A quantitative understanding of microRNA- mediated competing endogenous RNA regulation

MicroRNA （miRNA） plays key roles in post-transcriptional regulations. Recently, a competing endogenous RNA （ceRNA） hypothesis has been proposed that miRNA targets could communicate and regulate each other through titrating shared miRNAs, which provides a new layer of gene regulation. Though a number of ceRNAs playing biological functions have been identified, the ceRNA hypothesis remains controversial. Recent experimental and theoretical studies argued that the modulation of a single RNA species could hardly change the expression level of competing miRNA targets through ceRNA effect under normal physiological conditions. Here, we reviewed a common framework to model miRNA regulations, and summarized the current theoretical and experimental studies for quantitative understanding ceRNA effect. By revisiting a coarse-grained ceRNA model, we proposed that network topology could significantly influence the competing effect and ceRNA regulation at protein level could be much stronger than that at RNA level. We also provided a conditional independent binding equation to describe miRNA relative repression on different target, which could be applied to quantify siRNA off-target effect.

Regulation of Flowering Time by MicroRNAs

The shoot apical meristem（SAM） continuously produces lateral organs in plants.Based on the identity of the lateral organs,the life cycle of a plant can be divided into two phases： vegetative and reproductive.The SAM produces leaves during the vegetative phase,whereas it gives rise to flowers in the reproductive phase（reviewed in Poethig,2003）.The floral transition,namely the switch from vegetative to reproductive growth,

Single-cell Transcriptomes Reveal Characteristics of MicroRNAs in Gene Expression Noise Reduction

Isogenic cells growing in identical environments show cell-to-cell variations because of the stochasticity in gene expression.High levels of variation or noise can disrupt robust gene expression and result in tremendous consequences for cell behaviors.In this work,we showed evidence from single-cell RNA sequencing data analysis that microRNAs(miRNAs)can reduce gene expression noise at the mRNA level in mouse cells.We identified that the miRNA expression level,number of targets,target pool abundance,and miRNA-target interaction strength are the key features contributing to noise repression.miRNAs tend to work together in cooperative subnetworks to repress target noise synergistically in a cell type-specific manner.By building a physical model of post-transcriptional regulation and observing in synthetic gene circuits,we demonstrated that accelerated degradation with elevated transcriptional activation of the miRNA target provides resistance to extrinsic fluctuations.Together,through the integrated analysis of single-cell RNA and miRNA expression profiles,we demonstrated that miRNAs are important post-transcriptional regulators for reducing gene expression noise and conferring robustness to biological processes.

Molecular mechanism of microRNA125 regulating human coagulation factor IX gene with nonsense mutation

Objective To construct human coagulation factorⅨmini-gene(Mini-h F9)and some nonsense mutants,detect the levels of the Mini-h F9 mRNA,and analyze the molecular mechanism of microRNA125 regulating F9gene with nonsense mutation.Methods Three nonsense mutants were obtained by using PCR mutagenesis to ana-

The Integrative Studies on the Functional A-to-I RNA Editing Events in Human Cancers

Adenosine-to-inosine(A-to-I)RNA editing,constituting nearly 90%of all RNA editing events in humans,has been reported to contribute to the tumorigenesis in diverse cancers.However,the comprehensive map for functional A-to-I RNA editing events in cancers is still insufficient.To fill this gap,we systematically and intensively analyzed multiple tumorigenic mechanisms of A-to-I RNA editing events in samples across 33 cancer types from The Cancer Genome Atlas.For individual candidate among1,500,000 quantified RNA editing events,we performed diverse types of downstream functional annotations.Finally,we identified 24,236 potentially functional A-to-I RNA editing events,including the cases in APOL1,IGFBP3,GRIA2,BLCAP,and miR-589-3p.These events might play crucial roles in the scenarios of tumorigenesis,due to their tumor-related editing frequencies or probable effects on altered expression profiles,protein functions,splicing patterns,and microRNA regulations of tumor genes.Our functional A-to-I RNA editing events(https://ccsm.uth.edu/CAeditome/)will help better understand the cancer pathology from the A-to-I RNA editing aspect.

Shortening of the 3＇ untranslated region： an important mechanism leading to overexpression of HMGA2 in serous ovarian cancer

Background Oncofetal protein high-mobility-group AT-hook protein 2 （HMGA2） is reactivated in serous ovarian cancer （SOC） and its overexpression correlates with poor prognosis.To explore the mechanism,we investigated whether HMGA2 could avoid microRNA regulation due to gene truncation or 3＇ UTR shortening by alternative polyadenylation.Methods Real-time reverse transcription polymerase chain reaction （RT-PCR） was used to evaluate the abundance of different regions of HMGA2 mRNA in 46 SOC samples.Rapid amplification of cDNA 3＇ ends （3＇ RACE） and Southern blotting were used to confirm the shortening of 3＇ untranslated region （UTR）.5＇ RACE and Southern blotting were used to prove the mRNA decay.Results No significant difference in the ratio of the stable coding region to the fragile region was observed between SOC and control normal fallopian tubes,indicating that the HMGA2 gene is not truncated in SOC.Varying degrees of 3＇ UTR shortening in SOC samples were observed by comparing the abundance of the proximal region and distal region of the HMGA2 3＇ UTR.The ratio of the proximal to the distal region of the 3＇ UTR correlated significantly with expression of the HMGA2 coding region in SOC （r=0.579,P ＜0.01）.Moreover,although the abundance of the HMGA2 coding region varied,all samples,including the very low expressed samples,exhibit relatively high levels of the proximal 3＇ UTR region,suggesting a dynamic decay of HMGA2 mRNA from the 5＇ end.The shortening of 3＇ UTR and the decay from the 5＇ end were confirmed by 3＇ RACE,5＇ RACE and subsequent Southern blotting.Conclusion Heterogeneous 3＇ UTR lengths render HMGA2 susceptible to different levels of negative regulation by microRNAs,which represents an important mechanism of HMGA2 reactivation in SOC.

Dioxin induces expression of hsa-mi R-146b-5p in human neuroblastoma cells

Dioxin can cause a series of neural toxicological effects. Micro RNAs（mi Rs） play important roles in regulating nervous system function and mediating cellular responses to environmental pollutants, such as dioxin. Hsa-mi R-146 b-5 p appears to be involved in neurodegenerative diseases and brain tumors. However, little is known about effects of dioxin on the expression of hsa-mi R-146 b-5 p. We found that the hsa-mi R-146 b-5 p expression and its promoter activity were significantly increased in dioxin treated SK-N-SH cells, a human-derived neuroblastoma cell line. Potential roles of hsa-mi R-146 b-5 p in mediating neural toxicological effects of dioxin may be due to the regulation of certain target genes. We further confirmed that hsa-mi R-146 b-5 p significantly suppressed acetylcholinesterase（ACh E） activity and targeted the3′-untranslated region of the ACh E T subunit, which has been down-regulated in dioxin treated SK-N-SH cells. Functional bioinformatic analysis showed that the known and predicted target genes of hsa-mi R-146 b-5 p were involved in some brain functions or cyto-toxicities related to known dioxin effects, including synapse transmission, in which ACh E may serve as a responsive gene for mediating the effect.