植物学报 ›› 2024, Vol. 59 ›› Issue (6): 950-962.DOI: 10.11983/CBB24075 cstr: 32102.14.CBB24075
收稿日期:
2024-05-13
接受日期:
2024-07-23
出版日期:
2024-11-10
发布日期:
2024-08-08
通讯作者:
*李文学, 中国农业科学院作物科学研究所研究员, 博士生导师。2009年入选教育部“新世纪优秀人才支持计划”; 2017年入选科技部创新人才推进计划“中青年科技创新领军人才”, 同年入选国家级人才计划。主要从事玉米适应养分胁迫及抗倒伏的分子机制研究。相关成果以通讯作者身份发表在Science、Nucleic Acids Res、Mol Plant、New Phytol、Plant Physiol及Plant J等期刊上。相关科研成果荣获北京市科学技术进步奖一等奖和教育部科技进步二等奖各1项。E-mail: liwenxue@caas.cn
基金资助:
Received:
2024-05-13
Accepted:
2024-07-23
Online:
2024-11-10
Published:
2024-08-08
Contact:
*E-mail: liwenxue@caas.cn
摘要: 长链非编码RNA (long non-coding RNA, lncRNA)广泛存在于真核生物基因组中, 在维持生物体正常生命活动中发挥重要作用。近年来, 通过高通量测序和生物信息学分析在植物中发掘到大量的lncRNA。已有研究证实lncRNA在调控植物生长发育和逆境响应中发挥重要作用。由于基因组复杂且遗传操作过程繁琐, lncRNA在玉米(Zea mays)中的研究远落后于拟南芥(Arabidopsis thaliana)和水稻(Oryza sativa)。玉米作为我国主要粮食作物, 对于保障国家粮食安全至关重要。玉米还是遗传学与基因组学领域重要的模式植物。了解lncRNA在玉米中的研究进展有助于理解lncRNA的生物学功能。挖掘并解析lncRNA参与玉米生长发育和逆境响应的分子调控网络, 可为玉米遗传改良提供新的分子靶点。该文总结了lncRNA的来源、分类和作用机制, 并讨论了玉米中lncRNA的发掘及其在调控生长发育和逆境响应中的生物学功能, 最后展望了lncRNA在玉米中的研究方向。
杜庆国, 李文学. lncRNA调控玉米生长发育和非生物胁迫研究进展. 植物学报, 2024, 59(6): 950-962.
Qingguo Du, Wenxue Li. Research Progress in the Regulation of Development and Stress Responses by Long Non-coding RNAs in Maize. Chinese Bulletin of Botany, 2024, 59(6): 950-962.
图1 长链非编码RNA (lncRNA)的分类 蓝色框代表mRNA的外显子, 红色线表示lncRNA转录本, 黑色箭头表示转录方向。
Figure 1 The classification of long non-coding RNA (lncRNA) Blue boxes indicate the exon of mRNA, red lines represent lncRNA, black arrows indicate the direction of transcription.
数据库 | 物种及主要功能 | 网址 | 参考文献 |
---|---|---|---|
PlantNATsDB | 玉米、水稻、小麦和拟南芥等69个物种; NAT数据库, NAT调控网络 | Chen et al., | |
PLncDB V2.0 | 玉米、水稻、小麦和拟南芥等80个物种; lncRNA基因组位置、序列、结构、表达模式、表观遗传及调控网络 | Jin et al., | |
PNRD | 玉米、水稻和拟南芥等150个物种; lncRNA和小分子非编码RNA (sRNA)序列、结构、表达模式和功能 | Yi et al., | |
LncPheDB | 玉米、小麦、水稻和高粱等9个物种; lncRNA序列、农艺性状表型和单核苷酸多态性 | Lou et al., | |
GreeNC 2.0 | 玉米、水稻和拟南芥等96个物种; lncRNA序列及种间和种内lncRNA序列聚类分析 | Di Marsico et al., | |
wLNCdb | 小麦; lncRNA序列、表达模式、共表达基因和单核苷酸多态性 | Zhang et al., | |
RiceLncPedia | 水稻; lncRNA表达谱、基因组变异、lncRNA- miRNA相互作用、转座因子相关lncRNA以及lncRNA与农艺性状的关联 | Zhang et al., | |
scPLAD | 拟南芥; 单细胞水平lncRNA图谱浏览器 | He et al., |
表1 植物长链非编码RNA (lncRNA)数据库
Table 1 Summary of database depositing plant long non-coding RNA (lncRNA)
数据库 | 物种及主要功能 | 网址 | 参考文献 |
---|---|---|---|
PlantNATsDB | 玉米、水稻、小麦和拟南芥等69个物种; NAT数据库, NAT调控网络 | Chen et al., | |
PLncDB V2.0 | 玉米、水稻、小麦和拟南芥等80个物种; lncRNA基因组位置、序列、结构、表达模式、表观遗传及调控网络 | Jin et al., | |
PNRD | 玉米、水稻和拟南芥等150个物种; lncRNA和小分子非编码RNA (sRNA)序列、结构、表达模式和功能 | Yi et al., | |
LncPheDB | 玉米、小麦、水稻和高粱等9个物种; lncRNA序列、农艺性状表型和单核苷酸多态性 | Lou et al., | |
GreeNC 2.0 | 玉米、水稻和拟南芥等96个物种; lncRNA序列及种间和种内lncRNA序列聚类分析 | Di Marsico et al., | |
wLNCdb | 小麦; lncRNA序列、表达模式、共表达基因和单核苷酸多态性 | Zhang et al., | |
RiceLncPedia | 水稻; lncRNA表达谱、基因组变异、lncRNA- miRNA相互作用、转座因子相关lncRNA以及lncRNA与农艺性状的关联 | Zhang et al., | |
scPLAD | 拟南芥; 单细胞水平lncRNA图谱浏览器 | He et al., |
图2 植物体内长链非编码RNA (lncRNA)的作用机制 (A) lncRNA参与染色质修饰; (B) lncRNA作为诱饵与转录调节子结合; (C) lncRNA作为小分子非编码RNA (sRNA)前体; (D) lncRNA编码产生小多肽顺式或反式调控目标基因; (E) lncRNA作为竞争性内源RNA抑制体内miRNA的积累; (F) lncRNAs调控染色质环的形成
Figure 2 Representative models for the roles of plant long non-coding RNA (lncRNA) (A) lncRNAs mediate the coordinated switching of chromatin states; (B) lncRNAs act as a bait by binding to transcriptional regulators; (C) lncRNAs act as precursors of sRNA; (D) lncRNAs can translated into small peptides to regulate target genes in cis or in trans; (E) lncRNAs act as a target mimic for miRNA; (F) lncRNAs regulate the formation of chromatin loops
lncRNA ID | lncRNA分子调控机制 | 功能 | 参考文献 |
---|---|---|---|
ZM401 | 调控花粉发育关键基因ZmADS2、MZm3-3和ZmC5的表达 | 花粉发育 | Ma et al., |
GARR2 | 调控赤霉素和生长素通路中相关基因的表达 | 响应赤霉素, 调控株高 | Li et al., |
cis-NATZmNAC48 | 负调控ZmNAC48的表达, 影响叶片气孔关闭 | 干旱 | Mao et al., |
MSTRG8888.1 | 通过靶向bHLH转录因子, 影响下游耐盐相关基因的表达 | 盐胁迫 | Liu et al., |
PILNCR1 | 作为竞争性内源RNA分子结合ZmmiRNA399, 并抑制ZmmiRNA399对靶基因ZmPHO2的切割 | 磷酸盐胁迫 | Du et al., |
PILNCR2 | 与ZmPHT1s形成双链结构, 保护ZmPHT1s不被ZmmiR399切割 | 磷酸盐胁迫 | Wang et al., |
表2 玉米长链非编码RNA (lncRNA)的功能
Table 2 Function of long non-coding RNA (lncRNA) in maize
lncRNA ID | lncRNA分子调控机制 | 功能 | 参考文献 |
---|---|---|---|
ZM401 | 调控花粉发育关键基因ZmADS2、MZm3-3和ZmC5的表达 | 花粉发育 | Ma et al., |
GARR2 | 调控赤霉素和生长素通路中相关基因的表达 | 响应赤霉素, 调控株高 | Li et al., |
cis-NATZmNAC48 | 负调控ZmNAC48的表达, 影响叶片气孔关闭 | 干旱 | Mao et al., |
MSTRG8888.1 | 通过靶向bHLH转录因子, 影响下游耐盐相关基因的表达 | 盐胁迫 | Liu et al., |
PILNCR1 | 作为竞争性内源RNA分子结合ZmmiRNA399, 并抑制ZmmiRNA399对靶基因ZmPHO2的切割 | 磷酸盐胁迫 | Du et al., |
PILNCR2 | 与ZmPHT1s形成双链结构, 保护ZmPHT1s不被ZmmiR399切割 | 磷酸盐胁迫 | Wang et al., |
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