植物体内调控miRNA合成与功能的机制研究进展

microRNA(miRNA)能够在转录后水平通过剪切或抑制翻译对靶mRNA进行调节,并且广泛参与植物的生长发育、生物胁迫和非生物胁迫等过程,因此引起了众多研究者的关注。随着对miRNA研究的深入,人们发现miRNA从转录到转录后成熟再到行使功能的过程中,会受到很多因子的调控。这些因子可以是蛋白质、核酸序列、基因、甚至miRNA本身,由于这些因子的参与,使得miRNA调节的生物学过程更具复杂性和灵活性。本文从转录、加工、活性调节和反馈调控等层次综述了近年来调控植物miRNA合成与功能方面取得的进展,以期为miRNA调控机制的研究提供理论基础和新思路。     

Identification and characterization of new plant microRNAs using EST analysis

Seventy-five previously known plant microRNAs (miRNAs) were classified into 14 families according to their gene sequence identity. A total of 18,694 plant expressed sequence tags (EST) were found in the GenBank EST databases by comparing all previously known Arabidopsis miRNAs to GenBank‘s plant EST databases with BLAST algorithms. After removing the EST sequences with high numbers (more than 2) of mismatched nucleotides, a total of 812 EST contigs were identified. After predicting and scoring the RNA secondary structure of the 812 EST sequences using mFold software, 338 new potential miRNAs were identified in 60 plant species, miRNAs are widespread. Some microRNAsmay highly conserve in the plant kingdom, and they may have the same ancestor in very early evolution. There is no nucleotide substitution in most miRNAs among many plant species. Some of the new identified potential miRNAs may be induced and regulated by environmental biotic and abiotic stresses. Some may be preferentially expressed in specific tissues, and are regulated by developmental switching. These findings suggest that EST analysis is a good alternative strategy for identifying new miRNA candidates, their targets, and other genes. A large number of miRNAs exist in different plant species and play important roles in plant developmental switching and plant responses to environmental abiotic and biotic stresses as well as signal transduction. Environmental stresses and developmental switching may be the signals for synthesis and regulation of miRNAs in plants. A model for miRNA induction and expression, and gene regulation by miRNA is hypothesized.     

Sequence variation of MicroRNAs and their binding sites in Arabidopsis

Major differences exist between plants and animals both in the extent of microRNA (miRNA)-based gene regulation and the sequence complementarity requirements for miRNA-messenger RNA pairing. Whether these differences affect how these sites evolve at the molecular level is unknown. To determine the extent of sequence variation at miRNAs and their targets in a plant species, we resequenced 16 miRNA families (66 miRNAs in total) and all 52 of the characterized binding sites for these miRNAs in the plant model Arabidopsis (Arabidopsis thaliana), accounting for around 50% of the known miRNAs and binding sites in this species. As has been shown previously in humans, we find that both miRNAs and their target binding sites have very low nucleotide variation and divergence compared to their flanking sequences in Arabidopsis, indicating strong purifying selection on these sites in this species. Sequence data flanking the mature miRNAs, however, exhibit normal levels of polymorphism for the accessions in this study and, in some cases, nonneutral evolution or subtle effects on predicted pre-miRNA secondary structure, suggesting that there is raw material for the differential function of miRNA alleles. Overall, our results show that despite differences in the architecture of miRNA-based regulation, miRNAs and their targets are similarly constrained in both plants and animals.     

MicroRNAs--micro in size but macro in function

MicroRNAs (miRNAs) are endogenous small RNAs that can regulate target mRNAs by binding to their 3'-UTRs. A single miRNA can regulate many mRNA targets, and several miRNAs can regulate a single mRNA. These have been reported to be involved in a variety of functions, including developmental transitions, neuronal patterning, apoptosis, adipogenesis metabolism and hematopoiesis in different organisms. Many oncogenes and tumor suppressor genes are regulated by miRNAs. Studies conducted in the past few years have demonstrated the possible association between miRNAs and several human malignancies and infectious diseases. In this article, we have focused on the mechanism of miRNA biogenesis and the role of miRNAs in human health and disease.     

Biogenesis, evolution, and functions of plant microRNAs

This review focuses on the biological role of one class of plant small RNAs, ～22-nt microRNAs (miRNAs). The majority of plant miRNA targets are genes encoding the effector factors of cell signaling pathways. The regulation of their expression is necessary for both ontogenesis and rapid response of plants to biotic and abiotic stress factors. We also summarized current views on the biogenesis and evolution of plant miRNAs as well as the techniques used for their investigation.     

生物信息学在植物miRNA研究中的应用

植物miRNA的研究已经从小规模实验向大规模计算分析方向发展,生物信息学的应用成为当前植物miRNA研究的热点问题。本文回顾了最近几年生物信息学在植物miRNA研究中取得的最新进展,简要介绍了植物miRNA的形成及其作用方式,重点对植物miRNA的计算识别、靶基因预测、启动子分析方法进行了讨论,并对相关的数据库资源进行了总结,最后展望了该领域研究的发展方向,将为植物miRNA的计算研究提供理论指导。