Abstract
Mature microRNAs (miRNAs) are processed from primary transcripts (pri-miRNAs), and their expression is controlled at transcriptional and post-transcriptional levels. However, how regulation at multiple levels achieves precise control remains elusive. Using published and new datasets, we profile a time course of mature and pri-miRNAs in Drosophila embryos and reveal the dynamics of miRNA production and degradation as well as dynamic changes in pri-miRNA isoform selection. We found that 5' nucleotides influence stability of mature miRNAs. Furthermore, distinct half-lives of miRNAs from the mir-309 cluster shape their temporal expression patterns, and the importance of rapid degradation of the miRNAs in gene regulation is detected as distinct evolutionary signatures at the target sites in the transcriptome. Finally, we show that rapid degradation of miR-3/-309 may be important for regulation of the planar cell polarity pathway component Vang. Altogether, the results suggest that complex mechanisms regulate miRNA expression to support normal development.
Highlights
Gene expression is regulated at multiple levels involving transcriptional and post-transcriptional mechanisms
We found that the derived target allele frequencies (DAF) was generally lower for maternal mRNAs than zygotic mRNAs for miR-3/–309 target sites, whereas target sites for the other four miRNAs in maternal and zygotic gene sets showed more similar DAF distributions (Figure 7G, Supplementary file 6)
PiRNA reads gradually decreased during embryogenesis, consistent with previous reports (Brennecke et al, 2008)
Summary
Gene expression is regulated at multiple levels involving transcriptional and post-transcriptional mechanisms. Small RNAs including microRNAs (miRNAs) play central roles in post-transcriptional regulation of protein-coding genes. MiRNAs are transcribed as primary transcripts (primiRNAs) by RNA polymerase II and their molecular architectures resemble those of mRNAs (Kim et al, 2009). The majority of miRNAs are processed from pri-miRNAs by a two-step cleavage mechanism involving two RNase III-class enzymes, Drosha and Dicer (Okamura, 2012). The resulting 21-23nt miRNA duplexes are loaded onto Argonaute family proteins and subsequently unwound to form mature effector complexes that regulate expression of target mRNAs. Analogous to regulation of protein-coding genes, expression of miRNAs is regulated at both transcriptional and post-transcriptional levels (Ha and Kim, 2014).
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