Complementarity to an miRNA seed region is sufficient to induce moderate repression of a target transcript in the unicellular green algaChlamydomonas reinhardtii

Tomohito Yamasaki; Adam Voshall; Eun-Jeong Kim; Etsuko Moriyama; Heriberto Cerutti; Takeshi Ohama

doi:10.1111/tpj.12354

Predicting effective microRNA target sites in mammalian mRNAs

eLife ◽

10.7554/elife.05005 ◽

2015 ◽

Vol 4 ◽

Cited By ~ 2438

Author(s):

Vikram Agarwal ◽

George W Bell ◽

Jin-Wu Nam ◽

David P Bartel

Keyword(s):

Regulatory Networks ◽

Quantitative Model ◽

Seed Region ◽

Microrna Target ◽

Functional Sites ◽

Uv Crosslinking ◽

Gene Regulatory ◽

Mirna Seed ◽

Better Than

MicroRNA targets are often recognized through pairing between the miRNA seed region and complementary sites within target mRNAs, but not all of these canonical sites are equally effective, and both computational and in vivo UV-crosslinking approaches suggest that many mRNAs are targeted through non-canonical interactions. Here, we show that recently reported non-canonical sites do not mediate repression despite binding the miRNA, which indicates that the vast majority of functional sites are canonical. Accordingly, we developed an improved quantitative model of canonical targeting, using a compendium of experimental datasets that we pre-processed to minimize confounding biases. This model, which considers site type and another 14 features to predict the most effectively targeted mRNAs, performed significantly better than existing models and was as informative as the best high-throughput in vivo crosslinking approaches. It drives the latest version of TargetScan (v7.0; targetscan.org), thereby providing a valuable resource for placing miRNAs into gene-regulatory networks.

Clustering Pattern and Functional Effect of SNPs in Human miRNA Seed Regions

International Journal of Genomics ◽

10.1155/2018/2456076 ◽

2018 ◽

Vol 2018 ◽

pp. 1-4 ◽

Cited By ~ 2

Author(s):

Sha He ◽

Haiyan Ou ◽

Cunyou Zhao ◽

Jian Zhang

Keyword(s):

Genetic Variation ◽

Target Genes ◽

Current Knowledge ◽

Seed Region ◽

Functional Effect ◽

Mirna Clusters ◽

Vital Effects ◽

Computational Analyses ◽

Clustering Pattern ◽

Mirna Seed

miRNAs are a class of noncoding RNAs important in posttranscriptional repressors and involved in the regulation of almost every biological process by base paring with target genes through sequence in their seed regions. Genetic variations in the seed regions have vital effects on gene expression, phenotypic variation, and disease susceptibility in humans. The distribution pattern of genetic variation in miRNA seed regions might be related to miRNA function and is worth paying more attention to. We here employed computational analyses to explore the clustering pattern and functional effect of SNPs in human miRNA seed regions. A total of 1879 SNPs were mapped to 1226 human miRNA seed regions. We found that miRNAs with SNPs in their seed region are significantly enriched in miRNA clusters. We also found that SNPs in clustered miRNA seed regions have a lower functional effect than have SNPs in nonclustered miRNA seed regions. Additionally, we found that clustered miRNAs with SNPs in seed regions are involved in more pathways. Overall, our results demonstrate that SNPs in clustered miRNA seed regions can take part in more intricate and complex gene-regulating networks with lower functional cost by functional complementarity. Moreover, our results also broaden current knowledge on the genetic variation in human miRNA seed regions.

Noncanonical targeting contributes significantly to miRNA-mediated regulation

10.1101/2020.07.07.191023 ◽

2020 ◽

Author(s):

Jennifer Y. Tan ◽

Baroj Abdulkarim ◽

Ana C. Marques

Keyword(s):

Previous Analysis ◽

Target Prediction ◽

Seed Region ◽

Biological Processes ◽

Mirna Target Prediction ◽

Mirna Targets ◽

Sequence Complementarity ◽

Health And Disease ◽

The Impact ◽

Mirna Seed

ABSTRACTDetermining which genes are targeted by miRNAs is crucial to elucidate their contributions to diverse biological processes in health and disease. Most miRNA target prediction tools rely on the identification of complementary regions between transcripts and miRNAs. Whereas important for target recognition, the presence of complementary sites is not sufficient to identify transcripts targeted by miRNAs.Here, we describe an unbiased statistical genomics approach that explores genetically driven changes in gene expression between human individuals. Using this approach, we identified transcripts that respond to physiological changes in miRNA levels. We found that a much smaller fraction of mRNAs expressed in lymphoblastoid cell lines (LCLs) than what is predicted by other tools is targeted by miRNAs. We estimate that each miRNA has a relatively small number of targets. The transcripts we predict to be miRNA targets are enriched in AGO-binding and previously validated miRNAs target interactions, supporting the reliability of our predictions. Consistent with previous analysis, these targets are also enriched among dosage sensitive and highly controlled genes.Almost a third of genes we predict to be miRNA targets lack sequence complementarity to the miRNA seed region (noncanonical targets). These noncanonical targets have higher complementary with the miRNA 3’ end. The impact of miRNAs on the levels of their canonical or noncanonical targets is identical supporting the relevance of this poorly explored mechanism of targeting.

From life to death: microRNAs in the fine tuning of the heart

microRNA Diagnostics and Therapeutics ◽

10.2478/micrnat-2014-0003 ◽

2014 ◽

Vol 1 (1) ◽

Author(s):

Sayantan Nath ◽

S I Rizvi ◽

Munish Kumar

Keyword(s):

Fine Tuning ◽

Untranslated Regions ◽

Seed Region ◽

Cardiovascular Disorders ◽

Cardiovascular Development ◽

Rna Sequences ◽

Mrna Targets ◽

Mirna Seed ◽

Potential Therapeutics ◽

Specific Mrna

AbstractThe heart is one of the most important vital organs, and any malfunctioning of the heart and its blood vessels may contribute to cardiovascular disorders. Diseases of the cardiovascular system represent the most common cause of human morbidity and mortality around the globe. Thus, there is always a need for innovative new therapies and diagnostics for cardiovascular disorders. In the past decades, a plethora of tiny, endogenous, singlestranded RNA sequences called microRNAs (miRNAs) has been studied meticulously in cardiovascular development and pathophysiology, providing a new dimension to the heart’s biology. miRNAs posttranscriptional inhibit the gene expression of specific mRNA targets through Watson– Crick base pairing between the miRNA “seed region” and the 3′ untranslated regions (UTRs) of target mRNAs. Better recognized as “master switches”, miRNAs are emerging as vital regulators of mammalian cardiovascular development and disease and thus are helpful in understanding therapeutic targets and diagnostics for a variety of cardiovascular disorders. In this review, a detailed discussion of the roles of various microRNAs in cardiovascular development and pathophysiology with potential therapeutics is considered.

The microRNA gene <i>bta-mir-2313</i> in cattle: an atlas of regulatory elements and an association analysis with growth and carcass traits in the Slovenian Simental cattle breed

Archives Animal Breeding ◽

10.5194/aab-61-271-2018 ◽

2018 ◽

Vol 61 (3) ◽

pp. 271-278 ◽

Cited By ~ 2

Author(s):

Špela Malovrh ◽

Tanja Kunej ◽

Milena Kovač ◽

Peter Dovč

Keyword(s):

Expression Profiles ◽

Carcass Traits ◽

Mirna Gene ◽

Cattle Breed ◽

Regulatory Elements ◽

Phenotypic Traits ◽

Seed Region ◽

Microrna Gene ◽

Simmental Cattle ◽

Mirna Seed

Abstract. MicroRNAs (miRNA) are a class of non-coding RNAs important in posttranscriptional regulation of target genes. Regulation requires complementarity between the target mRNA and the miRNA region responsible for their recognition and binding, also called the seed region. Previous studies have proven that expression profiles and genetic variations of miRNA genes (miR-SNP; SNP – single nucleotide polymorphism) and their target sites (miR-TS-SNPs) have an impact on phenotypic variation and disease susceptibility in human, animal models, and livestock. MicroRNA-associated polymorphisms therefore represent biomarker potential for phenotypic traits in livestock. Effects of miRNA gene polymorphisms on phenotypic traits have been studied in several animal species but much less in cattle. The aim of the present study was therefore to analyze the genetic variability in the bta-mir-2313 gene and test associations with growth and carcass traits of the Slovenian Simmental cattle breed. Additionally, validated and predicted genomic information related to the miRNA gene bta-mir-2313 has been obtained and presented as an atlas of miRNA regulatory elements. Sanger sequencing has been used for biomarker development and genotyping of 145 animals of Slovenian dual-purpose Simmental cattle. Out of nine known polymorphisms located within pre-miRNA regions, one mature miRNA seed SNP was polymorphic in the Slovenian Simmental cattle breed. An additional three polymorphisms were identified within the flanking pri-miRNA regions. There was no significant effect of polymorphisms on 18 tested fattening and carcass traits; however, validated polymorphisms could now be tested in association with other traits in other cattle populations. The microRNA gene bta-mir-2313 warrants further genetic and functional analyses since it overlaps with a large number of quantitative trait loci (QTL), has over 3100 predicted targets and highly polymorphic mature seed regions, and is located within protein-coding gene GRAMD1B, previously associated with production traits in cattle. Mature miRNA seed SNPs present important genomic loci for functional studies because they could affect the gain/loss of downstream targets and should be systematically studied in cattle.

Widespread siRNA "off-target" transcript silencing mediated by seed region sequence complementarity

RNA ◽

10.1261/rna.25706 ◽

2006 ◽

Vol 12 (7) ◽

pp. 1179-1187 ◽

Cited By ~ 575

Author(s):

A. L. Jackson

Keyword(s):

Seed Region ◽

Region Sequence ◽

Target Transcript ◽

Sequence Complementarity

Beyond the seed: structural basis for supplementary microRNA targeting

10.1101/476960 ◽

2018 ◽

Author(s):

Jessica Sheu-Gruttadauria ◽

Yao Xiao ◽

Luca F. R. Gebert ◽

Ian J. MacRae

Keyword(s):

Mirna Target ◽

Target Recognition ◽

Structural Basis ◽

Seed Region ◽

Base Pairs ◽

Argonaute Proteins ◽

Target Rna ◽

Mirna Seed ◽

Mirna Targeting

AbstractmicroRNAs (miRNA) guide Argonaute proteins to mRNAs targeted for repression. Target recognition occurs primarily through the miRNA seed region, composed of guide (g) nucleotides g2–g8. However, nucleotides beyond the seed are also important for some known miRNA-target interactions. Here, we report the structure of human Argonaute2 (Ago2) engaged with a target RNA recognized through both miRNA seed and supplementary (g13–g16) regions. Ago2 creates a “supplementary chamber” that accommodates up to 5 miRNA-target base pairs. Seed and supplementary chambers are adjacent to each other, and can be bridged by an unstructured target loop of 1–15 nucleotides. Opening of the supplementary chamber may be constrained by tension in the miRNA 3' tail as increases in miRNA length stabilize supplementary interactions. Contrary to previous reports, we demonstrate optimal supplementary interactions can increase target affinity >20-fold. These results provide a mechanism for extended miRNA-targeting, suggest a function for 3' isomiRs in tuning miRNA targeting specificity, and indicate that supplementary interactions may contribute more to target recognition than is widely appreciated.

Pairing to the microRNA 3′ region occurs through two alternative binding modes, with affinity shaped by nucleotide identity as well as pairing position

10.1101/2021.04.13.439700 ◽

2021 ◽

Author(s):

Sean E. McGeary ◽

Namita Bisaria ◽

David P. Bartel

Keyword(s):

Nucleotide Identity ◽

Seed Region ◽

List Type ◽

Binding Modes ◽

High Affinity ◽

The Many ◽

Insight Into ◽

Mirna Seed ◽

Mirna Targeting

ABSTRACTMicroRNAs (miRNAs), in association with Argonaute (AGO) proteins, direct repression by pairing to sites within mRNAs. Compared to pairing preferences of the miRNA seed region (nucleotides 2–8), preferences of the miRNA 3′ region are poorly understood, due to the sparsity of measured affinities for the many pairing possibilities. We used RNA bind-n-seq with purified AGO2–miRNA complexes to measure relative affinities of >1,000 3′-pairing architectures for each miRNA. In some cases, optimal 3′ pairing increased affinity by >500-fold. Some miRNAs had two high-affinity 3′-pairing modes—one of which included additional nucleotides bridging seed and 3′ pairing to enable high-affinity pairing to miRNA nucleotide 11. The affinity of binding and the position of optimal pairing both tracked with the occurrence of G or oligo(G/C) nucleotides within the miRNA. These and other results advance understanding of miRNA targeting, providing insight into how optimal 3′ pairing is determined for each miRNA.HIGHLIGHTSRNA bind-n-seq reveals relative affinities of >1,000 3′-pairing architecturesTwo distinct 3′-binding modes can enhance affinity, by >500-fold in some instancesG and oligo(G/C) residues help define the miRNA 3′ segment most critical for pairingSeed mismatch identity can influence the contribution of compensatory 3′ pairing

Lentivirus-mediated long-term overexpression of specific microRNA for complementary miRNA pairs in mammalian cells

10.1101/717330 ◽

2019 ◽

Author(s):

Shupei Qiao ◽

Yufang Zhao ◽

Kai Li ◽

Yulu Sun ◽

Liuke Sun ◽

...

Keyword(s):

Mirna Expression ◽

Mammalian Cells ◽

Expression System ◽

Seed Region ◽

Future Studies ◽

Mirna Degradation ◽

Mirna Seed

AbstractThe establishment of a method that would overexpress or suppress of specific microRNA activity is essential for the functional analysis of these molecules and for the development of miRNA therapeutic applications. There already exist excellent ways to inhibit miRNA function in vitro and in vivo by overexpressing miRNA target sequences, which include miRNA ‘decoys’, ‘sponges’, or ‘antagomirs’ that are complementary to an miRNA seed region. Conversely, no methods to induce stable gain-of-function phenotypes for specific miRNAs have, as yet, been reported. Furthermore, the discovery of complementary miRNA pairs raises suspicion regarding the existing methods used for miRNA overexpression. In our study, we will study whether the traditional methods for miRNA overexpression can be used for specific miRNA overexpression while complementary miRNA pairs exist. In addition, we test various miRNA-expression cassettes that were designed to efficiently overexpress specific miRNA through the shRNA lentivirus expression system. We report the optimal conditions that were established for the design of such miRNA-expression cassettes. We finally demonstrate that the miRNA-expression cassettes achieve efficient and long-term overexpression of specific miRNAs. Meanwhile, our results also support the notion that miRNA–miRNA interactions are implicated in potential, mutual regulatory patterns and beyond the seed sequence of miRNA, extensive pairing interactions between a miRNA and its target also lead to target-directed miRNA degradation. Our results indicate that our method offers a simple and efficient means to over-express the specific miRNA with long-term which will be very useful for future studies in miRNA biology, as well as contributed to the development of miRNA-based therapy for clinical applications.

A-to-I editing in the miRNA seed region regulates target mRNA selection and silencing efficiency

Nucleic Acids Research ◽

10.1093/nar/gku662 ◽

2014 ◽

Vol 42 (15) ◽

pp. 10050-10060 ◽

Cited By ~ 35

Author(s):

Hideaki Kume ◽

Kimihiro Hino ◽

Josephine Galipon ◽

Kumiko Ui-Tei

Keyword(s):

Gene Expression Regulation ◽

Seed Region ◽

Rna Sequences ◽

Protein Coding ◽

Adenosine Deaminases ◽

Target Mrnas ◽

Non Coding Rna ◽

The Difference ◽

Mirna Seed

Abstract Hydrolytic deamination of adenosine to inosine (A-to-I) by adenosine deaminases acting on RNA (ADARs) is a post-transcriptional modification which results in a discrepancy between genomic DNA and the transcribed RNA sequence, thus contributing to the diversity of the transcriptome. Inosine preferentially base pairs with cytidine, meaning that A-to-I modifications in the mRNA sequences may be observed as A-to-G substitutions by the protein-coding machinery. Genome-wide studies have revealed that the majority of editing events occur in non-coding RNA sequences, but little is known about their functional meaning. MiRNAs are small non-coding RNAs that regulate the expression of target mRNAs with complementarities to their seed region. Here, we confirm that A-to-I editing in the miRNA seed duplex globally reassigns their target mRNAs in vivo, and reveal that miRNA containing inosine in the seed region exhibits a different degree of silencing efficiency compared to the corresponding miRNA with guanosine at the same position. The difference in base-pairing stability, deduced by melting temperature measurements, between seed-target duplexes containing either C:G or I:C pairs may account for the observed silencing efficiency. These findings unequivocally show that C:G and I:C pairs are biologically different in terms of gene expression regulation by miRNAs.