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

## TL;DR

This study explores how histone acetylation influences gene activity during plant cell embryogenesis, revealing key genes and regulators involved in the process.

## Contribution

The study identifies histone acetylation-regulated genes and master regulators involved in somatic embryogenesis in Arabidopsis.

## Key findings

- TSA treatment upregulates transcription factors essential for auxin-induced embryogenesis, including LEC1/LEC2, FUS3, and WUS/WOXs.
- TSA-induced transcriptomes show extensive upregulation of stress-related genes and accumulation of stress hormones like SA and ABA.
- Polarity-related genes such as AIL7/PLT7 and LBD18 are identified as responding to TSA treatment during embryogenesis.

## Abstract

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.

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.

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

The online version contains supplementary material available at 10.1186/s12864-024-10623-5.