Dicer结构和功能研究进展

摘要: Dicer蛋白是RNA干扰机制的关键组分, 负责siRNA和miRNA的产生。它主要由RNA解旋酶结构域、PAZ结构域、RNaseⅢ结构域和双链RNA结合结构域构成。Dicer的结构特点决定了它所产生的小RNA的结构特点。不同生物体具有不同数量的Dicer, 各Dicer既有功能上各自独立的特点, 同时又有功能的冗余和交叉, 而在进化过程中, Dicer的数量逐渐减少, 功能却逐步整合从而表现出多功能的特点。对Dicer结构和功能进行深入研究, 有助于了解Dicer乃至整个RNAi及相关途径的作用机制, 也有助于揭示它们在进化过程中所表现出的规律和特点。文章对上述Dicer结构及功能特点作简要综述。     

In vivo structure-function analysis of human Dicer reveals directional processing of precursor miRNAs

Dicer is an RNase III family endoribonuclease and haploinsufficient tumor suppressor that processes mature miRNAs from the 5' (5p) or 3' (3p) arm of hairpin precursors. In murine Dicer knockout fibroblasts, we expressed human Dicer with point mutations in the RNase III, helicase, and PAZ domains and characterized miRNA expression by Northern blot and massively parallel sequencing of small RNAs. We report that inactivation of the RNase IIIA domain results in complete loss of 3p-derived mature miRNAs, but only partial reduction in 5p-derived mature miRNAs. Conversely, inactivation of the RNase IIIB domain by mutation of D1709, a residue mutated in a subset of nonepithelial ovarian cancers, results in complete loss of 5p-derived mature miRNAs, including the tumor-suppressive let-7 family, but only partial reduction in 3p-derived mature miRNAs. Mutation of the PAZ domain results in global reduction of miRNA processing, while mutation of the Walker A motif in the helicase domain of Dicer does not alter miRNA processing. These results provide insight into the biochemical activity of human Dicer in vivo and, furthermore, suggest that mutation of the clinically relevant residue D1709 within the RNase IIIB results in a uniquely miRNA-haploinsufficient state in which the let-7 family of tumor suppressor miRNAs is lost while a complement of 3p-derived miRNAs remains expressed.     

Functional parameters of Dicer-independent microRNA biogenesis

Until recently, a Dicer-class RNase III enzyme was believed to be essential for microRNA (miRNA) biogenesis in all animals. The conserved vertebrate locus mir-451 defies this expectation and instead matures by direct cleavage of its pre-miRNA hairpin via the Slicer activity of Argonaute2 (Ago2). In this study, we used structure-function analysis to define the functional parameters of Ago2-mediated miRNA biogenesis. These include (1) the requirement for base-pairing at most, but not all, positions within the pre-mir-451 stem; (2) surprisingly little influence of the 5'-nucleotide on Ago sorting; (3) substantial influence of Ago protein stoichiometry on mir-451 maturation; (4) strong influence of G:C content in the distal stem on 3' resection of cleaved mir-451 substrates; and (5) the influence of hairpin length on substrate utilization by Ago2 and Dicer. Unexpectedly, we find that certain hairpin lengths confer competence to mature via both Dicer-mediated and Ago2-mediated pathways, and we show, in fact, that a conventional shRNA can traverse the Dicer-independent pathway. Altogether, these data inform the design of effective Dicer-independent substrates for gene silencing and reveal novel aspects of substrate handling by Ago proteins.     

Ssa miRNAs DB: Online repository of in silico predicted miRNAs in Salmo salar

The Atlantic salmon (Salmo salar) is a very valuable commercial salmonid species. As with other aquaculture species, intensive aquaculture of Atlantic salmon often faces disease problems especially in early life stages which can limit stable production of the species. 'Ssa miRNAs DB', a bioinformatics and manually curated database, aims at providing a comprehensive resource of microRNA in Altantic salmon, with a user friendly interface for a convenient retrieval of each entry by microRNA ID or target gene. The current version of Ssa miRNAs DB involved the prediction of 41 and 266 homologous and novel microRNAs, respectively. AVAILABILITY: The database is available for free at http://www.molgenv.com/ssa_mirnas_db_home.php.     

病毒miRNA与免疫逃逸

微小RNA（microRNA,miRNA）是一种非编码的小分子RNA,长度一般在22 nt左右,通过与mRNA 3＇UTR的特异性结合介导转录后调控过程。现已鉴定出的miRNA涵盖了从植物到人类的多个物种,并参与了调节生长、免疫、凋亡等多种生命活动。最近发现,DNA病毒感染宿主时也能编码产生miRNA,并在病毒免疫逃逸中扮演着重要角色。病毒感染是一个复杂的过程,病毒需要逃脱免疫系统才能对宿主产生持续性感染,而病毒miRNA能调控宿主和自身基因表达,帮助病毒感染宿主,且因其本身没有免疫原性,而成为病毒逃避免疫应答的重要工具,但其中的分子机制尚不十分清楚。该文就病毒miRNA如何调控病毒自身与宿主基因进行免疫逃逸的近期研究作一综述。     

Loss of functional Dicer in mouse radial glia cell-autonomously prolongs cortical neurogenesis

Radial glia of the mouse cerebral cortex emerge from neuroepithelial stem cells around embryonic day 11 and produce excitatory cortical neurons until a few days before birth. The molecular mechanisms that regulate the end of cortical neurogenesis remain largely unknown. Here we investigated if the Dicer-dependent microRNA (miRNA) pathway is involved. By electroporating a cre-recombinase expression vector into the cortex of E13.5 embryos carrying a conditional allele of Dicer1, we induced mosaic recombination causing Dicer1 deletion and reporter activation in a subset of radial glia. We analysed the long-term fates of their progeny. We found that mutant radial glia produced abnormally large numbers of Cux1-positive neurons, many of which populated the superficial cortical layers. Injections of the S-phase marker bromodeoxyuridine between postnatal days 3 and 14 showed that much of this population was generated postnatally. Our findings suggest a role for Dicer-dependent processes in limiting the timespan of cortical neurogenesis.     

The use of miRNA microarrays for the analysis of cancer samples with global miRNA decrease

Recent studies have established that mutations or deletions in microRNA (miRNA) processing enzymes resulting in a global decrease of miRNA expression are frequent across cancers and can be associated with a poorer prognosis. While very popular in miRNA profiling studies, it remains unclear whether miRNA microarrays are suited or not to accurately detecting global miRNA decreases seen in cancers. In this work, we analyzed the miRNA profiles of samples with global miRNA decreases using Affymetrix miRNA microarrays following the inducible genetic deletion of Dicer1. Surprisingly, up to a third of deregulated miRNAs identified upon Dicer1 depletion were found to be up-regulated following standard robust multichip average (RMA) background correction and quantile normalization, indicative of normalization bias. Our comparisons of five preprocess steps performed at the probe level demonstrated that the use of cyclic loess relying on non-miRNA small RNAs present on the Affymetrix platform significantly improved specificity and sensitivity of detection of decreased miRNAs. These findings were validated in samples from patients with prostate cancer, where conjugation of robust normal-exponential background correction with cyclic loess normalization and array weights correctly identified the greatest number of decreased miRNAs, and the lowest amount of false-positive up-regulated miRNAs. These findings highlight the importance of miRNA microarray normalization for the detection of miRNAs that are truly differentially expressed and suggest that the use of cyclic loess based on non-miRNA small RNAs can help to improve the sensitivity and specificity of miRNA profiling in cancer samples with global miRNA decrease.     

综述与专论：微RNA在大脑新皮层层次形成中的调控作用

种类多样的神经元有序排列和特异性的连接形成了大脑新皮层的6层组织,从而构成了神经系统高级功能的核心。了解大脑新皮层发育形成的机制将为理解哺乳动物乃至人类的生理与行为提供理论基础,也为神经系统疾病诊疗带来重大影响。本文以微RNA（microRNAs,miRNAs）为对象,结合笔者实验室工作,总结近年来所发现的miRNAs在大脑皮层层次形成过程中的研究进展,特别是在神经干细胞时序性命运决定、投射神经元多样性的形成、神经元放射状迁移,以及分裂后神经元进一步命运特化等方面的进展,为大脑皮层的发育机制研究提供新的思路。     

microRNA研究进展

小分子RNA家族中的一员——microRNA,是一段非常短的非编码RNA序列,对多种生物学过程起调控作用。本文试从microRNA的结构特点、合成及作用机制和功能等方面对microRNA的研究进展作一个简单回顾。     

Role of Dicer1 in thyroid cell proliferation and differentiation

DICER1 plays a central role in the biogenesis of microRNAs and it is important for normal development. Altered microRNA expression and DICER1 dysregulation have been described in several types of tumors, including thyroid carcinomas. Recently, our group identified a new somatic mutation (c.5438A>G; E1813G) within DICER1 gene of an unknown function. Herein, we show that DICER1 is overexpressed, at mRNA level, in a significant-relative number of papillary (70%) and anaplastic (42%) thyroid carcinoma samples, whereas is drastically downregulated in all the analyzed human thyroid carcinoma cell lines (TPC-1, BCPAP, FRO and 8505c) in comparison with normal thyroid tissue samples. Conversely, DICER1 is downregulated, at protein level, in PTC in comparison with normal thyroid tissues. Our data also reveals that DICER1 overexpression positively regulates thyroid cell proliferation, whereas its silencing impairs thyroid cell differentiation. The expression of DICER1 gene mutation (c.5438A>G; E1813G) negatively affects the microRNA machinery and cell proliferation as well as upregulates DICER1 protein levels of thyroid cells but has no impact on thyroid differentiation. In conclusion, DICER1 protein is downregulated in papillary thyroid carcinomas and affects thyroid proliferation and differentiation, while DICER1 gene mutation (c.5438A>G; E1813G) compromises the DICER1 wild-type-mediated microRNA processing and cell proliferation.     

人乳汁中microRNA的稳定性研究

为了研究人乳汁中的microRNAs(miRNAs)在体外储存状态下的稳定性。本研究采用模拟体外乳汁储存条件,对乳汁进行室温孵育24h,反复冻融6次,100℃孵育10min,以及模拟体内消化环境(RNA酶A/T137℃孵育1h)的处理条件,通过实时荧光定量PCR(qRT-PCR)方法检测处理前后乳汁中9个内源性免疫相关和1个外源性人工合成miRNA的相对表达量变化差异。研究结果显示:处理前后乳汁中内源性miRNAs和外源性miRNA均显著性降解(p<0.01)。内源性miRNAs降解为初始量的25%～70%之间,而外源性miRNA则急剧降解至初始量的0.06%～0.96%。我们的实验表明人乳汁中内源性的miRNAs较外源性miRNAs在体外不同环境下具有更强的稳定性。