Bahar Yilmazel, Yanhui Hu, Frederic Sigoillot, Jennifer A Smith, Caroline E Shamu, Norbert Perrimon, and Stephanie E Mohr 14 "Online GESS prediction of miRNAlike offtarget effects in largescale RNAi screen data by seed region analysis" BMC Bioinformatics, 15, Pp 192Basepairing of the socalled miRNA "seed" region with mRNAs identifies many thousands of putative targets Evaluating the strength of the resulting mRNA repression remains challenging, but is essential for a biologically informative ranking of potential miRNA targetsCanonically, miRNA targeting is reliant on base pairing of the seed region, nucleotides 2–7, of the miRNA to sites in mRNA 3′ untranslated regions Recently, the 3′ half of the miRNA has gained attention for newly appreciated roles in regulating target specificity and regulation
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Seed region of mirna-A mismatch tolerance test assay, based on pools of transgenic strains, revealed that target hybridization to nucleotides of the seed region, at the 5′ end of an miRNA, was sufficient to induce moderate repression of expression In contrast, pairing to the 3′ region of the miRNA was not critical for silencingThe seed sequence or seed region is a conserved heptametrical sequence which is mostly situated at positions 27 from the miRNA 5´end Even though base pairing of miRNA and its target mRNA does not match perfect, the "seed sequence" has to be perfectly complementary
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Defined as six or seven nucleotides between the nucleotides 27 or 28 of the miRNA 5' end that are responsible for mRNA binding 11(Figure (Figure11C) Seed Pairing Is Enriched in miRNATarget Sites The miRNA sequence can be separated into five functional domains that affect miRNAtarget recognition 5′ anchor (nt 1), seed sequence (nts 2–8), central region (nts 9–12), 3′ supplementary region (nts 13–16), and 3′ tail (nts 17–22) (Wee et al, 12)Online GESS prediction of miRNAlike offtarget effects in largescale RNAi screen data by seed region analysis Bahar Yilmazel1, Yanhui Hu1, Frederic Sigoillot2, Jennifer A Smith3, Caroline E Shamu3, Norbert Perrimon1,4 and Stephanie E Mohr1* Abstract Background RNA interference (RNAi) is an effective and important tool used to study gene
MicroRNAs (miRNAs) bind to mRNAs and target them for translational inhibition or transcriptional degradation It is thought that most miRNAmRNA interactions involve the seed region at the 5′ end of the miRNA The importance of seed sites is supported by experimental evidence, although there is growing interest in interactions mediated by the central region of the miRNA To characterize the basepairing patterns of miRNAtarget interaction, we searched for overrepresented sequence elements in all the targets discovered for each miRNA For most of the top expressed miRNAs, highly enriched sequence motifs emerged as complementary to the extended miRNA seed region (nucleotides 1–8 of miRNA) (Fig 4A and S7 Fig) The impact of miRNA seed types on target downregulation Previous studies have identified several major types of canonical miRNA target sites, including those matching to the 6mer, 7mer, or 8mer miRNA seed sequences (Table 2)Sequence conservation analysis suggested that target sites pairing to longer miRNA seeds are more conserved across species and thus are
Results from luciferasereporter assays and global expression data confirmed previous observations that the siRNA seed region is the primary determinant for offtarget gene recognition and bindingMicroRNAs (miRNAs) are key regulators of sequencespecific gene silencing However, crucial factors that determine the efficacy of miRNAmediated target gene silencing are poorly understood Here we mathematized basepairing stability and showed that miRNAs with an unstable 5′ terminal duplex and stable seedtarget duplex exhibit strong silencing activityAs a result, we identified 48 SNPs in human miRNA seed regions and thousands of SNPs in 3' untranslated regions with the potential to either disturb or create miRNAtarget interactions Furthermore, we experimentally confirmed seven lossoffunction SNPs and one gainoffunction SNP by luciferase assay
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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, weIn molecular genetics, the three prime untranslated region (3′UTR) is the section of messenger RNA (mRNA) that immediately follows the translation termination codonThe 3′UTR often contains regulatory regions that posttranscriptionally influence gene expression During gene expression, an mRNA molecule is transcribed from the DNA sequence and is later translated into a proteinSOFTWARE Open Access Online GESS prediction of miRNAlike offtarget effects in largescale RNAi screen data by seed region analysis Bahar Yilmazel1, Yanhui Hu1, Frederic Sigoillot2, Jennifer A Smith3, Caroline E Shamu3, Norbert Perrimon1,4 and Stephanie E Mohr1* Abstract
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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 basepairing stability, deduced by melting temperature measurements, between seedtarget duplexes containing either CG or IC pairs may account for Bases 2–8 (seed region) from the 5′end of the mature miRNA are critical determinants of target complementarity 22 Premature forms of a miRNAMouse let7 miRNA populations exhibit RNA editing that is constrained in the 5'seed/ cleavage/anchor regions and stabilize predicted mmulet7amRNA duplexes 11
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After the siRNA seed region anneals, the catalytic RNase H domain of Argonaute then subjects perfectly complementary mRNA sequences 10 nucleotides from the 5' end of the incorporated siRNA strand to nucleolytic degradation, resulting inTargetScan does its own classification of miRNAs into families, based on identical seed region, so miRNA family classification and, even more likely, nomenclature can differ between these databases In TargetScan 5 Custom, nonconserved target sites are not shown; Part of a miRNA is a 2–8base pair long seed region in their 5′ end The interaction happens between these seed regions and complementary "seed matches" on the target sites of the mRNAs 7
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For the 1226 human miRNAs with SNPs in their seed region, 314 (256%) of them are located in miRNA clusters, whereas among the 1587 human miRNAs without SNPs in their seed region, only 3 (2%) of them are located in miRNA clusters (P = 606 x 10sup4, chi square test) (Table S2) miRNAs from the same cluster have the tendency toTargetScan predicts biological targets of miRNAs by searching for the presence of conserved 8mer, 7mer, and 6mer sites that match the seed region of each miRNA (Lewis et al, 05)As an option, predictions with only poorly conserved sites are also providedThe most critical region for complementarity is the seed region (nucleotides 2–7 from the 5'terminus of the miRNA) 4,7 Aside from the seed region, other criteria have been established that can enhance miRNAmediated repression including complementarity at position 8 and the presence of an adenosine residue opposite the first miRNA
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MiRNA seed region is more critical than the 3′ region for target recognition in A thaliana (Mallory et al, 04) Moreover, plant and algal small RNAs also induce translational repression of perfectly complementary target mRNAs without, or with only minimal, transcript destabiliTargetScan predicts biological targets of miRNAs by searching for the presence of 8mer, 7mer, and 6mer sites that match the seed region of each miRNA As an option, only conserved sites are predicted Also identified are sites with mismatches in the seed region that are compensated by conserved 3' pairing and centered sitesThe latest version of this resource was released in August 15 miRSearch
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SCIENTIFIC REPORTS srep 1 wwwnaturecomscientificreports Long noncoding RNAs harboring miRNA seed regions are enriched in prostate cancer exosomes Alireza Ahadi1,2, Samuel Brennan3, Paul J Kennedy2,4, Gyorgy Hutvagner2 & Nham Tran2,5 Long noncoding RNAs (lncRNAs) form the largest transcript class in the human transcriptomeTargetScan is a target prediciton tool that predicts biological targets of miRNAs by searching for the presence of conserved 8mer and 7mer sites that match the seed region of each miRNA The target prediction software is frequently updated;I microRNA si appaiano all'mRNA target attraverso i nucleotidi 28 del miRNA (seed region) e il sito complementare della regione 3'UTR dell'mRNA bersaglio PDF PDF
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A mismatch tolerance test assay, based on pools of transgenic strains, revealed that target hybridization to nucleotides of the seed region, at the 5′ end of an miRNA, was sufficient to induce moderate repression of expression In contrast, pairing to the 3′ region of the miRNA was not critical for silencingComplementarity to an miRNA Seed Region Is Sufficient to Induce Moderate Repression of a Target Transcript in the Unicellular Green Alga Chlamydomonas reinhardtii Tomohito Yamasaki,1 Adam Voshall,2 EunJeong Kim,2 Etsuko Moriyama,2 Heriberto Cerutti,2 and Takeshi Ohama1 1Specifically, seedbased canonical target recognition was dependent on the GC content of the miRNA seed For miRNAs with low GC content of the seed region, noncanonical targeting was the dominant mechanism for target recognition
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For the 1226 human miRNAs with SNPs in their seed region, 314 (256%) of them are located in miRNA clusters, whereas among the 1587 human miRNAs without SNPs in their seed region, only 3 (2%) of them are located in miRNA clusters (P = 606 × 10 −4, χ 2 test) (Table S2) miRNAs from the same cluster have the tendency to regulate the One class of pattern consists of perfect WatsonCrick binding at the 5'end of the miRNA This region is known as "seedregion" and found at the 27 base of the miRNA This region is able to suppress the target mRNAs without having a complete base pairing at Further studies revealed that the pairing of miRNA position 8 was dispensable in many cases, indicating that the seed region can be as
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However, this information is available for annotated miRNAs This mature miRNA SNP (miRSNP) is located within the "seed region";The seedregion are rare and comprise less than 1% of the miRNA The role of miRNAs in processes such as maturation of the related SNPs 22 mammalian kidney was recently established by the podocyte MicroRNA associated single nucleotide polymorphisms specific inactivation of Dicer, the RNAse III endonuclease (miRSNPs) found on miRNA target
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And some miRNA nucleotides are more important than others (8, 9) Specifically, pairing to the miRNA "seed region" (nt 2 to 7 or 2 to 8, from the 5′ end) is the most evolutionarily conserved feature of miRNA targets in animals (10–14) Crystal structures of human Argonaute proteins show nt 2 to 6 of the guide RNA bound Furthermore, we evaluated the silencing efficiencies of miRNAs with the same seven nucleotide compositions in their seed regions (A = 3, U =
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