Denoising feedback loops by thresholding--a new role for microRNAs.
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Animals↗
Biomedical subjects
Stephen M Cohen
Publications and source records attributed to Stephen M Cohen.
On the role of glypicans in the process of morphogen gradient formation.
Glypicans are cell surface molecules that influence signaling and gradient formation of secreted morphogens and growth factors. Several distinct functions have been ascribed to glypicans including acting as co-receptors for signaling proteins. Recent data show that glypicans are also necessary for morphogen propagation in the tissue. In the present study, a model describing the interaction of a morphogen with glypicans is formulated, analyzed and compared with measurements of the effect of glypican Dally-like (Dlp) overexpression on Wingless (Wg) morphogen signaling in Drosophila melanogaster wing imaginal discs. The model explains the opposing effect that Dlp overexpression has on Wg signaling in the distal and proximal regions of the disc and makes a number of quantitative predictions for further experiments. In particular, our model suggests that Dlp acts by allowing Wg to diffuse on cell surface while protecting it from loss and degradation, and that Dlp rather than acting as Wg co-receptor competes with receptors for morphogen binding.
Animals↗
Structural insights into the Notch-modifying glycosyltransferase Fringe.
Fringe proteins are beta1,3-N-acetylglucosaminyltransferases that modify Notch receptors, altering their ligand-binding specificity to regulate Notch signaling in development. We present the crystal structure of mouse Manic Fringe bound to UDP and manganese. The structure reveals amino acid residues involved in recognition of donor substrates and catalysis, and a putative binding pocket for acceptor substrates. Mutations of several invariant residues in this pocket impair Fringe activity in vivo.
Animals↗
The Hippo pathway regulates the bantam microRNA to control cell proliferation and apoptosis in Drosophila.
The Hippo signaling pathway acts upon the Yorkie transcriptional activator to control tissue growth in Drosophila. Activated Yorkie drives growth by stimulating cell proliferation and inhibiting apoptosis, but how it achieves this is not understood. Yorkie is known to activate Cyclin E (CycE) and the apoptosis inhibitor DIAP1. However, overexpression of these targets is not sufficient to cause tissue overgrowth. Here we show that Yorkie also activates expression of the bantam microRNA, a known regulator of both proliferation and apoptosis. bantam overexpression mimics Yorkie activation while loss of bantam function slows the rate of cell proliferation. bantam is necessary for Yorkie-induced overproliferation and bantam overexpression is sufficient to rescue survival and proliferation of yorkie mutant cells. Finally, we show that bantam levels are regulated during both developmentally programmed proliferation arrest and apoptosis. In summary, the results show that the Hippo pathway regulates expression of bantam to control tissue growth in Drosophila.
Animals↗
Developmental biology. Mixed messages in early development.
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3' Untranslated Regions↗
Drosophila lacking microRNA miR-278 are defective in energy homeostasis.
The mechanisms that control energy homeostasis and tissue growth during development are closely linked through the insulin signal transduction pathway. Changes in the level of insulin and other hormones reflect the nutritional status of the animal to control circulating sugar levels and fat metabolism. Systemic defects in insulin responsiveness can lead to elevated circulating glucose levels and fat accumulation. Here we present evidence that the microRNA miR-278 plays a role in the control of energy homeostasis in Drosophila. miR-278 mutants have elevated insulin production and are correspondingly lean. Despite the elevated insulin levels, miR-278 mutants have elevated circulating sugar, mobilized from adipose-tissue glycogen stores. We provide evidence that miR-278 mutants are insulin resistant and that miR-278 acts through regulation of the expanded transcript.
Animals↗
An evaluation of the efficacy of a cyclosporine-based dry eye therapy when used with marketed artificial tears as supportive therapy in dry eye.
PURPOSE: To evaluate the efficacy of marketed artificial tears in relieving the signs and symptoms of dry eye when used as supportive therapy to a cyclosporine-based ophthalmic emulsion. METHODS: Sixty-one patients were enrolled in this randomized, investigator-masked, parallel study of 6 months' duration. Eligible patients needed a Schirmer I score without anesthesia of 7 mm or less at day -7 and to answer that they needed artificial tears at least "some of the time." Corneal staining of 3 or more (National Eye Institute grid, 15 points) at day -7 and day 0 in the same eye was also required. Patients were randomized to one of three regimens: Restasis (0.05% cyclosporine) twice per day with Systane used a minimum of once per day (Restasis + Systane); Restasis twice per day with Refresh Tears used a minimum of once per day (Restasis + Refresh); and Systane alone used four times per day. Signs and symptoms were measured at days -7, 0, 7, 14, 28, 42, 120, and 180. RESULTS: A statistical difference was seen in favor of Restasis + Systane versus Restasis + Refresh for corneal staining (P = 0.0048) change from baseline and a trend (P = 0.0725) for increased tear film breakup time at 6 months. There were no differences between treatment groups for Schirmer score, conjunctival staining, or conjunctival injection. Significant differences were seen in favor of Restasis + Systane versus Restasis + Refresh for less ocular burning (P = 0.0210), stinging (P = 0.0314), grittiness (P = 0.0128), and dryness (P = 0.0132). Systane was better than Restasis + Refresh for less burning (P = 0.0288), dryness (P = 0.0480), and scratchiness (P = 0.0294). CONCLUSIONS: Results indicate that the choice of concomitant therapy used with Restasis has significant effects on outcome measures. Both supportive therapies were compatible with Restasis.
Adult↗
Genome-wide analysis of mRNAs regulated by Drosha and Argonaute proteins in Drosophila melanogaster.
RNA silencing pathways are conserved gene regulation mechanisms that elicit decay and/or translational repression of mRNAs complementary to short interfering RNAs and microRNAs (miRNAs). The fraction of the transcriptome regulated by these pathways is not known, but it is thought that each miRNA may have hundreds of targets. To identify transcripts regulated by silencing pathways at the genomic level, we examined mRNA expression profiles in Drosophila melanogaster cells depleted of four Argonaute paralogs (i.e., AGO1, AGO2, PIWI, or Aubergine) that play essential roles in RNA silencing. We also profiled cells depleted of the miRNA-processing enzyme Drosha. The results reveal that transcripts differentially expressed in Drosha-depleted cells have highly correlated expression in the AGO1 knockdown and are significantly enriched in predicted and validated miRNA targets. The levels of a subset of miRNA targets are also regulated by AGO2. Moreover, AGO1 and AGO2 silence the expression of a common set of mobile genetic elements. Together, these results indicate that the functional overlap between AGO1 and AGO2 in Drosophila is more important than previously thought.
Animals↗
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.
3' Untranslated Regions↗
Gain-of-function screen for genes that affect Drosophila muscle pattern formation.
This article reports the production of an EP-element insertion library with more than 3,700 unique target sites within the Drosophila melanogaster genome and its use to systematically identify genes that affect embryonic muscle pattern formation. We designed a UAS/GAL4 system to drive GAL4-responsive expression of the EP-targeted genes in developing apodeme cells to which migrating myotubes finally attach and in an intrasegmental pattern of cells that serve myotubes as a migration substrate on their way towards the apodemes. The results suggest that misexpression of more than 1.5% of the Drosophila genes can interfere with proper myotube guidance and/or muscle attachment. In addition to factors already known to participate in these processes, we identified a number of enzymes that participate in the synthesis or modification of protein carbohydrate side chains and in Ubiquitin modifications and/or the Ubiquitin-dependent degradation of proteins, suggesting that these processes are relevant for muscle pattern formation.
Animals↗
Not miR-ly muscular: microRNAs and muscle development.
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Animals↗
4E-BP functions as a metabolic brake used under stress conditions but not during normal growth.
4E-BP is an important regulator of overall translation levels in cells. By binding eIF4E, 4E-BP impairs recruitment of the 40S ribosomal subunit to the cap structure present at the 5'-end of all eukaryotic cellular mRNAs. 4E-BP activity is controlled by TOR (Target of Rapamycin). 4E-BP has been studied extensively in cell culture; however, the biological role of 4E-BP in developing organisms is unclear to date. Since TOR has been shown to control tissue growth during animal development, 4E-BP has also been assumed to serve as a growth regulator. Here, we study the relevance of 4E-BP function for organismal development, and present evidence for an alternate view. We show that 4E-BP strongly affects fat metabolism in Drosophila. We suggest that 4E-BP works as a metabolic brake that is activated under conditions of environmental stress to control fat metabolism. 4E-BP mutants lack this regulation, reducing their ability to survive under unfavorable conditions.
Animals↗
molting defective is required for ecdysone biosynthesis.
20-hydroxyecdysone was discovered as the major biologically active insect steroid hormone half a century ago, yet much remains to be learned about its biosynthesis and its activities. 20-hydroxyecdysone controls many biological processes, including progression between larval stages, entry to pupariation and metamorphosis. A number of genes required for 20-hydroxyecdysone production have been identified, including those encoding enzymes that mediate four of the late steps of biosynthesis. A second smaller group of low ecdysone mutants do not encode enzymes. Here, we report identification of one such gene, which we call molting defective, on the basis of its lethal phenotype. molting defective encodes a nuclear zinc finger protein required for ecdysone biosynthesis.
Animals↗
A genetic screen in Drosophila for identifying novel components of the hedgehog signaling pathway.
The Hedgehog signaling pathway plays an essential role in the pattern formation and development of metazoan animals. Misregulation of Hedgehog signaling has also been associated with the formation of multiple types of cancer. For these reasons, the Hedgehog pathway has attracted considerable interest. Many proteins required in the Hedgehog pathway have been identified, and while much has been learned about their function in signal transduction, it is clear that this complement of proteins does not comprise the full set necessary for Hedgehog signal transduction. Because significant gaps remain in our knowledge of the molecules required for Hedgehog signaling, we performed an enhancer/suppressor screen in Drosophila melanogaster to identify novel components of the pathway. In addition to the isolation of new alleles of the known pathway components patched and smoothened, this screen identified 14 novel complementation groups and a larger number of loci represented by single alleles. These groups include mutations in the genes encoding the translation factors eRF1 and eIF1A and the kinesin-like protein Pavarotti. It also identified mutations in a gene whose product is necessary for the movement of Hedgehog protein through tissues.
Amino Acid Sequence↗
Boundary formation in the Drosophila wing: functional dissection of Capricious and Tartan.
Cells in multicellular organisms often do not intermingle freely with each other. Differential cell affinities contribute to organizing cells into different tissues. Drosophila limbs and rhombomeres of the vertebrate hindbrain are subdivided into compartments. Cells in adjacent compartments do not mix. The wing primordium is subdivided into dorsal (D) and ventral (V) compartments by the activity of the LIM-homeodomain protein Apterous in D cells. The leucine-rich repeats transmembrane proteins Capricious and Tartan have been shown to contribute to formation of the affinity boundary between dorsal and ventral compartments. Here, we have carried out a structure-function analysis of Capricious and Tartan. We present evidence that both the extracellular and intracellular domains are required for the establishment of a DV affinity boundary. Our data suggest that the extracellular domains of Capricious and Tartan may work as ligands of an unknown D cell surface protein. Their intracellular domains may be required to transduce a signal necessary for the establishment of the DV boundary.
Animals↗
Drosophila Melted modulates FOXO and TOR activity.
The insulin/PI3K signaling pathway controls both tissue growth and metabolism. Here, we identify Melted as a new modulator of this pathway in Drosophila. Melted interacts with both Tsc1 and FOXO and can recruit these proteins to the cell membrane. We provide evidence that in the melted mutant, TOR activity is reduced and FOXO is activated. The melted mutant condition mimics the effects of nutrient deprivation in a normal animal, producing an animal with 40% less fat than normal.
Adipose Tissue↗
Tumor suppressor properties of the ESCRT-II complex component Vps25 in Drosophila.
We have found that the Drosophila gene vps25 possesses several properties of a tumor suppressor. First, vps25 mutant cells activate Notch and Dpp receptor signaling, inducing ectopic organizers in developing eyes and limbs and consequent overproliferation of both mutant and nearby wild-type cells. Second, as the mutant cells proliferate, they lose their epithelial organization and undergo apoptosis. Strikingly, when apoptosis of mutant cells is blocked, tumor-like overgrowths are formed that are capable of metastasis. vps25 encodes a component of the ESCRT-II complex, which sorts membrane proteins into multivesicular bodies during endocytic trafficking to the lysosome. Activation of Notch and Dpp receptor signaling in mutant cells results from an endocytic blockage that causes accumulation of these receptors and other signaling components in endosomes. These results highlight the importance of endocytic trafficking in regulating signaling and epithelial organization and suggest a possible role for ESCRT components in human cancer.
Animals↗
Ligand-binding and signaling properties of the Ax[M1] form of Notch.
The Abruptex class of Notch alleles has attracted interest because they exhibit some properties that are best explained in terms of increased activity and others that are best explained in terms of reduced activity in vivo. Here, we report a comparison of the properties of Abruptex[M1] and wild-type Notch as ligand binding receptors. Abruptex[M1] showed less activity than wild-type Notch in its ability to bind Delta and Serrate and was expressed at reduced levels on the cell surface. When differences in expression level were taken into account, Abruptex[M1] was comparable to Notch in its sensitivity to ligand-induced activation of reporter gene expression. Abruptex[M1] was also comparable to Notch in its requirement for modification by Fringe and in being sensitive to cis-dowregulation by co-expressed ligands. By the available criteria Abruptex[M1] exhibits less activity than Notch. To explain the ectopic activity of Abruptex[M1] in vivo we suggest that it may be necessary to invoke an altered response to an as yet unidentified ligand or cofactor.
Alleles↗