植物表观转录组学：调控逆境响应的分子机制与抗逆育种展望

doi:10.3864/j.issn.0578-1752.2026.19.001

Abstract

Abstract:

As a critical interface bridging environmental cues and gene expression, plant RNA modifications (the epitranscriptome) empower sessile plants to adapt rapidly to fluctuating environments. This review provides a comprehensive overview of the regulatory mechanisms underlying key modifications, such as N⁶-methyladenosine (m⁶A), 5-methylcytosine (m⁵C), and organellar C-to-U editing, under abiotic (salt, drought, extreme temperatures, heavy metals) and biotic stress conditions. We elucidate how these modifications orchestrate hormone signaling, reactive oxygen species (ROS) homeostasis, and energy metabolism by fine-tuning transcript stability (e.g., SbABA2 in sorghum), translation efficiency (e.g., CBFs in Arabidopsis), and protein structure (e.g., mitochondrial NAD9 in wheat). The emerging significance of modifications on long non-coding RNAs (lncRNAs) in stress resilience is also explored. Technologically, we critically evaluate MeRIP-seq, miCLIP, and Nanopore Direct RNA Sequencing (DRS), highlighting the superiority of Nanopore DRS in resolving full-length transcripts within complex plant genomes, particularly in forestry species. Moreover, advances in functional verification tools, including DART-FISH and CRISPR-dCas13-mediated targeted editing, are presented. Concluding with a forward-looking perspective, we propose an epitranscriptome engineering strategy based on "target mining-precision editing-germplasm creation" to facilitate the breeding of high-yielding, stress-tolerant crops.

Key words: RNA modification, m⁶A, stress response, single-molecule sequencing, CRISPR imaging, epitranscriptome

ZHANG Ce, ZHANG YanYan, LIU XuanDong, LU DuXian, LIN JinXing, CUI YaNing. Plant Epitranscriptomics: Molecular Mechanisms Regulating Stress Responses and Prospects for Stress-Resistant Breeding[J].Scientia Agricultura Sinica, 2026, 59(19): 4195-4207.

Figures/Tables 3

Table 1

Major types of plant RNA modifications and their biochemical characteristics"

修饰分类 Modification category	修饰类型 Modification type	生化特征/原理 Biochemical characteristics/mechanism	主要功能/调控作用 Main function/regulatory role	参考文献 References
甲基化修饰Methylation	N⁶-甲基腺嘌呤m⁶A N⁶-methyladenosine m⁶A	在腺嘌呤的N⁶位引入甲基基团，由甲基转移酶复合物识别RRACH基序催化形成 Methyl group is introduced at the N⁶ position of adenine; catalyzed by the methyltransferase complex recognizing the RRACH motif	在转录后水平精确调控RNA的剪接、翻译和降解等关键过程 Precisely regulates key post-transcriptional processes such as RNA splicing, translation, and degradation	[4]
	N¹-甲基腺苷m¹A N¹-methyladenosine m¹A	在腺苷N¹位引入甲基，破坏经典Watson-Crick碱基配对，促使形成Hoogsteen配对 Methyl group introduced at the N¹ position of adenosine; disrupts canonical Watson-Crick base pairing and promotes Hoogsteen pairing	广泛参与RNA稳定性调控与翻译效率调节，在tRNA中促进翻译，在mRNA中多表现为翻译抑制 Widely regulates RNA stability and translation efficiency; promotes translation in tRNA, while often manifesting as translation repression in mRNA	[5]
	5-甲基胞嘧啶m⁵C 5-methylcytosine m⁵C	胞嘧啶第五位碳的甲基化，以S-腺苷甲硫氨酸为甲基供体，主要由NSUN家族甲基转移酶催化 Methylation at the 5th carbon of cytosine using S-adenosylmethionine (SAM) as the methyl donor; mainly catalyzed by the NSUN family of methyltransferases	参与mRNA核质转运，增强3′-UTR区域稳定性，调控可变剪接事件 Participates in mRNA nucleocytoplasmic transport, enhances 3′-UTR stability, and regulates alternative splicing events	[6-7]
异构化修饰Isomerization	假尿苷Ψ Pseudouridine	尿苷经由异构化反应形成的C5-C1糖苷键结构产物。结构转变显著增强RNA分子的结构刚性 Product of C5-C1 glycosidic bond formation via uridine isomerization. This structural shift significantly enhances the structural rigidity of the RNA molecule	通过影响RNA稳定性，核质运输，翻译效率等代谢环节，拓展表观转录组调控的复杂性边界 Expands the complexity of epitranscriptomic regulation by influencing metabolic steps such as RNA stability, nucleocytoplasmic transport, and translation efficiency	[8-9]
脱氨编辑Deamination editing	C-to-U编辑植物细胞器主导（注：A-to-I编辑）C-to-U editingplant organelle dominant (A-to-I Editing)	胞嘧啶（C）脱氨基转化为尿嘧啶（U），主要PPR蛋白家族识别并招募编辑酶催化，常发生于线粒体和叶绿体mRNA中 Deamination of cytosine (C) to uracil (U); primarily recognized by the PPR protein family which recruits editing enzymes; commonly occurs in mitochondrial and chloroplast mRNA 在高等植物中极罕见，主要存在于动物或真菌中，植物中主要表现为上述C-to-U类型 Rare in higher plants (mainly found in animals/fungi); plants primarily exhibit the C-to-U type mentioned above	修复基因组中的T-to-C突变，恢复保守氨基酸序列；在逆境下通过改变蛋白二级结构维持细胞器功能稳态 Corrects genomic T-to-C mutations to restore conserved amino acid sequences; maintains organelle functional homeostasis under stress by altering protein secondary structure	[10]

Table 1

Fig. 1

Table 2

Quantitative comparison of performance parameters and applicability of mainstream detection technologies"

技术类别 Technology category	具体方法 Specific method	核心原理 Core principle	分辨率 Resolution	样本起始量 Input RNA amount	定量能力 Quantification capability	优势与局限 Advantages & limitations
高通量测序High-throughput sequencing	甲基化RNA免疫共沉淀测序MeRIP-seq	抗体富集+NGS Antibody enrichment+NGS	~100 nt	常规: >100 μg Routine: >100 μg 优化: ~500 ng Optimized: ~500 ng	相对定量，Peak富集度 Relative quantification, Peak enrichment	优势：通量高，技术成熟，适合初筛 Pros: High throughput, mature technology, suitable for initial screening 局限：分辨率低，依赖抗体特异性，无法精确定位 Cons: Low resolution, relies on antibody specificity, cannot pinpoint exact locations
	甲基化诱导交联免疫共沉淀miCLIP	抗体交联+逆转录突变 Antibody cross-linking+RT mutation	单碱基Single-base	>10 μg	半定量 Semi-quantitative	优势：单碱基分辨率 Pros: Single-base resolution 局限：建库复杂，交联效率低，丢失部分低丰度位点 Cons: Complex library prep, low cross- linking efficiency, loss of some low- abundance sites
	无偏倚亚硫酸氢盐测序UBS-seq	高温重亚硫酸盐处理 High-temp bisulfite treatment	单碱基Single-base	10-20 ng	绝对定量，m⁵C比例 Absolute quantification, m⁵C ratio	优势：反应时间缩短13倍，DNA损伤极低，超高灵敏度 Pros: Reaction time shortened by 13x, extremely low nucleic acid damage, ultra-high sensitivity 局限：仅适用于m⁵C Cons: Only applicable to m⁵C
	亚硫酸氢盐诱导缺失测序BID-seq	重亚硫酸盐诱导缺失 Bisulfite-induced deletion	单碱基Single-base	10-20 ng	绝对定量，Ψ比例 Absolute quantification, Ψ ratio	优势：首次实现Ψ绝对定量,无化学背景噪声 Pros: First realization of absolute Ψ quantification, no chemical background noise 局限：需精确控制反应条件 Cons: Requires precise control of reaction conditions
单分子测序Single molecule sequencing	纳米孔直接RNA测序Nanopore DRS	电流信号直接读取 Direct current signal reading	单碱基Single-base	>500 ng (polyA+)	绝对定量，修饰比例 Absolute quantification, modification fraction	优势：全长读取,无PCR偏好，适合高GC/复杂基因组（如林木） Pros: Full-length reading, no PCR bias, suitable for high GC/complex genomes (e.g., forest trees) 局限：错误率相对较高，需机器学习算法校正 Cons: Relatively high error rate, requires machine learning algorithms for correction
位点验证 Site validation	基于单碱基延伸与连接的qPCR扩增技术SELECT	连接酶介导qPCR Ligase-mediated qPCR	位点特异Site-specific	~10 ng	相对定量，Ct值 Relative quantification, Ct value	优势：低成本，无需测序，适合大样本验证 Pros: Low cost, no sequencing needed, suitable for large sample validation 局限：只能检测已知位点，非高通量 Cons: Can only detect known sites, not high-throughput
原位成像In situ imaging	基于靶点邻近脱氨的荧光原位杂交技术DART-FISH	APOBEC1编辑+Padlock探针 APOBEC1 editing + Padlock probes	单细胞Single-cell	原位细胞 In situ cell	可视定性 Visual qualitative	优势：空间分辨率，区分修饰/非修饰转录本 Pros: Spatial resolution, distinguishes modified/unmodified transcripts 局限：探针设计复杂，通量低 Cons: Complex probe design, low throughput

Table 2

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