相关基因在 SE 诱导中的作用。