A deeply conserved, noncanonical miRNA hosted by ribosomal DNA

Chak, Li-Ling; Mohammed, Jaaved; Lai, Eric C.; Tucker‐Kellogg, Greg; Okamura, Katsutomo

doi:10.1261/rna.049098.114

Cited by 49 publications

(54 citation statements)

References 57 publications

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“…Bioinformatics analysis was performed as previously described (Chak et al, 2015). Briefly, adaptors were removed using cutadapt (Martin, 2009), mapped to the dm3 Drosophila genome and the spike-in sequences using bowtie -q -S -v 0 -a –best -M 1 (Langmead et al, 2009).…”

Section: Methodsmentioning

confidence: 99%

The Drosophila Dicer-1 Partner Loquacious Enhances miRNA Processing from Hairpins with Unstable Structures at the Dicing Site

Lim

Chou

et al. 2016

Cell Reports

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In Drosophila, Dicer-1 binds Loquacious-PB (Loqs-PB) as its major co-factor. Previous analyses indicated that loqs mutants only partially impede miRNA processing but the activity of minor isoforms or maternally deposited Loqs was not eliminated in these studies. We addressed this by generating a cell line from loqs null embryos, and found that only ~40% of miRNAs showed clear Loqs-dependence. Genome-wide comparison of the hairpin structure and Loqs-dependence suggested that Loqs substrates are influenced by base-pairing status at the dicing site. Artificial alteration of base-pairing stability at this position in model miRNA hairpins resulted in predicted changes in the Loqs-dependence, providing evidence for this hypothesis. Finally, we found that evolutionarily young miRNA genes tended to be Loqs-dependent. We propose that Loqs may have roles in assisting the de novo emergence of miRNA genes by facilitating dicing of suboptimal hairpin substrates.

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Section: Methodsmentioning

confidence: 99%

The Drosophila Dicer-1 Partner Loquacious Enhances miRNA Processing from Hairpins with Unstable Structures at the Dicing Site

Lim

Chou

et al. 2016

Cell Reports

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“…However, some conserved miRNAs continue to be found, many of which derive from unusual genomic locations or non-canonical pathways, perhaps explaining why they were overlooked earlier. For example, deeply-conserved, non-canonical, dme-mir-10404 was recently reported to be processed from the internal spacer regions of highly repetitive rRNA loci [32]. Indeed, we find this miRNA is well-cloned from across the Drosophilid phylogeny ( Supplementary Figure S7 ).…”

Section: Resultsmentioning

confidence: 56%

Deep experimental profiling of microRNA diversity, deployment, and evolution across theDrosophilagenus

Flynt

Panzarino

Siepel

et al. 2017

Preprint

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Comparative genomic analyses of microRNAs (miRNAs) have yielded myriad insights into their biogenesis and regulatory activity. While miRNAs have been deeply annotated in a small cohort of model organisms, evolutionary assessments of miRNA flux are clouded by the functional uncertainty of orthologs in related species, and insufficient data regarding the extent of species-specific miRNAs. We address this by generating a comparative small RNA (sRNA) catalog of unprecedented breadth and depth across the Drosophila genus, extending our extant deep analyses of D. melanogaster with sRNA data from multiple tissues of 11 other fly species. Aggregate analysis of several billion sRNA reads permits curation of accurate and holistic compendia of miRNAs across this genus, providing abundant opportunities to identify species- and clade-specific variation in miRNA identity, abundance, and processing. Amongst well-conserved miRNAs, we observe unexpected cases of clade-specific variation in 5′ end precision, occasional antisense loci, and some putatively non-canonical loci. We also employ strict criteria to identify a massive set (649) of novel, evolutionarily-restricted miRNAs. Amongst the bulk collection of species-restricted miRNAs, two notable subpopulations of rapidly-evolving miRNAs are splicing-derived mirtrons and testis-restricted, clustered (TRC) canonical miRNAs. We quantify rates of miRNA birth and death using our annotation and a phylogenetic model for estimating rates of miRNA turnover in the presence of annotation uncertainty. We show striking differences in birth and death rates across miRNA classes defined by biogenesis pathway, genomic clustering, and tissue restriction, and even identify variation heterogeneity amongst Drosophila clades. In particular, distinct molecular rationales underlie the distinct evolutionary behavior of different miRNA classes. We broaden observations made from D. melanogaster as Drosophilid-wide principles for opposing evolutionary viewpoints for miRNA maintenance. Mirtrons are associated with a high rate of 3′ untemplated addition, a mechanism that impedes their biogenesis, whereas TRC miRNAs appear to evolve under positive selection. Altogether, these data reveal miRNA diversity amongst Drosophila species and permit future discoveries in understanding their emergence and evolution.

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“…For example, collected embryos from population cages have been used very successfully in immunoprecipitation assays [6][7][8] , mass collection of larval tissues from dissociated larvae has demonstrated to be a very good source for 3C experiments 4 and RNA preparations 15 , and heads from adult flies have been utilized for ChIP experiments 16 . In addition, adults are often needed to make fly extracts for tissue culture 17 .…”

Section: Discussionmentioning

confidence: 99%

Maintenance of a <em>Drosophila melanogaster</em> Population Cage

Caravaca

Lei

2016

JoVE

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Large quantities of DNA, RNA, proteins and other cellular components are often required for biochemistry and molecular biology experiments. The short life cycle of Drosophila enables collection of large quantities of material from embryos, larvae, pupae and adult flies, in a synchronized way, at a low economic cost. A major strategy for propagating large numbers of flies is the use of a fly population cage. This useful and common tool in the Drososphila community is an efficient way to regularly produce milligrams to tens of grams of embryos, depending on uniformity of developmental stage desired. While a population cage can be time consuming to set up, maintaining a cage over months takes much less time and enables rapid collection of biological material in a short period. This paper describes a detailed and flexible protocol for the maintenance of a Drosophila melanogaster population cage, starting with 1.5 g of harvested material from the previous cycle.

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A deeply conserved, noncanonical miRNA hosted by ribosomal DNA

Cited by 49 publications

References 57 publications

The Drosophila Dicer-1 Partner Loquacious Enhances miRNA Processing from Hairpins with Unstable Structures at the Dicing Site

The Drosophila Dicer-1 Partner Loquacious Enhances miRNA Processing from Hairpins with Unstable Structures at the Dicing Site

Deep experimental profiling of microRNA diversity, deployment, and evolution across theDrosophilagenus

Maintenance of a <em>Drosophila melanogaster</em> Population Cage

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