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

RNA ◽  
2006 ◽  
Vol 12 (7) ◽  
pp. 1179-1187 ◽  
Author(s):  
A. L. Jackson
Keyword(s):  
Seed Region ◽  
Region Sequence ◽  
Target Transcript ◽  
Sequence Complementarity

scholarly journals Noncanonical targeting contributes significantly to miRNA-mediated regulation

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.

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

2013 ◽  
Vol 76 (6) ◽  
pp. 1045-1056 ◽  
Author(s):  
Tomohito Yamasaki ◽  
Adam Voshall ◽  
Eun-Jeong Kim ◽  
Etsuko Moriyama ◽  
Heriberto Cerutti ◽  
...  
Keyword(s):  
Seed Region ◽  
Target Transcript ◽  
Mirna Seed

scholarly journals SCOPE enables type III CRISPR-Cas diagnostics using flexible targeting and stringent CARF ribonuclease activation

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Jurre A. Steens ◽  
Yifan Zhu ◽  
David W. Taylor ◽  
Jack P. K. Bravo ◽  
Stijn H. P. Prinsen ◽  
...  
Keyword(s):  
Immune Response ◽  
Diagnostic Tool ◽  
Nasal Swab ◽  
Rna Binding ◽  
Seed Region ◽  
Base Pairing ◽  
Specific Detection ◽  
Type Iii ◽  
Single Host ◽  
Target Rna

AbstractCharacteristic properties of type III CRISPR-Cas systems include recognition of target RNA and the subsequent induction of a multifaceted immune response. This involves sequence-specific cleavage of the target RNA and production of cyclic oligoadenylate (cOA) molecules. Here we report that an exposed seed region at the 3′ end of the crRNA is essential for target RNA binding and cleavage, whereas cOA production requires base pairing at the 5′ end of the crRNA. Moreover, we uncover that the variation in the size and composition of type III complexes within a single host results in variable seed regions. This may prevent escape by invading genetic elements, while controlling cOA production tightly to prevent unnecessary damage to the host. Lastly, we use these findings to develop a new diagnostic tool, SCOPE, for the specific detection of SARS-CoV-2 from human nasal swab samples, revealing sensitivities in the atto-molar range.

scholarly journals Epigenetic Regulation of MicroRNA Clusters and Families during Tumor Development

Cancers ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 1333
Author(s):  
Jana Gregorova ◽  
Petra Vychytilova-Faltejskova ◽  
Sabina Sevcikova
Keyword(s):  
Histone Modifications ◽  
Sequence Similarity ◽  
Tumor Development ◽  
Hematologic Malignancies ◽  
Seed Region ◽  
Cancer Therapies ◽  
Rna Molecules ◽  
Physiological Processes ◽  
Close Relationship ◽  
Aberrant Dna Methylation

MicroRNAs are small non-coding single-stranded RNA molecules regulating gene expression on a posttranscriptional level based on the seed sequence similarity. They are frequently clustered; thus, they are either simultaneously transcribed into a single polycistronic transcript or they may be transcribed independently. Importantly, microRNA families that contain the same seed region and thus target related signaling proteins, may be localized in one or more clusters, which are in a close relationship. MicroRNAs are involved in basic physiological processes, and their deregulation is associated with the origin of various pathologies, including solid tumors or hematologic malignancies. Recently, the interplay between the expression of microRNA clusters and families and epigenetic machinery was described, indicating aberrant DNA methylation or histone modifications as major mechanisms responsible for microRNA deregulation during cancerogenesis. In this review, the most studied microRNA clusters and families affected by hyper- or hypomethylation as well as by histone modifications are presented with the focus on particular mechanisms. Finally, the diagnostic and prognostic potential of microRNA clusters and families is discussed together with technologies currently used for epigenetic-based cancer therapies.

scholarly journals MicroRNA Zma-miR528 Versatile Regulation on Target mRNAs during Maize Somatic Embryogenesis

2021 ◽  
Vol 22 (10) ◽  
pp. 5310
Author(s):  
Eduardo Luján-Soto ◽  
Vasti T. Juárez-González ◽  
José L. Reyes ◽  
Tzvetanka D. Dinkova
Keyword(s):  
Somatic Embryogenesis ◽  
Immature Embryo ◽  
Inverse Correlation ◽  
Total Rna ◽  
Target Mrnas ◽  
Sequence Complementarity ◽  
Low Levels ◽  
Embryogenic Callus Induction ◽  
Regenerated Plantlets ◽  
Polysome Fraction

MicroRNAs (miRNAs) are small non-coding RNAs that regulate the accumulation and translation of their target mRNAs through sequence complementarity. miRNAs have emerged as crucial regulators during maize somatic embryogenesis (SE) and plant regeneration. A monocot-specific miRNA, mainly accumulated during maize SE, is zma-miR528. While several targets have been described for this miRNA, the regulation has not been experimentally confirmed for the SE process. Here, we explored the accumulation of zma-miR528 and several predicted targets during embryogenic callus induction, proliferation, and plantlet regeneration using the maize cultivar VS-535. We confirmed the cleavage site for all tested zma-miR528 targets; however, PLC1 showed very low levels of processing. The abundance of zma-miR528 slightly decreased in one month-induced callus compared to the immature embryo (IE) explant tissue. However, it displayed a significant increase in four-month sub-cultured callus, coincident with proliferation establishment. In callus-regenerated plantlets, zma-miR528 greatly decreased to levels below those observed in the initial explant. Three of the target transcripts (MATE, bHLH, and SOD1a) showed an inverse correlation with the miRNA abundance in total RNA samples at all stages. Using polysome fractionation, zma-miR528 was detected in the polysome fraction and exhibited an inverse distribution with the PLC1 target, which was not observed at total RNA. Accordingly, we conclude that zma-miR528 regulates multiple target mRNAs during the SE process by promoting their degradation, translation inhibition or both.

scholarly journals MicroRNA expression profile in Lampetra morii upon Vibrio anguillarum infection and miR-4561 characterization targeting lip

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Lie Ma ◽  
Meng Gou ◽  
Zeyu Du ◽  
Ting Zhu ◽  
Jun Li ◽  
...  
Keyword(s):  
Immune Regulation ◽  
Genetic Information ◽  
Vibrio Anguillarum ◽  
Microrna Expression ◽  
Seed Region ◽  
Bacterial Clearance ◽  
Embryonic Cells ◽  
Immunological Stress ◽  
Expression Atlas ◽  
Induced Apoptosis

AbstractAs a critical evolutionary pivot between invertebrates and vertebrates, lampreys provide rich genetic information. Lamprey immune protein (LIP) is a key immune regulator. MicroRNAs, well-conserved in the response to immunological stress, remain understudied in lamprey immunity. We generated a lamprey microRNA expression atlas, using deep sequencing, upon Vibrio anguillarum infection. Using comparative methods, we found that miR-4561 potentially regulates innate immunity via interaction with lip. We found a sequence in the 3′-UTR region of LIP mRNA complementary to the miR-4561 seed region; miR-4561 expression was negatively correlated with LIP. During V. anguillarum infection, miR-4561 inhibited LIP expression and bacterial clearance. Notably, LIP expression in supraneural body cells was necessary for the Gram-negative immune response. Additionally, we observed that overexpression of miR-4561 induced apoptosis in embryonic cells, suggesting a role in embryonic development. Collectively, we show lamprey microRNAs may significantly affect gene regulation and provide new insights on LIP-mediated immune regulation.

Azadirachta indica MicroRNAs: Genome-Wide Identification, Target Transcript Prediction, and Expression Analyses

2021 ◽  
Author(s):  
Raja Rajakani ◽  
Pravin Prakash ◽  
Dolly Ghosliya ◽  
Ranjana Soni ◽  
Arpita Singh ◽  
...  
Keyword(s):  
Azadirachta Indica ◽  
Genome Wide ◽  
Target Transcript
Sign in / Sign up

Export Citation Format

Share Document