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Annual Review of Genetics

Volume 49, 2015

A Uniform System for the Annotation of Vertebrate microRNA Genes and the Evolution of the Human microRNAome

Abstract

Although microRNAs (miRNAs) are among the most intensively studied molecules of the past 20 years, determining what is and what is not a miRNA has not been straightforward. Here, we present a uniform system for the annotation and nomenclature of miRNA genes. We show that less than a third of the 1,881 human miRBase entries, and only approximately 16% of the 7,095 metazoan miRBase entries, are robustly supported as miRNA genes. Furthermore, we show that the human repertoire of miRNAs has been shaped by periods of intense miRNA innovation and that mature gene products show a very different tempo and mode of sequence evolution than star products. We establish a new open access database—MirGeneDB ()—to catalog this set of miRNAs, which complements the efforts of miRBase but differs from it by annotating the mature versus star products and by imposing an evolutionary hierarchy upon this curated and consistently named repertoire.

Keyword(s): genome duplication, miRBase, MirGeneDB, miRNA, molecular evolution, vertebrate

Erratum

An erratum has been published for this article:
A Uniform System for the Annotation of Vertebrate microRNA Genes and the Evolution of the Human microRNAome
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/content/journals/10.1146/annurev-genet-120213-092023
2015-11-23
2025-04-29
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A Uniform System for the Annotation of Vertebrate microRNA Genes and the Evolution of the Human microRNAome
Annual Review of Genetics 49, 213 (2015); https://doi.org/10.1146/annurev-genet-120213-092023
/content/journals/10.1146/annurev-genet-120213-092023
/content/journals/10.1146/annurev-genet-120213-092023
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Supplementary Data

  • Supplemental Figures 1–4 (PDF)

    Supplemental Table 1. Measurements on read length, complementarity, loop length, and time of acquisition for all accepted miRNA genes in five taxa, human, zebrafish, nudibranch, fruit fly and nematode. These are the data for what is presented in Table 1, Figure 3A, and Figure 5. The mature and star sequences for human from genes that were acquired by the time of the last common ancestor of tetrapods were used to generate the sequence logos in Fig. 6D. (XLSX)

    Supplemental Table 2. Our evaluation of all metazoan microRNAs deposited at miRBase as of version 21. These are the data for Figure 3B. (XLSX)

    Supplemental Table 3. The proposed nomenclature system for all multi-gene families for six vertebrate taxa, human, mouse, chicken, anolis lizard, frog and zebrafish. (PDF)

    Supplemental Table 4. The gain and loss of miRNAs for every node given in Figure 5. (XLSX)

    Supplemental Table 5. The data for the mutational profiles of all 234 miRNA genes reconstructed as present in the last common ancestor of tetrapods. These are the data for the mutational profiles presented in Fig. 6A and C, and the rates estimates presented in Fig. 6B and Table 3. (XLSX)

    Supplemental Table 6. miRNAs deposited at MirGeneDB.org that either differ in sequence (red) and/or genome coordinates (yellow) from what is deposited at miRBase. Concordant entries are shown in green. (XLSX)

  • Article Type: Review Article

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