Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2013 Sep;19(9):1295-308.
doi: 10.1261/rna.039248.113. Epub 2013 Jul 23.

The impact of age, biogenesis, and genomic clustering on Drosophila microRNA evolution

Jaaved Mohammed  1 , Alex S Flynt, Adam Siepel, Eric C Lai
Affiliations

The impact of age, biogenesis, and genomic clustering on Drosophila microRNA evolution

Jaaved Mohammed et al. RNA. 2013 Sep.

Abstract

The molecular evolutionary signatures of miRNAs inform our understanding of their emergence, biogenesis, and function. The known signatures of miRNA evolution have derived mostly from the analysis of deeply conserved, canonical loci. In this study, we examine the impact of age, biogenesis pathway, and genomic arrangement on the evolutionary properties of Drosophila miRNAs. Crucial to the accuracy of our results was our curation of high-quality miRNA alignments, which included nearly 150 corrections to ortholog calls and nucleotide sequences of the global 12-way Drosophilid alignments currently available. Using these data, we studied primary sequence conservation, normalized free-energy values, and types of structure-preserving substitutions. We expand upon common miRNA evolutionary patterns that reflect fundamental features of miRNAs that are under functional selection. We observe that melanogaster-subgroup-specific miRNAs, although recently emerged and rapidly evolving, nonetheless exhibit evolutionary signatures that are similar to well-conserved miRNAs and distinct from other structured noncoding RNAs and bulk conserved non-miRNA hairpins. This provides evidence that even young miRNAs may be selected for regulatory activities. More strikingly, we observe that mirtrons and clustered miRNAs both exhibit distinct evolutionary properties relative to solo, well-conserved miRNAs, even after controlling for sequence depth. These studies highlight the previously unappreciated impact of biogenesis strategy and genomic location on the evolutionary dynamics of miRNAs, and affirm that miRNAs do not evolve as a unitary class.

Keywords: Drosophila; microRNA clusters; microRNA evolution; mirtrons; structure evolution.

PubMed Disclaimer

Figures

FIGURE 1.
FIGURE 1.
Examples of miRNA alignment corrections. Original and corrected orthologs identified in genome assembly search; (A) dwi-mir-318, and in trace-data search; (B) dpe-mir-285. (C) Four miRNA orthologs missing from trace data, but recovered after targeted PCR and sequencing of genomic gaps. (D) Validation of genuine substitutions based on trace evidence within the mature and star regions of mir-316, an otherwise well-conserved miRNA. (E) Genomic base corrections within the dsi-mir-4916, dsi-mir-985, and der-mir-985 orthologs based on trace-data evidence.
FIGURE 2.
FIGURE 2.
Age distribution of 238 D. melanogaster miRNAs and mirtrons within 12 Drosophila species. miRNAs are further classified into three presence–depth groups: pan-Drosophilid, Sophophoran, and melanogaster subgroup. The number of D. melanogaster canonical miRNAs (green) and mirtrons (red) with putative functional orthologs up to the indicated branch are labeled within the tree. The numbers of miRNAs with confident lineage- or species-specific miRNA death events are shown in squares at their respective branch. The total numbers of canonical miRNAs and mirtrons for each of the three presence–depth groups are shown above.
FIGURE 3.
FIGURE 3.
Primary sequence and secondary structure evolutionary characteristics for miRNAs and other structured RNA classes. (A) Diagram of an extended hairpin partitioning scheme for which phyloP conservation scores were computed. (B,C) Mean phyloP conservation scores computed within extended partitions for (B) 116 pan-Drosophilid miRNAs and (C) 37 melanogaster-subgroup miRNAs. Mirtrons, melanogaster-only, and “3-species” canonical miRNAs and CDS miRNAs were excluded. Error bars indicate the standard error of the mean. Horizontal dashed lines portray the mean phyloP conservation score for other reference genomic classes. Blue values specify the number of miRNAs represented within the partition, and lack of a number indicates that all miRNAs are represented. (D,E) Properties of structure evolution for miRNAs, non-miRNA conserved hairpin structures, and other structured RNAs (snRNAs, tRNAs). Numbers on the x-axis indicate the number of loci represented in each class. Melanogaster-subgroup miRNAs have (D) proportions of free-energy difference and (E) consistent-to-compensatory substitution ratios (CCSRs), which are similar to pan-Drosophilid miRNAs but distinct from other structured RNAs.
FIGURE 4.
FIGURE 4.
Characteristics of mirtrons and clustered canonical miRNAs. (A) Classification of canonical miRNAs and mirtrons by mature and star arm conservation patterns. Pan-Drosophilid miRNA genes with both mature and star arm divergences are generally either clustered canonical miRNAs or mirtrons, whereas melanogaster-subgroup genes show homogeneity in arm divergences. (B) Alignment for dme-mir-1011, a pan-Drosophilid mirtron with divergent mature and star arms, and seed mutations. These patterns are discordant from solo canonical miRNAs. (C) Proportions of solo to clustered miRNAs at differing presence–depth groups. Melanogaster-subgroup miRNAs are rarely clustered, unlike older miRNAs. (D,E) Similar to mirtrons, clustered miRNAs also show dual arm divergences like dme-mir-309, a pan-Drosophilid miRNA (D), and mir-2498, a melanogaster-subgroup miRNA (E). The functional 7- to 8-nt “seed” regions within pan-Drosophilid clustered miRNAs are ultraconserved, unlike recently evolved clustered miRNAs. Not all clustered miRNAs evolve similarly, however; mir-309 is the only miRNA to have divergent mature and star sequence (yellow and blue stars), unlike other members of its cluster. (F) Illustration of dynamic miRNA turnover with miRNA clusters. In the mir-959 → 964 cluster, several members have emerged and died across Drosophilid evolution. The absence of mir-959 and mir-961 from ancestral outgroup insect species suggests that these miRNAs were born during Drosophilid radiation.
FIGURE 5.
FIGURE 5.
PhyloP conservation score profile and variance for three miRNA classes with different biogenesis and emergence properties. miRNA classes include solo and clustered canonical miRNAs, and mirtrons. (A,B) Partition-specific conservation scores for (A) pan-Drosophilid and (B) melanogaster-subgroup miRNAs and mirtrons. Pan-Drosophilid mirtrons show partition-specific patterns similar to canonical miRNAs, such as higher conservation of paired than unpaired duplex sites. (C) Variance of conservation scores per miRNA class. At all presence–depths, clustered miRNAs have greater variance of phyloP scores than other miRNA classes. Numbers within each panel (A,B) or on the x-axis (C) indicate the number of miRNAs present in each class.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Altuvia Y, Landgraf P, Lithwick G, Elefant N, Pfeffer S, Aravin A, Brownstein MJ, Tuschl T, Margalit H 2005. Clustering and conservation patterns of human microRNAs. Nucleic Acids Res 33: 2697–2706 - PMC - PubMed
    1. Aravin A, Lagos-Quintana M, Yalcin A, Zavolan M, Marks D, Snyder B, Gaasterland T, Meyer J, Tuschl T 2003. The small RNA profile during Drosophila melanogaster development. Dev Cell 5: 337–350 - PubMed
    1. Auyeung VC, Ulitsky I, McGeary SE, Bartel DP 2013. Beyond secondary structure: Primary-sequence determinants license Pri-miRNA hairpins for processing. Cell 152: 844–858 - PMC - PubMed
    1. Axtell MJ, Westholm JO, Lai EC 2011. Vive la différence: Biogenesis and evolution of microRNAs in plants and animals. Genome Biol 12: 221. - PMC - PubMed
    1. Batzoglou S, Jaffe DB, Stanley K, Butler J, Gnerre S, Mauceli E, Berger B, Mesirov JP, Lander ES 2002. ARACHNE: A whole-genome shotgun assembler. Genome Res 12: 177–189 - PMC - PubMed

Publication types

LinkOut - more resources