Transcriptomic analysis reveals the key role of histone deacetylation via mediating different phytohormone signalings in fiber initiation of cotton

Zhenzhen Wei; Yonghui Li; Faiza Ali; Ye Wang; Jisheng Liu; Zuoren Yang; Zhi Wang; Yadi Xing; Fuguang Li

doi:10.1186/s13578-022-00840-4

Transcriptomic analysis reveals the key role of histone deacetylation via mediating different phytohormone signalings in fiber initiation of cotton

Cell Biosci. 2022 Jul 12;12(1):107. doi: 10.1186/s13578-022-00840-4.

Authors

Zhenzhen Wei^#¹, Yonghui Li^#¹, Faiza Ali¹, Ye Wang², Jisheng Liu^{1

2}, Zuoren Yang^{1

2}, Zhi Wang^{1

2

3

4}, Yadi Xing⁵, Fuguang Li^{6

7}

Affiliations

¹ Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China.
² State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
³ National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572024, Hainan, China.
⁴ Sanya Institute, Zhengzhou University, Sanya, 572024, Hainan, China.
⁵ Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China. xingyadi@zzu.edu.cn.
⁶ Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China. aylifug@caas.cn.
⁷ State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China. aylifug@caas.cn.

^# Contributed equally.

Abstract

Background: Histone deacetylation is one of the most important epigenetic modifications and plays diverse roles in plant development. However, the detailed functions and mechanisms of histone deacetylation in fiber development of cotton are still unclear. HDAC inhibitors (HDACi) have been commonly used to study the molecular mechanism underlying histone deacetylation or to facilitate disease therapy in humans through hindering the histone deacetylase catalytic activity. Trichostatin A (TSA)-the most widely used HDACi has been extensively employed to determine the role of histone deacetylation on different developmental stages of plants.

Results: Through in vitro culture of ovules, we observed that exogenous application of TSA was able to inhibit the fiber initiation development. Subsequently, we performed a transcriptomic analysis to reveal the underlying mechanisms. The data showed that TSA treatment resulted in 4209 differentially expressed genes, which were mostly enriched in plant hormone signal transduction, phenylpropanoid biosynthesis, photosynthesis, and carbon metabolism pathways. The phytohormone signal transduction pathways harbor the most differentially expressed genes. Deeper studies showed that some genes promoting auxin, Gibberellic Acid (GA) signaling were down-regulated, while some genes facilitating Abscisic Acid (ABA) and inhibiting Jasmonic Acid (JA) signaling were up-regulated after the TSA treatments. Further analysis of plant hormone contents proved that TSA significantly promoted the accumulation of ABA, JA and GA₃.

Conclusions: Collectively, histone deacetylation can regulate some key genes involved in different phytohormone pathways, and consequently promoting the auxin, GA, and JA signaling, whereas repressing the ABA synthesis and signaling to improve the fiber cell initiation. Moreover, the genes associated with energy metabolism, phenylpropanoid, and glutathione metabolism were also regulated by histone deacetylation. The above results provided novel clues to illuminate the underlying mechanisms of epigenetic modifications as well as related different phytohormones in fiber cell differentiation, which is also very valuable for the molecular breeding of higher quality cotton.

Keywords: Fiber initiation; HDAC inhibitor; Histone deacetylation; Phytohormones; TSA.

Abstract

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