Evolution of complexity in miRNA-mediated gene regulation systems

Using Arabidopsis microRNA (miRNA)-mediated gene regulation system as a model, we investigated how complex systems evolve with special attention to selection to maintain the systems. We found that the copy number of miRNA genes within each system is a key factor to determine the complexity of the system, indicating a crucial role of gene duplication to increase the complexity. Furthermore, we show that the mode of selection to maintain the systems depend on their complexity levels.     

The GW/WG repeats of Drosophila GW182 function as effector motifs for miRNA-mediated repression

The control of messenger RNA (mRNA) function by micro RNAs (miRNAs) in animal cells requires the GW182 protein. GW182 is recruited to the miRNA repression complex via interaction with Argonaute protein, and functions downstream to repress protein synthesis. Interaction with Argonaute is mediated by GW/WG repeats, which are conserved in many Argonaute-binding proteins involved in RNA interference and miRNA silencing, from fission yeast to mammals. GW182 contains at least three effector domains that function to repress target mRNA. Here, we analyze the functions of the N-terminal GW182 domain in repression and Argonaute1 binding, using tethering and immunoprecipitation assays in Drosophila cultured cells. We demonstrate that its function in repression requires intact GW/WG repeats, but does not involve interaction with the Argonaute1 protein, and is independent of the mRNA polyadenylation status. These results demonstrate a novel role for the GW/WG repeats as effector motifs in miRNA-mediated repression.     

Tethering of human Ago proteins to mRNA mimics the miRNA-mediated repression of protein synthesis

MicroRNAs (miRNAs) are approximately 21-nt-long RNAs involved in regulating development, differentiation, and other processes in eukaryotes. In metazoa, nearly all miRNAs control gene expression by imperfectly base-pairing with the 3'-untranslated region (3'-UTR) of target mRNAs and repressing protein synthesis by an unknown mechanism. It is also unknown whether miRNA-mRNA duplexes containing mismatches and bulges provide specific features that are recognized by factors mediating the repression. miRNAs form part of ribonucleoprotein complexes, miRNPs, that contain Argonaute (Ago) and other proteins. Here we demonstrate that effects of miRNAs on translation can be mimicked in human HeLa cells by the miRNA-independent tethering of Ago proteins to the 3'-UTR of a reporter mRNA. Inhibition of protein synthesis occurred without a change in the reporter mRNA level and was dependent on the number, but not the position, of the hairpins tethering hAgo2 to the 3'-UTR. These findings indicate that a primary function of miRNAs is to guide their associated proteins to the mRNA.     

Computational analysis of miRNA-mediated repression of translation: implications for models of translation initiation inhibition

The mechanism by which miRNAs inhibit translation has been under scrutiny both in vivo and in vitro. Divergent results have led to the suggestion that miRNAs repress translation by a variety of mechanisms including blocking the function of the cap in stimulating translation. However, these analyses largely only examine the final output of the multistep process of translation. This raises the possibility that when different steps in translation are rate limiting, miRNAs might show different effects on protein production. To examine this possibility, we modeled the process of translation initiation and examined how the effects of miRNAs under different conditions might be explained. Our results suggest that different effects of miRNAs on protein production in separate experiments could be due to differences in rate-limiting steps. This analysis does not rule out that miRNAs directly repress the function of the cap structure, but it demonstrates that the observations used to argue for this effect are open to alternative interpretations. Taking all the data together, our analysis is consistent with the model that miRNAs may primarily repress translation initiation at a late step.     

The miRNA-mediated post-transcriptional regulation of maize response to nitrate

Stress responses depend on the correct regulation of gene expression. The discovery that abiotic as well as biotic stresses can regulate miRNA levels, coupled with the identification and functional analyses of stress-associated genes as miRNA targets, provided clues about the vital role that several miRNAs may play in modulating plant resistance to stresses. Nitrogen availability seriously affects crops productivity and environment and the understanding of the miRNA-guided stress regulatory networks should provide new tools for the genetic improvement of nitrogen use efficiency of crops. A recent study revealed the potential role of a number of nitrate-responsive miRNAs in the maize adaptation to nitrate fluctuations. In particular, results obtained suggested that a nitrate depletion might regulate the expression of genes involved in the starvation adaptive response, by affecting the spatio-temporal expression patterns of specific miRNAs.     

miRNA在植物病原调控方面的研究进展

miRNA是一类在真核生物体内普遍存在的,长度在22 nt左右的单链小RNA分子。大量研究发现,miRNA可广泛参与植物的生长发育、新陈代谢、物质运输、逆境响应及病原防御等多种生理生化过程。目前已经从植物中鉴定到大量的miRNA,但其中参与植物病原调控相关miRNA的研究较少。miRNA作为一种重要的转录调控因子,可参与调控病原相关分子模式触发的免疫反应和效应因子触发的免疫反应。拟南芥中,miRNA393通过靶向生长素受体基因对植物生长素进行负调控,从而在抵御细菌侵染方面发挥作用;水稻中,miRNA528可响应水稻条纹病毒(RSV)的侵染,人为提高miRNA528水平有助于维持水稻对RSV的抗性。阐述了miRNA的作用机制,与植物细菌、真菌和病毒侵染相关的miRNA研究进展,总结了葡萄,苹果,梨和桃等具有重要经济价值果树中病原调控相关miRNA研究情况,旨在为今后miRNA在植物,特别是在果树抗病研究方面提供全面的理论依据。     

miRNAs: whys and wherefores of miRNA-mediated regulation

MiRNAs are assumed to be important in animal development and physiology, but their specific roles in vivo are still poorly understood. New bioinformatic and genetic studies are setting the stage for unraveling the specific biological functions of miRNAs.     

The complexity of HDL

Plasma high-density lipoprotein cholesterol (HDL-C) levels are inversely associated with coronary artery disease risk in large epidemiologic studies. This rule, however, has many exceptions in individual patients, and evidence suggests that other facets of high-density lipoprotein particle biology not captured by measuring HDL-C levels are responsible for HDL's effects in vivo. This article reviews the evidence for the protective nature of HDL, current evidence from animal and human studies regarding HDL-based therapies, the major steps in HDL particle formation and metabolism, alterations leading to dysfunctional HDL in diabetes and inflammatory states, and potential alternatives to HDL-C to measure HDL function and predict its protective value clinically.     

The complexity of mucins

Mucins represent the main components of gel-like secretions, or mucus, secreted by mucosae or some exocrine glands. These high-molecular-weight glycoproteins are characterized by the large number of carbohydrate chains O-glycosidically linked to the peptide. The determination of mucin molecular weight and conformation has been controversial for several reasons: 1) the methods used to solubilize mucus and to purify mucins are different and 2) the molecules have a strong tendency to aggregate or to bind to other molecules (peptides or lipids). Recently, electron microscopy has shown the filamentous shape of most mucins and their polydisperse character which, in some secretions, might correspond to a polymorphism of the peptide part of these molecules. The recent development of high pressure liquid chromatography and high-resolution proton NMR spectroscopy has allowed major progress in the structural study of mucin carbohydrate chains. These chains may have from 1 to about 20 sugars and bear different antigenic determinants, such as A, B, H, I, i, X, Y or Cad antigens. In some mucins, such as human respiratory mucins, the carbohydrate chain diversity is remarkable, which raises many questions. Mucins are molecules located at the interface between mucosae and the external environment. The carbohydrate chain diversity might allow many interactions between mucins and microorganisms and play a major role in the colonization or the defense of mucosae.     

The complexity of simplicity

What is the minimum number of genes or functions necessary to support cellular life? The concept of a 'minimal genome' has become popular, but is it a useful concept, and if so, what might a minimal genome encode? We argue that the concept may be useful, even though the goal of defining a general minimal genome may never be attained.     

miRNA-mediated functional changes through co-regulating function related genes

Background

microRNAs play important roles in various biological processes involving fairly complex mechanism. Analysis of genome-wide miRNA microarray demonstrate that a single miRNA can regulate hundreds of genes, but the regulative extent on most individual genes is surprisingly mild so that it is difficult to understand how a miRNA provokes detectable functional changes with such mild regulation.

Results

To explore the internal mechanism of miRNA-mediated regulation, we re-analyzed the data collected from genome-wide miRNA microarray with bioinformatics assay, and found that the transfection of miR-181b and miR-34a in Hela and HCT-116 tumor cells regulated large numbers of genes, among which, the genes related to cell growth and cell death demonstrated high Enrichment scores, suggesting that these miRNAs may be important in cell growth and cell death. MiR-181b induced changes in protein expression of most genes that were seemingly related to enhancing cell growth and decreasing cell death, while miR-34a mediated contrary changes of gene expression. Cell growth assays further confirmed this finding. In further study on miR-20b-mediated osteogenesis in hMSCs, miR-20b was found to enhance osteogenesis by activating BMPs/Runx2 signaling pathway in several stages by co-repressing of PPARγ, Bambi and Crim1.

Conclusions

With its multi-target characteristics, miR-181b, miR-34a and miR-20b provoked detectable functional changes by co-regulating functionally-related gene groups or several genes in the same signaling pathway, and thus mild regulation from individual miRNA targeting genes could have contributed to an additive effect. This might also be one of the modes of miRNA-mediated gene regulation.     

The structural complexity of DNA templates—Implications on cellular complexity

A previously formulated procedure for the quantitative evaluation of the complexities of molecules and biostructures is applied to assess the complexities of selected genomic DNA sequences. These include: (1) Several E. coli genes, including lacI, as examples of DNA sequences which are nearly as complex as possible (relative complexity=∼1). This is verified by the Lempel-Ziv (LZ) complexity analysis. (2) The telomere of a yeast chromosome, which has a considerable number of regular features that reduce complexity; the telomere shows indeed a lower structural complexity value. (3) A segment of human DNA, gene p53, which has a certain number of regular features such as 29 interspersed alu elements; these features cause a certain reduction in the complexity of the p53 gene, but do not invalidate the (previous) overall conclusion that template complexity is very high. The close to maximal complexity of the transcribed regions of p53 is validated by the LZ compression analysis. The general conclusion is that DNA base sequence composition is the dominant factor determining cellular complexity. The high complexity of DNA arrived at is a direct consequence of the template character of DNA and reflects the role of genomic DNA as a principal regulating element of a cell. It will be a challenge to find systems of lower complexity with the ability to respond to challenges from the environment to the extent that DNA templated systems do. Cellular complexity and template directed activity are thus highly intertwined properties, at the heart of many developmental, behavioral and evolutionary processes.