Wang Zhihan, Li Shunyuan, Wu Hongkai, Huang Linzhou, Fu Liangbo, Zhan Chengfang, Lu Xueli, Yang Long, Dai Liping, Zeng Dali
College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou 311300, China.
State Key Laboratory for Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 311400, China.
Genes (Basel). 2025 Apr 3;16(4):429. doi: 10.3390/genes16040429.
CCCH zinc finger proteins (OsC3Hs) are a class of transcriptional regulators that play important roles in plant development and stress responses. Although their functional significance has been widely studied in model species, comprehensive genome-wide characterization of CCCH proteins in rice () remains limited.
Using CCCH proteins as references, we identified the CCCH gene family in rice and analyzed the physicochemical properties, subcellular localization, conserved structures, phylogeny, cis-regulatory elements, synteny analysis, spatiotemporal expression patterns, and expression patterns under drought, ABA, and MeJA treatments for the identified CCCH family members.
The results showed that the rice CCCH family comprises 73 members, which are unevenly distributed across the 12 chromosomes. Phylogenetic analysis classified them into 11 subfamilies. Subcellular localization indicated that most members are localized in the nucleus. The upstream regions of CCCH promoters contain a large number of cis-regulatory elements related to plant hormones and biotic stress responses. Most genes respond to drought, abscisic acid (ABA), and methyl jasmonate (MeJA) treatments. was highly expressed under drought, ABA, and MeJA treatments. Haplotype analysis of this gene revealed two major allelic variants (H1 and H2), with H1 predominantly found in japonica rice and associated with increased grain width and 1000-grain weight. Functional validation using a chromosome segment substitution line (CSSL1) confirmed these findings.
CCCH genes play important roles in rice growth, development, and stress responses. Additionally, we validated that OsC3H36 is associated with rice grain width and 1000-grain weight.
CCCH锌指蛋白（OsC3Hs）是一类转录调节因子，在植物发育和胁迫反应中发挥重要作用。尽管它们的功能意义已在模式物种中得到广泛研究，但水稻中CCCH蛋白的全基因组综合表征仍然有限。
以CCCH蛋白为参考，我们鉴定了水稻中的CCCH基因家族，并分析了已鉴定的CCCH家族成员的理化性质、亚细胞定位、保守结构、系统发育、顺式调控元件、共线性分析、时空表达模式以及干旱、脱落酸（ABA）和茉莉酸甲酯（MeJA）处理下的表达模式。
结果表明，水稻CCCH家族由73个成员组成，它们不均匀地分布在12条染色体上。系统发育分析将它们分为11个亚家族。亚细胞定位表明，大多数成员定位于细胞核。CCCH启动子的上游区域包含大量与植物激素和生物胁迫反应相关的顺式调控元件。大多数基因对干旱、脱落酸（ABA）和茉莉酸甲酯（MeJA）处理有反应。在干旱、ABA和MeJA处理下高表达。对该基因的单倍型分析揭示了两个主要的等位基因变体（H1和H2），其中H1主要存在于粳稻中，并与粒宽和千粒重增加相关。使用染色体片段代换系（CSSL1）进行的功能验证证实了这些发现。
CCCH基因在水稻生长、发育和胁迫反应中发挥重要作用。此外，我们验证了OsC3H36与水稻粒宽和千粒重相关。
