The full-length transcripts and promoter analysis of intergenic microRNAs in Drosophila melanogaster

Qian, Jinjun; Zhang, Zan; Liang, Jingdong; Ge, Qiongqiong; Duan, Xuchu; Ma, Fei; Li, Fēi

doi:10.1016/j.ygeno.2011.02.004

Cited by 23 publications

(16 citation statements)

References 41 publications

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“…Importantly, the dual firefly/Renilla luciferase reporter system allows internal normalization of LUC expression. For example, using site-directed mutagenesis and dual LUC assays, Qian et al (2011) identified TFBSs in the promoters of the Drosophila intergenic miRNAs bantam and miR-276a. Promoter bashing in combination with sensitive reporter systems is still a powerful tool for dissecting functional regions and for empirically determining or confirming predicted TFBSs in miRNA or PCG promoters, but mutagenesis can be laborious and timeconsuming in plants, particularly due to the necessity of obtaining transgenics.…”

Section: Techniques That Bash Promoter Bashing: Tf Binding Validationmentioning

confidence: 99%

Small Genetic Circuits and MicroRNAs: Big Players in Polymerase II Transcriptional Control in Plants

et al. 2016

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ORCID IDs: 0000-0001-6793-6151 (M.M.); 0000-0002-0105-6431 (S.A.F.)RNA Polymerase II (Pol II) regulatory cascades involving transcription factors (TFs) and their targets orchestrate the genetic circuitry of every eukaryotic organism. In order to understand how these cascades function, they can be dissected into small genetic networks, each containing just a few Pol II transcribed genes, that generate specific signal-processing outcomes. Small RNA regulatory circuits involve direct regulation of a small RNA by a TF and/or direct regulation of a TF by a small RNA and have been shown to play unique roles in many organisms. Here, we will focus on small RNA regulatory circuits containing Pol II transcribed microRNAs (miRNAs). While the role of miRNA-containing regulatory circuits as modular building blocks for the function of complex networks has long been on the forefront of studies in the animal kingdom, plant studies are poised to take a lead role in this area because of their advantages in probing transcriptional and posttranscriptional control of Pol II genes. The relative simplicity of tissue-and cell-type organization, miRNA targeting, and genomic structure make the Arabidopsis thaliana plant model uniquely amenable for small RNA regulatory circuit studies in a multicellular organism. In this Review, we cover analysis, tools, and validation methods for probing the component interactions in miRNA-containing regulatory circuits. We then review the important roles that plant miRNAs are playing in these circuits and summarize methods for the identification of small genetic circuits that strongly influence plant function. We conclude by noting areas of opportunity where new plant studies are imminently needed.

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Section: Techniques That Bash Promoter Bashing: Tf Binding Validationmentioning

confidence: 99%

Small Genetic Circuits and MicroRNAs: Big Players in Polymerase II Transcriptional Control in Plants

et al. 2016

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“…Sokol and Ambros (2005) showed that the muscle-specific transcription factors Twist (Twi) and Mef2 are key activators of miR-1 in Drosophila. Genomic studies have also identified regulators of miRNAs, such as Dorsal (Dl), c-Myc (Diminutive -FlyBase) and Ecdysone (Zeitlinger et al, 2007;Qian et al, 2011;Sempere et al, 2003). However, for many miRNAs, particularly those differentially expressed across developmental stages, the regulatory networks that control their transcription remain unknown.…”

Section: Introductionmentioning

confidence: 99%

Co-activation of microRNAs by Zelda is essential for early Drosophila development

Nien

Liang

et al. 2014

Development

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Transcription factors and microRNAs (miRNAs) are two important classes of trans-regulators in differential gene expression. Transcription factors occupy cis-regulatory motifs in DNA to activate or repress gene transcription, whereas miRNAs specifically pair with seed sites in target mRNAs to trigger mRNA decay or inhibit translation. Dynamic spatiotemporal expression patterns of transcription factors and miRNAs during development point to their stage-and tissuespecific functions. Recent studies have focused on miRNA functions during development; however, much remains to explore regarding how the expression of miRNAs is initiated and how dynamic miRNA expression patterns are achieved by transcriptional regulatory networks at different developmental stages. Here, we focused on the identification, regulation and function of miRNAs during the earliest stage of Drosophila development, when the maternal-tozygotic transition (MZT) takes place. Eleven miRNA clusters comprise the first set of miRNAs activated in the blastoderm embryo. The transcriptional activator Zelda is required for their proper activation and regulation, and Zelda binding observed in genome-wide binding profiles is predictive of enhancer activity. In addition, other blastoderm transcription factors, comprising both activators and repressors, the activities of which are potentiated and coordinated by Zelda, contribute to the accurate temporal and spatial expression of these miRNAs, which are known to function in diverse developmental processes. Although previous genetic studies showed no early phenotypes upon loss of individual miRNAs, our analysis of the miR-1; miR-9a double mutant revealed defects in gastrulation, demonstrating the importance of co-activation of miRNAs by Zelda during the MZT.

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“…MiRs were first discovered in the nematode Caenorhabditis elegans by Rosalind C. Lee in 1993 [ 2 ]. Since then, abundant miRs were found in many species such as plants, animals and human being [ 3 , 4 , 5 ], and regarded as a class of highly conserved RNA in the course of evolution. So far, more than 1000 miRs are predicted in human genome, and regulate about 30% of human genes [ 6 , 7 ].…”

Section: Introductionmentioning

confidence: 99%

MicroRNA-1 in Cardiac Diseases and Cancers

Dong

Wang

et al. 2014

Korean J Physiol Pharmacol

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MicroRNAs (miRs) are endogenous ≈22-nt non-coding RNAs that participate in the regulation of gene expression at post-transcriptional level. MiR-1 is one of the muscle-specific miRs, aberrant expression of miR-1 plays important roles in many physiological and pathological processes. In this review, we focus on the recent studies about miR-1 in cardiac diseases and cancers. The findings indicate that miR-1 may be a novel, important biomarker, and a potential therapeutic target in cardiac diseases and cancers.

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The full-length transcripts and promoter analysis of intergenic microRNAs in Drosophila melanogaster

Cited by 23 publications

References 41 publications

Small Genetic Circuits and MicroRNAs: Big Players in Polymerase II Transcriptional Control in Plants

Small Genetic Circuits and MicroRNAs: Big Players in Polymerase II Transcriptional Control in Plants

Co-activation of microRNAs by Zelda is essential for early Drosophila development

MicroRNA-1 in Cardiac Diseases and Cancers

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