Requirements for Mediator Complex Subunits Distinguish Three Classes of Notch Target Genes at the Drosophila Wing Margin

Spatial and temporal gene regulation relies on a combinatorial code of sequence-specific transcription factors that must be integrated by the general transcriptional machinery. A key link between the two is the mediator complex, which consists of a core complex that reversibly associates with the accessory kinase module. We show here that genes activated by Notch signaling at the dorsal-ventral boundary of the Drosophila wing disc fall into three classes that are affected differently by the loss of kinase module subunits. One class requires all four kinase module subunits for activation, while the others require only Med12 and Med13, either for activation or for repression. These distinctions do not result from different requirements for the Notch coactivator Mastermind or the corepressors Hairless and Groucho. We propose that interactions with the kinase module through distinct cofactors allow the DNA-binding protein Suppressor of Hairless to carry out both its activator and repressor functions

The retinal determination gene dachshund restricts cell proliferation by limiting the activity of the Homothorax-Yorkie complex

The Drosophila transcriptional co-activator protein Yorkie and its vertebrate orthologs YAP and TAZ are potent oncogenes, whose activity is normally kept in check by the upstream Hippo kinase module. Upon its translocation into the nucleus, Yorkie forms complexes with several tissue-specific DNA-binding partners, which help to define the tissue-specific target genes of Yorkie. In the progenitor cells of the eye imaginal disc, the DNA-binding transcription factor Homothorax is required for Yorkie-promoted proliferation and survival through regulation of the bantam microRNA (miRNA). The transit from proliferating progenitors to cell cycle quiescent precursors is associated with the progressive loss of Homothorax and gain of Dachshund, a nuclear protein related to the Sno/Ski family of co-repressors. We have identified Dachshund as an inhibitor of Homothorax-Yorkie-mediated cell proliferation. Loss of dachshund induces Yorkie-dependent tissue overgrowth. Conversely, overexpressing dachshund inhibits tissue growth, prevents Yorkie or Homothorax-mediated cell proliferation of disc epithelia and restricts the transcriptional activity of the Yorkie-Homothorax complex on the bantam enhancer in Drosophila cells. In addition, Dachshund collaborates with the Decapentaplegic receptor Thickveins to repress Homothorax and Cyclin B expression in quiescent precursors. The antagonistic roles of Homothorax and Dachshund in Yorkie activity, together with their mutual repression, ensure that progenitor and precursor cells are under distinct proliferation regimes. Based on the crucial role of the human dachshund homolog DACH1 in tumorigenesis, our work suggests that DACH1 might prevent cellular transformation by limiting the oncogenic activity of YAP and/or TAZ.Spanish Ministry of Economy and Competitiveness (MINECO), EU Feder Funds: (BFU2012-34324), Consolider 'From Genes to Shape' (MICINN), FCT fellowships: (SFRH/BPD/46983/2008, IF/01031/2012)

The Big Bang of tissue growth: Apical cell constriction turns into tissue expansion

How tissue growth is regulated during development and cancer is a fundamental question in biology. In this issue, Tsoumpekos et al. (2018. J. Cell Biol. https://doi.org/10.1083/jcb.201705104) and Forest et al. (2018. J. Cell Biol. https://doi.org/10.1083/jcb.201705107) identify Big bang (Bbg) as an important growth regulator of the Drosophila melanogaster wing imaginal disc.Research in the Janody laboratory is supported by funds from Fundação para a Ciência e Tecnologia (FCT; PTDC/BIA-BCM/121455/ 2010) and from FCT cofinanced by European Regional Development Fund through Programa Operacional Competitividade e Internacional-ização (POCI-01-0145-FEDER-016390). Florence Janody is the recipient of Fundação para a Ciência e Tecnologia IF/01031/2012

The spectraplakin Dystonin antagonizes YAP activity and suppresses tumourigenesis

Aberrant expression of the Spectraplakin Dystonin (DST) has been observed in various cancers, including those of the breast. However, little is known about its role in carcinogenesis. In this report, we demonstrate that Dystonin is a candidate tumour suppressor in breast cancer and provide an underlying molecular mechanism. We show that in MCF10A cells, Dystonin is necessary to restrain cell growth, anchorage-independent growth, self-renewal properties and resistance to doxorubicin. Strikingly, while Dystonin maintains focal adhesion integrity, promotes cell spreading and cell-substratum adhesion, it prevents Zyxin accumulation, stabilizes LATS and restricts YAP activation. Moreover, treating DST-depleted MCF10A cells with the YAP inhibitor Verteporfin prevents their growth. In vivo, the Drosophila Dystonin Short stop also restricts tissue growth by limiting Yorkie activity. As the two Dystonin isoforms BPAG1eA and BPAG1e are necessary to inhibit the acquisition of transformed features and are both downregulated in breast tumour samples and in MCF10A cells with conditional induction of the Src proto-oncogene, they could function as the predominant Dystonin tumour suppressor variants in breast epithelial cells. Thus, their loss could deem as promising prognostic biomarkers for breast cancer.The authors acknowledge the support of the Bloomington Drosophila Stock Centre, the National Institute of Genetics (NIG-Fly) the services of the Animal, Imaging and Cytometry and Genomics facilities at Instituto Gulbenkian de Ciência, and of the i3S Scientific Platforms, including the Cell Culture and Genotyping (CCGen) and the Genomics (GenCore) platforms, as well as the Bioimaging and the Advanced Light Microscopy platforms. We are also grateful to M. J. Amorim and N. Tapon for reagents and to A. Monteiro for fly food preparation. We specially thank K. Struhl for providing the TAM-inducible ER-Src and PBabe cell lines and Rafeeq Mir, Eurico Morais-de-Sá, Archana Pawar and Carla Oliveira for comments on the manuscript. This work was supported by funds from Fundação para a Ciência e Tecnologia (FCT), co-financed by Fundo Europeu de Desenvolvimento Regional (FEDER) through Programa Operacional Competitividade e Internacionalização (POCI) (POCI-01-0145-FEDER-016390) and the Laço Grant in breast cancer 2015 to F.J. The i3S Bioimaging and Advanced Light Microscopy scientific platforms are both member of the national infrastructure PPBI-Portuguese Platform of BioImaging, supported by POCI-01-0145-FEDER-022122. P.J. was the recipient of fellowships from FCT (PD/ BD/52439/2013). F.J. was the recipient of IF/01031/2012

Detection of markers for discrete phenotypes

Motivation: Capturing the molecular diversity of living cells is not straightforward. One approach is to measure molecular markers that serve as indicators of specific biological conditions or phenotypes. This is particularly relevant in modern medicine to provide precise diagnostics and pinpoint the best treatment for each patient. The challenge is to select a minimal set of markers whose activity patterns are in correspondence with the phenotypes of interest. Results: This article approaches the marker detection problem in the context of discrete phenotypes which arise, for example, from Boolean models of cellular networks. Mathematically this poses a combinatorial optimization problem with many answers. We propose a solution to this optimization problem that is based on the modelling language answer set programming (ASP). A case study of a death cell receptor network illustrates the methodology. Discussion and code: For code, discussions and reporting errors visit https://github.com/hklarner/detection_of_markers_for_discrete_phenotypes

A Novel Pzg-NURF Complex Regulates Notch Target Gene Activity

The Putzig (Pzg) protein is associated with the NURF nucleosome remodeling complex, thereby promoting Notch target gene expression. Our findings suggest a novel Pzg-NURF complex that is responsible for the epigenetic regulation of Notch target genes

Bovine proteins containing poly-glutamine repeats are often polymorphic and enriched for components of transcriptional regulatory complexes

peer-reviewedBackground: About forty human diseases are caused by repeat instability mutations. A distinct subset of these diseases is the result of extreme expansions of polymorphic trinucleotide repeats; typically CAG repeats encoding poly-glutamine (poly-Q) tracts in proteins. Polymorphic repeat length variation is also apparent in human poly-Q encoding genes from normal individuals. As these coding sequence repeats are subject to selection in mammals, it has been suggested that normal variations in some of these typically highly conserved genes are implicated in morphological differences between species and phenotypic variations within species. At present, poly-Q encoding genes in non-human mammalian species are poorly documented, as are their functions and propensities for polymorphic variation. Results: The current investigation identified 178 bovine poly-Q encoding genes (Q ≥ 5) and within this group, 26 genes with orthologs in both human and mouse that did not contain poly-Q repeats. The bovine poly-Q encoding genes typically had ubiquitous expression patterns although there was bias towards expression in epithelia, brain and testes. They were also characterised by unusually large sizes. Analysis of gene ontology terms revealed that the encoded proteins were strongly enriched for functions associated with transcriptional regulation and many contributed to physical interaction networks in the nucleus where they presumably act cooperatively in transcriptional regulatory complexes. In addition, the coding sequence CAG repeats in some bovine genes impacted mRNA splicing thereby generating unusual transcriptional diversity, which in at least one instance was tissue-specific. The poly-Q encoding genes were prioritised using multiple criteria for their likelihood of being polymorphic and then the highest ranking group was experimentally tested for polymorphic variation within a cattle diversity panel. Extensive and meiotically stable variation was identified. Conclusions: Transcriptional diversity can potentially be generated in poly-Q encoding genes by the impact of CAG repeat tracts on mRNA alternative splicing. This effect, combined with the physical interactions of the encoded proteins in large transcriptional regulatory complexes suggests that polymorphic variations of proteins in these complexes have strong potential to affect phenotype.Dairy Australia (through the Innovative Dairy Cooperative Research Center

Mathematics and biology: a Kantian view on the history of pattern formation theory

Driesch’s statement, made around 1900, that the physics and chemistry of his day were unable to explain self-regulation during embryogenesis was correct and could be extended until the year 1972. The emergence of theories of self-organisation required progress in several areas including chemistry, physics, computing and cybernetics. Two parallel lines of development can be distinguished which both culminated in the early 1970s. Firstly, physicochemical theories of self-organisation arose from theoretical (Lotka 1910–1920) and experimental work (Bray 1920; Belousov 1951) on chemical oscillations. However, this research area gained broader acceptance only after thermodynamics was extended to systems far from equilibrium (1922–1967) and the mechanism of the prime example for a chemical oscillator, the Belousov–Zhabotinski reaction, was deciphered in the early 1970s. Secondly, biological theories of self-organisation were rooted in the intellectual environment of artificial intelligence and cybernetics. Turing wrote his The chemical basis of morphogenesis (1952) after working on the construction of one of the first electronic computers. Likewise, Gierer and Meinhardt’s theory of local activation and lateral inhibition (1972) was influenced by ideas from cybernetics. The Gierer–Meinhardt theory provided an explanation for the first time of both spontaneous formation of spatial order and of self-regulation that proved to be extremely successful in elucidating a wide range of patterning processes. With the advent of developmental genetics in the 1980s, detailed molecular and functional data became available for complex developmental processes, allowing a new generation of data-driven theoretical approaches. Three examples of such approaches will be discussed. The successes and limitations of mathematical pattern formation theory throughout its history suggest a picture of the organism, which has structural similarity to views of the organic world held by the philosopher Immanuel Kant at the end of the eighteenth century