DIANA-miRGen v3.0: accurate characterization of microRNA promoters and their regulators

Γεωργακίλας, Γεώργιος; Vlachos, Ioannis S.; Zagganas, Konstantinos; Vergoulis, Thanasis; Paraskevopoulou, Maria D.; Kanellos, Ilias; Tsanakas, Panayiotis; Dellis, Dimitris; Fevgas, Athanasios; Dalamagas, Theodore; Hatzigeorgiou, Artemis G.

doi:10.1093/nar/gkv1254

Cited by 55 publications

(50 citation statements)

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“…Manual curation furthermore identified the promoter for an additional 196, mostly intergenic, pre-miRNAs, thereby generating the—to our knowledge—largest miRNA promoter collection to date (Table S17, Figure S20a). Across the human robust set, an associated ENCODE RAMPAGE (RNA Annotation and Mapping of Promoters for the Analysis of Gene Expression 32 ) 5′ end was found within 300 base pairs of more than 75% of the FANTOM5 curated promoters both for intergenic and intronic miRNAs, outperforming the miRGen 33 , Chang et al 14 , miRStart 34 , and TSmiR 35 collections of miRNA promoter annotations (Figure S20b). The median distance between the FANTOM5 annotated miRNA promoter and the associated RAMPAGE 5′ end was 1 nucleotide, and was thereby closer than any of the existing miRNA promoter annotations (Figure S20c).…”

Section: Resultsmentioning

confidence: 99%

An integrated expression atlas of miRNAs and their promoters in human and mouse

Rie¹,

Abugessaisa²,

et al. 2017

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MicroRNAs (miRNAs) are short non-coding RNAs with key roles in cellular regulation. As part of the fifth edition of the Functional Annotation of Mammalian Genome (FANTOM5) project, we created an integrated expression atlas of miRNAs and their promoters by deep-sequencing 492 short RNA (sRNA) libraries, with matching Cap Analysis Gene Expression (CAGE) data, from 396 human and 47 mouse RNA samples. Promoters were identified for 1,357 human and 804 mouse miRNAs and showed strong sequence conservation between species. We also found that primary and mature miRNA expression levels were correlated, allowing us to use the primary miRNA measurements as a proxy for mature miRNA levels in a total of 1,829 human and 1,029 mouse CAGE libraries. We thus provide a broad atlas of miRNA expression and promoters in primary mammalian cells, establishing a foundation for detailed analysis of miRNA expression patterns and transcriptional control regions.

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Section: Resultsmentioning

confidence: 99%

An integrated expression atlas of miRNAs and their promoters in human and mouse

Rie¹,

Abugessaisa²,

et al. 2017

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“…In order to identify the regulation mechanism of miRNAs in Homo sapiens and Mus musculus (Georgakilas et al 2015), the DIANA-miRGen v3.0 using accurate cellline-specific miRNA gene transcription start sites (TSSs) and genome-wide maps of transcription factor binding sites were combined. GeneNetworkBuilder facilitates identification of the complex coregulatory network including TFs, miRNAs and mRNAs by combining binding site identifying and gene expression technologies such as chip-seq, chip-chip, microarray, and RNA-Seq (Ou and Zhu 2016).…”

Section: Discussionmentioning

confidence: 99%

Systems biology study of transcriptional and post-transcriptional co-regulatory network sheds light on key regulators involved in important biological processes in Citrus sinensis

Khodadadi¹,

Mehrabi²,

Najafi

et al. 2017

Physiol Mol Biol Plants

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Transcriptional and post-transcriptional regulators including transcription regulator, transcription factor and miRNA are the main endogenous molecular elements which control complex cellular mechanisms such as development, growth and response to biotic and abiotic stresses in a coordinated manner in plants. Utilizing the most recent information on such relationships in a plant species, obtained from high-throughput experimental technologies and advanced computational tools, we can reconstruct its co-regulatory network which consequently sheds light on key regulators involved in its important biological processes. In this article, combined systems biology approaches such as mining the literatures, various databases and network reconstruction, analysis, and visualization tools were employed to infer and visualize the coregulatory relationships between miRNAs and transcriptional regulators in Citrus sinensis. Using computationally and experimentally verified miRNA-target interactions and constructed co-expression networks on array-based data, 10 coregulatory networks and 10 corresponding subgraphs include FFL motifs were obtained for 10 distinct tissues/conditions. Then PPI subnetworks were extracted for transcripts/genes included in mentioned subgraphs in order to the functional analysis of extracted coregulatory circuits. These proposed coregulatory connections shed light on precisely identifying C. sinensis metabolic pathways key switches, which are demanded for ultimate goals such as genome editing.

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“…Colors are used to mark interactions also predicted by other algorithms ( 5 ). The MRE panel can be expanded for each interaction ( 6 ). This panel provides access to tools and metadata for the interacting miRNA and mRNA ( 7 ), as well as extensive information regarding the identifi ed binding sites ( 8 ).…”

Section: Selecting Candidate Mirnas For Downstream Studies From Ngs Dmentioning

confidence: 99%

“…Available utilities cover a very large scope of different needs and research scenarios, rendering DIANA website a one-stop-shop for miRNA analyses. The most commonly utilized databases and algorithms , include DIANA-microT-CDS [ 4 ], DIANA-TarBase v7.0 [ 3 ], DIANA-lncBase v2.0 [ 5 ], DIANAmiRGen v3.0 [ 6 ], DIANA-miRPath v3.0 [ 7 ], and DIANAmirExTra v2.0. A brief introduction to each tool is presented below:…”

Section: Introductionmentioning

confidence: 99%

“…DIANA-miRGen is a database of miRNA transription regulation [ 6 ]. DIANA-miRGen v3.0 comprises accurate cell-linespecifi c miRNA transcription start sites (TSS) and genome-wide maps of transcription factor (TF) binding sites derived from the in silico/experimental microTSS [ 9 ] framework and the analysis of more than seven billion next generation sequencing (NGS) reads.…”

Section: Introductionmentioning

confidence: 99%

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Functional Analysis of miRNAs Using the DIANA Tools Online Suite

Vlachos

Hatzigeorgiou

2016

Methods in Molecular Biology

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microRNAs (miRNAs) are central regulators of gene expression. They are actively studied for their involvement in numerous physiological and pathological conditions but also as diagnostic biomarkers or promising therapeutic targets. The increased complexity of the miRNA interactomes hinders straightforward interpretation of miRNA expression differences between states and conditions. To this end, functional analysis web servers process and combine experimental and in silico data, enabling researchers to uncover targeted pathways and transcriptional mechanisms that are hidden within numerous interactions and vast expression datasets. DIANA-tools ( www.microrna.gr ) is a web server hosting state-of-the-art utilities and databases for miRNA functional investigation. Available utilities cover a wide scope of different needs and research scenarios, rendering DIANA website a one-stop-shop for miRNA analyses. The most commonly utilized databases and algorithms include DIANA-microT-CDS, DIANA-TarBase v7.0, DIANA-lncBase v2.0, DIANA-miRGen v3.0, DIANA-miRPath v3.0, and DIANA-mirExTra v2.0.In the presented protocol, we will utilize different online tools in order to explore miRNA functions and to identify probable targets of interest for downstream analyses and wet lab experiments. The combined use of different applications from the DIANA suite can shed light to numerous different aspects of miRNA regulation and regulatory function, without the necessity for extensive bioinformatics expertise or computational infrastructure.

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DIANA-miRGen v3.0: accurate characterization of microRNA promoters and their regulators

Cited by 55 publications

References 55 publications

An integrated expression atlas of miRNAs and their promoters in human and mouse

An integrated expression atlas of miRNAs and their promoters in human and mouse

Systems biology study of transcriptional and post-transcriptional co-regulatory network sheds light on key regulators involved in important biological processes in Citrus sinensis

Functional Analysis of miRNAs Using the DIANA Tools Online Suite

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