miR-124 controls male reproductive success in Drosophila.

Many aspects of social behavior are controlled by sex-specific pheromones. Gender-appropriate production of the sexually dimorphic transcription factors doublesex and fruitless controls sexual differentiation and sexual behavior. miR-124 mutant males exhibited increased male-male courtship and reduced reproductive success with females. Females showed a strong preference for wild-type males over miR-124 mutant males when given a choice of mates. These effects were traced to aberrant pheromone production. We identified the sex-specific splicing factor transformer as a functionally significant target of miR-124 in this context, suggesting a role for miR-124 in the control of male sexual differentiation and behavior, by limiting inappropriate expression of the female form of transformer. miR-124 is required to ensure fidelity of gender-appropriate pheromone production in males. Use of a microRNA provides a secondary means of controlling the cascade of sex-specific splicing events that controls sexual differentiation in Drosophila. DOI:http://dx.doi.org/10.7554/eLife.00640.001.

An intuitive graphical visualization technique for the interrogation of transcriptome data.

The complexity of gene expression data generated from microarrays and high-throughput sequencing make their analysis challenging. One goal of these analyses is to define sets of co-regulated genes and identify patterns of gene expression. To date, however, there is a lack of easily implemented methods that allow an investigator to visualize and interact with the data in an intuitive and flexible manner. Here, we show that combining a nonlinear dimensionality reduction method, t-statistic Stochastic Neighbor Embedding (t-SNE), with a novel visualization technique provides a graphical mapping that allows the intuitive investigation of transcriptome data. This approach performs better than commonly used methods, offering insight into underlying patterns of gene expression at both global and local scales and identifying clusters of similarly expressed genes. A freely available MATLAB-implemented graphical user interface to perform t-SNE and nearest neighbour plots on genomic data sets is available at www.nimr.mrc.ac.uk/research/james-briscoe/visgenex.

Drosophila microRNAs 263a/b confer robustness during development by protecting nascent sense organs from apoptosis.

miR-263a/b are members of a conserved family of microRNAs that are expressed in peripheral sense organs across the animal kingdom. Here we present evidence that miR-263a and miR-263b play a role in protecting Drosophila mechanosensory bristles from apoptosis by down-regulating the pro-apoptotic gene head involution defective. Both microRNAs are expressed in the bristle progenitors, and despite a difference in their seed sequence, they share this key common target. In miR-263a and miR-263b deletion mutants, loss of bristles appears to be sporadic, suggesting that the role of the microRNAs may be to ensure robustness of the patterning process by promoting survival of these functionally specified cells. In the context of the retina, this mechanism ensures that the interommatidial bristles are protected during the developmentally programmed wave of cell death that prunes excess cells in order to refine the pattern of the pupal retina.

Recombinase-mediated cassette exchange provides a versatile platform for gene targeting: knockout of miR-31b.

A series of vectors has been designed to enhance the versatility of targeted homologous recombination. Recombinase-mediated cassette exchange permits sequential targeting at any locus and improves flexibility in making user-defined mutations. Application of RMCE to delete an intronic microRNA gene is described.

MicroRNAs in neurodegeneration.

microRNAs (miRNAs) act as post-transcriptional regulators of gene expression in diverse cellular and developmental processes. Many miRNAs are expressed specifically in the central nervous system, where they have roles in differentiation, neuronal survival, and potentially also in plasticity and learning. The absence of miRNAs in a variety of specific postmitotic neurons can lead to progressive loss of these neurons and behavioral defects reminiscent of the phenotypes seen in the pathologies of neurodegenerative diseases. Here, we review recent studies which provide a link between miRNA function and neurodegeneration. We also discuss evidence which might suggest involvement of miRNAs in the emergence or progression of neurodegenerative diseases.

Mei-P26 regulates microRNAs and cell growth in the Drosophila ovarian stem cell lineage.

Drosophila neuroblasts and ovarian stem cells are well characterized models for stem cell biology. In both cell types, one daughter cell self-renews continuously while the other undergoes a limited number of divisions, stops to proliferate mitotically and differentiates. Whereas neuroblasts segregate the Trim-NHL (tripartite motif and Ncl-1, HT2A and Lin-41 domain)-containing protein Brain tumour (Brat) into one of the two daughter cells, ovarian stem cells are regulated by an extracellular signal from the surrounding stem cell niche. After division, one daughter cell looses niche contact. It undergoes 4 transit-amplifying divisions to form a cyst of 16 interconnected cells that reduce their rate of growth and stop to proliferate mitotically. Here we show that the Trim-NHL protein Mei-P26 (refs 7, 8) restricts growth and proliferation in the ovarian stem cell lineage. Mei-P26 expression is low in stem cells but is strongly induced in 16-cell cysts. In mei-P26 mutants, transit-amplifying cells are larger and proliferate indefinitely leading to the formation of an ovarian tumour. Like brat, mei-P26 regulates nucleolar size and can induce differentiation in Drosophila neuroblasts, suggesting that these genes act through the same pathway. We identify Argonaute-1, a component of the RISC complex, as a common binding partner of Brat and Mei-P26, and show that Mei-P26 acts by inhibiting the microRNA pathway. Mei-P26 and Brat have a similar domain composition that is also found in other tumour suppressors and might be a defining property of a new family of microRNA regulators that act specifically in stem cell lineages.

Temporal reciprocity of miRNAs and their targets during the maternal-to-zygotic transition in Drosophila.

During oogenesis, female animals load their eggs with messenger RNAs (mRNAs) that will be translated to produce new proteins in the developing embryo. Some of these maternally provided mRNAs are stable and continue to contribute to development long after the onset of transcription of the embryonic (zygotic) genome. However, a subset of maternal mRNAs are degraded during the transition from purely maternal to mixed maternal-zygotic gene expression. In Drosophila, two independent RNA degradation pathways are used to promote turnover of maternal transcripts during the maternal-to-zygotic transition [1]. The first is driven by maternally encoded factors, including SMAUG [2], whereas the second is activated about 2 hr after fertilization, coinciding with the onset of zygotic transcription. Here, we report that a cluster of zygotically expressed microRNAs (miRNAs) targets maternal mRNAs for turnover, as part of the zygotic degradation pathway. miRNAs are small noncoding RNAs that silence gene expression by repressing translation of their target mRNAs and by promoting mRNA turnover. Intriguingly, use of miRNAs to promote mRNA turnover during the maternal-to-zygotic transition appears to be a conserved phenomenon because a comparable role was reported for miR-430 in zebrafish [3]. The finding that unrelated miRNAs regulate the maternal to zygotic transition in different animals suggests convergent evolution.

A single Hox locus in Drosophila produces functional microRNAs from opposite DNA strands.

MicroRNAs (miRNAs) are approximately 22-nucleotide RNAs that are processed from characteristic precursor hairpins and pair to sites in messages of protein-coding genes to direct post-transcriptional repression. Here, we report that the miRNA iab-4 locus in the Drosophila Hox cluster is transcribed convergently from both DNA strands, giving rise to two distinct functional miRNAs. Both sense and antisense miRNA products target neighboring Hox genes via highly conserved sites, leading to homeotic transformations when ectopically expressed. We also report sense/antisense miRNAs in mouse and find antisense transcripts close to many miRNAs in both flies and mammals, suggesting that additional sense/antisense pairs exist.

microRNA functions.

microRNAs (miRNAs) are small noncoding RNAs that play important roles in posttranscriptional gene regulation. In animal cells, miRNAs regulate their targets by translational inhibition and mRNA destabilization. Here, we review recent work in animal models that provide insight into the diverse roles of miRNAs in vivo.

Animal MicroRNAs confer robustness to gene expression and have a significant impact on 3'UTR evolution.

MicroRNAs are small noncoding RNAs that serve as posttranscriptional regulators of gene expression in higher eukaryotes. Their widespread and important role in animals is highlighted by recent estimates that 20%-30% of all genes are microRNA targets. Here, we report that a large set of genes involved in basic cellular processes avoid microRNA regulation due to short 3'UTRs that are specifically depleted of microRNA binding sites. For individual microRNAs, we find that coexpressed genes avoid microRNA sites, whereas target genes and microRNAs are preferentially expressed in neighboring tissues. This mutually exclusive expression argues that microRNAs confer accuracy to developmental gene-expression programs, thus ensuring tissue identity and supporting cell-lineage decisions.