Hot off the presses! Oct 18 Dev Cell

The Oct 18 issue of the Dev Cell is now up on Pubget (About Dev Cell): if you're at a subscribing institution, just click the link in the latest link at the home page. (Note you'll only be able to get all the PDFs in the issue if your institution subscribes to Pubget.)

Latest Articles Include:

• Deciphering Gene Expression Patterns
  - Dev Cell 21(4):e1 (2011)
  Large-scale studies in various model systems including Drosophila, fish, and the mouse have documented the exquisite temporal and spatial expression patterns of thousands of genes during development—making sense of it all is a major challenge in the field. The study by Yakoby and colleagues illustrates how very different expression patterns can be generated from a small number of initial patterns. By examining expression patterns for a large number of genes in the Drosophila follicle cell epithelium, the authors proposed that the various expression patterns could be explained by a simple combinatorial code based on six spatial building blocks and the operations of union, difference, intersection, and addition. Importantly, the six spatial building blocks can be linked to the activity of the epidermal growth factor receptor and bone morphogenetic protein signaling pathways that control gene expression along the dorsoventral and anteroposterior axes. A challenge for th! e future will be to see whether such a powerful approach can be applied to explain the diversity of patterns generated in more complex systems such as embryos. This PaperPick refers to "A Combinatorial Code for Pattern Formation in Drosophila Oogenesis" by N. Yakoby, C.A. Bristow, D. Gong, X. Schafer, J. Lembong, J.J. Zartman, M.S. Halfon, T. Schüpbach, and S.Y. Shvartsman, published in November 2008. Video Abstract
• Endoderm Formation: Not So Black and White Anymore
  - Dev Cell 21(4):e2 (2011)
  This study illustrates how the combination of innovative genetic mouse models, embryological experimentation, and live-imaging techniques can resolve longstanding questions in endoderm formation during early mouse development. Kwon et al. showed that cells recruited from the epiblast during germ layer formation in the mouse embryo are not always incorporated into the endoderm in the immediate vicinity of the primitive streak. Beyond demonstrating that the mouse is just like a chick in its strategy for definitive (gut) endoderm recruitment, this finding resolved the enigmatic observation that some epiblast-derived cells in the endoderm are localized further from the site of ingression than anticipated based on "conventional" wisdom. Through tracking of the distribution of the visceral endoderm pre-existing prior to gastrulation, descendants of the visceral endoderm were found, surprisingly, to colonize the embryonic gut, thus dispelling the myth that visceral endode! rm differs from the so-called "definitive" endoderm in its inability to contribute to the embryonic gut and that it is replaced wholesale by the nascent population recruited during gastrulation. This paper thus delineated a paradigm of mouse endoderm formation and presented us with the challenge of determining the ultimate fates of these visceral endoderm cells in the fetal and adult gut. This PaperPick refers to "The Endoderm of the Mouse Embryo Arises by Dynamic Widespread Intercalation of Embryonic and Extraembryonic Lineages," by G.S. Kwon, M. Viotti, and A.K. Hadjantonakis, published in October 2008. Video Abstract
• MINOS Is Plus: A Mitofilin Complex for Mitochondrial Membrane Contacts
  - Dev Cell 21(4):599-600 (2011)
  Cristae junctions mark the boundaries of respiratory compartments in the inner mitochondrial membrane. In this issue of Developmental Cell, identify a complex, MINOS, that organizes cristae junctions. Mitofilin/Fcj1, the central component of the MINOS complex, also connects the inner membrane to outer membrane protein import machinery.
• Cyclin beyond the Cell Cycle: New Partners at the Synapse
  - Dev Cell 21(4):601-602 (2011)
  In this issue of Developmental Cell, demonstrate that the cell-cycle regulator, cyclin E, sequesters Cdk5, a key regulator of neuronal development and synaptic plasticity. This cell-cycle-independent function of cyclin E reveals an exciting mode of Cdk5 regulation in postmitotic neurons and offers a window into evolutionary parsimony.
• The Hormone of Love Attracts a Partner for Life
  - Dev Cell 21(4):602-604 (2011)
  Neurovascular integration during embryonic development is essential for adult physiology. In this issue of Developmental Cell, report that hypothalamic neurons secrete oxytocin as a guidance cue for endothelial cells to establish their vascular supplyâ€"a prerequisite for neuroendocrine secretion from the neurohyophysis in adult life.
• Long, Saturated Chains: Tasty Domains for Kinases of Insulin Resistance
  - Dev Cell 21(4):604-606 (2011)
  The mechanistic basis of how cells respond to increased fatty acids (FAs) is murky but potentially involves receptor-mediated activation or inhibition by different FA classes. recently propose in Cell that expansion of intracellular membrane microdomains induced by saturated FA recruit and activate c-Src for JNK activation.
• Squeezing into Differentiation
  - Dev Cell 21(4):607-608 (2011)
  The earliest steps in tooth development depend on signaling interactions that result in the condensation of mandibular mesenchyme into the tooth bud. Reporting in this issue of Developmental Cell, find that chemotactic signals coordinate condensation and that the compressive force generated is sufficient to induce tooth bud gene expression.
• Bypassing Transcription: A Shortcut in Cytokinin-Auxin Interactions
  - Dev Cell 21(4):608-610 (2011)
  In this issue of Developmental Cell, uncover a transcription-independent molecular mechanism of interaction between auxin and cytokinin in the regulation of plant meristem function. By modulating endocytic trafficking of PIN1, cytokinin controls auxin flux and, therefore, auxin gradients.
• Animal Transcription Networks as Highly Connected, Quantitative Continua
  - Dev Cell 21(4):611-626 (2011)
  To understand how transcription factors function, it is essential to determine the range of genes that they each bind and regulate in vivo. Here I review evidence that most animal transcription factors each bind to a majority of genes over a quantitative series of DNA occupancy levels. These continua span functional, quasifunctional, and nonfunctional DNA binding events. Factor regulatory specificities are distinguished by quantitative differences in DNA occupancy patterns. I contrast these results with models for transcription networks that define discrete sets of direct target and nontarget genes and consequently do not fully capture the complexity observed in vivo.
• A Conserved Pbx-Wnt-p63-Irf6 Regulatory Module Controls Face Morphogenesis by Promoting Epithelial Apoptosis
  - Dev Cell 21(4):627-641 (2011)
  Morphogenesis of mammalian facial processes requires coordination of cellular proliferation, migration, and apoptosis to develop intricate features. Cleft lip and/or palate (CL/P), the most frequent human craniofacial birth defect, can be caused by perturbation of any of these programs. Mutations of WNT, P63, and IRF6 yield CL/P in humans and mice; however, how these genes are regulated remains elusive. We generated mouse lines lacking Pbx genes in cephalic ectoderm and demonstrated that they exhibit fully penetrant CL/P and perturbed Wnt signaling. We also characterized a midfacial regulatory element that Pbx proteins bind to control the expression of Wnt9b-Wnt3, which in turn regulates p63. Altogether, we establish a Pbx-dependent Wnt-p63-Irf6 regulatory module in midfacial ectoderm that is conserved within mammals. Dysregulation of this network leads to localized suppression of midfacial apoptosis and CL/P. Ectopic Wnt ectodermal expression in Pbx mutants rescues th! e clefting, opening avenues for tissue repair.
• The Hypothalamic Neuropeptide Oxytocin Is Required for Formation of the Neurovascular Interface of the Pituitary
  - Dev Cell 21(4):642-654 (2011)
  The hypothalamo-neurohypophyseal system (HNS) is the neurovascular structure through which the hypothalamic neuropeptides oxytocin and arginine-vasopressin exit the brain into the bloodstream, where they go on to affect peripheral physiology. Here, we investigate the molecular cues that regulate the neurovascular contact between hypothalamic axons and neurohypophyseal capillaries of the zebrafish. We developed a transgenic system in which both hypothalamic axons and neurohypophyseal vasculature can be analyzed in vivo. We identified the cellular organization of the zebrafish HNS as well as the dynamic processes that contribute to formation of the HNS neurovascular interface. We show that formation of this interface is regulated during development by local release of oxytocin, which affects endothelial morphogenesis. This cell communication process is essential for the establishment of a tight axovasal interface between the neurons and blood vessels of the HNS. We prese! nt a unique example of axons affecting endothelial morphogenesis through secretion of a neuropeptide.
• Cyclin E Constrains Cdk5 Activity to Regulate Synaptic Plasticity and Memory Formation
  - Dev Cell 21(4):655-668 (2011)
  Cyclin E is a component of the core cell cycle machinery, and it drives cell proliferation by regulating entry and progression of cells through the DNA synthesis phase. Cyclin E expression is normally restricted to proliferating cells. However, high levels of cyclin E are expressed in the adult brain. The function of cyclin E in quiescent, postmitotic nervous system remains unknown. Here we use a combination of in vivo quantitative proteomics and analyses of cyclin E knockout mice to demonstrate that in terminally differentiated neurons cyclin E forms complexes with Cdk5 and controls synapse function by restraining Cdk5 activity. Ablation of cyclin E led to a decreased number of synapses, reduced number and volume of dendritic spines, and resulted in impaired synaptic plasticity and memory formation in cyclin E-deficient animals. These results reveal a cell cycle-independent role for a core cell cycle protein, cyclin E, in synapse function and memory.
• MADD-4 Is a Secreted Cue Required for Midline-Oriented Guidance in Caenorhabditis elegans
  - Dev Cell 21(4):669-680 (2011)
  The netrins and slits are two families of widely conserved cues that guide axons and cells along the dorsal-ventral (D-V) axis of animals. These cues typically emanate from the dorsal or ventral midlines and provide spatial information to migrating cells by forming gradients along the D-V axis. Some cell types, however, extend processes to both the dorsal and ventral midlines, suggesting the existence of additional guidance cues that are secreted from both midlines. Here, we report that a previously uncharacterized protein called MADD-4 is secreted by the dorsal and ventral nerve cords of the nematode C. elegans to attract sensory axons and muscle membrane extensions called muscle arms. MADD-4's activity is dependent on UNC-40/DCC, a netrin receptor, which functions cell-autonomously to direct membrane extension. The biological role of MADD-4 orthologs, including ADAMTSL1 and 3 in mammals, is unknown. MADD-4 may therefore represent the founding member of a family of gu! idance proteins.
• A Syndecan-4 Hair Trigger Initiates Wound Healing through Caveolin- and RhoG-Regulated Integrin Endocytosis
  - Dev Cell 21(4):681-693 (2011)
  Cell migration during wound healing requires adhesion receptor turnover to enable the formation and disassembly of cell-extracellular matrix contacts. Although recent advances have improved our understanding of integrin trafficking pathways, it is not known how extracellular ligand engagement controls receptor dynamics. Using atomic force microscopy, we have measured cell avidity for fibronectin and defined a mechanism for the outside-in regulation of α5β1-integrin. Surprisingly, adhesive strength was attenuated by the syndecan-4-binding domain of fibronectin due to a rapid triggering of α5β1-integrin endocytosis. Association of syndecan-4 with PKCα was found to trigger RhoG activation and subsequent dynamin- and caveolin-dependent integrin uptake. Like disruption of syndecan-4 or caveolin, gene disruption of RhoG in mice was found to retard closure of dermal wounds due to a migration defect of the fibroblasts and keratinocytes of RhoG null mice. Thus, this syndec! an-4-regulated integrin endocytic pathway appears to play a key role in tissue repair.
• Dual Role of Mitofilin in Mitochondrial Membrane Organization and Protein Biogenesis
  - Dev Cell 21(4):694-707 (2011)
  The mitochondrial inner membrane consists of two domains, inner boundary membrane and cristae membrane that are connected by crista junctions. Mitofilin/Fcj1 was reported to be involved in formation of crista junctions, however, different views exist on its function and possible partner proteins. We report that mitofilin plays a dual role. Mitofilin is part of a large inner membrane complex, and we identify five partner proteins as constituents of the mitochondrial inner membrane organizing system (MINOS) that is required for keeping cristae membranes connected to the inner boundary membrane. Additionally, mitofilin is coupled to the outer membrane and promotes protein import via the mitochondrial intermembrane space assembly pathway. Our findings indicate that mitofilin is a central component of MINOS and functions as a multifunctional regulator of mitochondrial architecture and protein biogenesis.
• The Tetraspanin CD63 Regulates ESCRT-Independent and -Dependent Endosomal Sorting during Melanogenesis
  - Dev Cell 21(4):708-721 (2011)
  Cargo sorting to intraluminal vesicles (ILVs) of multivesicular endosomes is required for lysosome-related organelle (LRO) biogenesis. PMEL—a component of melanocyte LROs (melanosomes)—is sorted to ILVs in an ESCRT-independent manner, where it is proteolytically processed and assembled into functional amyloid fibrils during melanosome maturation. Here we show that the tetraspanin CD63 directly participates in ESCRT-independent sorting of the PMEL luminal domain, but not of traditional ESCRT-dependent cargoes, to ILVs. Inactivating CD63 in cell culture or in mice impairs amyloidogenesis and downstream melanosome morphogenesis. Whereas CD63 is required for normal PMEL luminal domain sorting, the disposal of the remaining PMEL transmembrane fragment requires functional ESCRTs but not CD63. In the absence of CD63, the PMEL luminal domain follows this fragment and is targeted for ESCRT-dependent degradation. Our data thus reveal a tight interplay regulated by CD63 betwe! en two distinct endosomal ILV sorting processes for a single cargo during LRO biogenesis.
• Rac1 Drives Melanoblast Organization during Mouse Development by Orchestrating Pseudopod- Driven Motility and Cell-Cycle Progression
  - Dev Cell 21(4):722-734 (2011)
  During embryogenesis, melanoblasts proliferate and migrate ventrally through the developing dermis and epidermis as single cells. Targeted deletion of Rac1 in melanoblasts during embryogenesis causes defects in migration, cell-cycle progression, and cytokinesis. Rac1 null cells migrate markedly less efficiently, but surprisingly, global steering, crossing the dermal/epidermal junction, and homing to hair follicles occur normally. Melanoblasts navigate in the epidermis using two classes of protrusion: short stubs and long pseudopods. Short stubs are distinct from blebs and are driven by actin assembly but are independent of Rac1, Arp2/3 complex, myosin, or microtubules. Rac1 positively regulates the frequency of initiation of long pseudopods, which promote migration speed and directional plasticity. Scar/WAVE and Arp2/3 complex drive actin assembly for long pseudopod extension, which also depends on microtubule dynamics. Myosin contractility balances the extension of lo! ng pseudopods by effecting retraction and allowing force generation for movement through the complex 3D epidermal environment.
• Dual Roles for Rac2 in Neutrophil Motility and Active Retention in Zebrafish Hematopoietic Tissue
  - Dev Cell 21(4):735-745 (2011)
  Neutrophil homeostasis is essential for host defense. Here we identify dual roles for Rac2 during neutrophil homeostasis using a zebrafish model of primary immune deficiency induced by the human inhibitory Rac2D57N mutation in neutrophils. Noninvasive live imaging of Rac2 morphants or Rac2D57N zebrafish larvae demonstrates an essential role for Rac2 in regulating 3D motility and the polarization of F-actin dynamics and PI(3)K signaling in vivo. Tracking of photolabeled Rac2-deficient neutrophils from hematopoietic tissue also shows increased mobilization into the circulation, indicating that neutrophil mobilization does not require traditionally defined cell motility. Moreover, excessive neutrophil retention in hematopoietic tissue resulting from a constitutively active CXCR4 mutation in zebrafish warts, hypogammaglobulinemia, infections, and myelokathexis (WHIM) syndrome is partially rescued by the inhibitory Rac2 mutation. These findings reveal that Rac2 signaling is! necessary for both neutrophil 3D motility and CXCR4-mediated neutrophil retention in hematopoietic tissue, thereby limiting neutrophil mobilization, a critical first step in the innate immune response.
• ATXN1 Protein Family and CIC Regulate Extracellular Matrix Remodeling and Lung Alveolarization
  - Dev Cell 21(4):746-757 (2011)
  Although expansion of CAG repeats in ATAXIN1 (ATXN1) causes Spinocerebellar ataxia type 1, the functions of ATXN1 and ATAXIN1-Like (ATXN1L) remain poorly understood. To investigate the function of these proteins, we generated and characterized Atxn1L−/− and Atxn1−/−; Atxn1L−/− mice. Atxn1L−/− mice have hydrocephalus, omphalocele, and lung alveolarization defects. These phenotypes are more penetrant and severe in Atxn1−/−; Atxn1L−/− mice, suggesting that ATXN1 and ATXN1L are functionally redundant. Upon pursuing the molecular mechanism, we discovered that several Matrix metalloproteinase (Mmp) genes are overexpressed and that the transcriptional repressor Capicua (CIC) is destabilized in Atxn1L−/− lungs. Consistent with this, Cic deficiency causes lung alveolarization defect. Loss of either ATXN1L or CIC derepresses Etv4, an activator for Mmp genes, thereby mediating MMP9 overexpression. These findings demonstrate a critical role of ATXN1/ATX! N1L-CIC complexes in extracellular matrix (ECM) remodeling during development and their potential roles in pathogenesis of disorders affecting ECM remodeling.
• Mechanochemical Control of Mesenchymal Condensation and Embryonic Tooth Organ Formation
  - Dev Cell 21(4):758-769 (2011)
  Mesenchymal condensation is critical for organogenesis, yet little is known about how this process is controlled. Here we show that Fgf8 and Sema3f, produced by early dental epithelium, respectively, attract and repulse mesenchymal cells, which cause them to pack tightly together during mouse tooth development. Resulting mechanical compaction-induced changes in cell shape induce odontogenic transcription factors (Pax9, Msx1) and a chemical cue (BMP4), and mechanical compression of mesenchyme is sufficient to induce tooth-specific cell fate switching. The inductive effects of cell compaction are mediated by suppression of the mechanical signaling molecule RhoA, and its overexpression prevents odontogenic induction. Thus, the mesenchymal condensation that drives tooth formation is induced by antagonistic epithelial morphogens that manifest their pattern-generating actions mechanically via changes in mesenchymal cell shape and altered mechanotransduction.
• Cell Identity Regulators Link Development and Stress Responses in the Arabidopsis Root
  - Dev Cell 21(4):770-782 (2011)
  Stress responses in plants are tightly coordinated with developmental processes, but interaction of these pathways is poorly understood. We used genome-wide assays at high spatiotemporal resolution to understand the processes that link development and stress in the Arabidopsis root. Our meta-analysis finds little evidence for a universal stress response. However, common stress responses appear to exist with many showing cell type specificity. Common stress responses may be mediated by cell identity regulators because mutations in these genes resulted in altered responses to stress. Evidence for a direct role for cell identity regulators came from genome-wide binding profiling of the key regulator SCARECROW, which showed binding to regulatory regions of stress-responsive genes. Coexpression in response to stress was used to identify genes involved in specific developmental processes. These results reveal surprising linkages between stress and development at cellular res! olution, and show the power of multiple genome-wide data sets to elucidate biological processes.
• A Muscle-Specific p38 MAPK/Mef2/MnSOD Pathway Regulates Stress, Motor Function, and Life Span in Drosophila
  - Dev Cell 21(4):783-795 (2011)
  Molecular mechanisms that concordantly regulate stress, life span, and aging remain incompletely understood. Here, we demonstrate that in Drosophila, a p38 MAP kinase (p38K)/Mef2/MnSOD pathway is a coregulator of stress and life span. Hence, overexpression of p38K extends life span in a MnSOD-dependent manner, whereas inhibition of p38K causes early lethality and precipitates age-related motor dysfunction and stress sensitivity, that is rescued through muscle-restricted (but not neuronal) add-back of p38K. Additionally, mutations in p38K are associated with increased protein carbonylation and Nrf2-dependent transcription, while adversely affecting metabolic response to hypoxia. Mechanistically, p38K modulates expression of the mitochondrial MnSOD enzyme through the transcription factor Mef2, and predictably, perturbations in MnSOD modify p38K-dependent phenotypes. Thus, our results uncover a muscle-restricted p38K-Mef2-MnSOD signaling module that influences life span a! nd stress, distinct from the insulin/JNK/FOXO pathway. We propose that potentiating p38K might be instrumental in restoring the mitochondrial detoxification machinery and combating stress-induced aging.
• Cytokinin Modulates Endocytic Trafficking of PIN1 Auxin Efflux Carrier to Control Plant Organogenesis
  - Dev Cell 21(4):796-804 (2011)
  Cytokinin is an important regulator of plant growth and development. In Arabidopsis thaliana, the two-component phosphorelay mediated through a family of histidine kinases and response regulators is recognized as the principal cytokinin signal transduction mechanism activating the complex transcriptional response to control various developmental processes. Here, we identified an alternative mode of cytokinin action that uses endocytic trafficking as a means to direct plant organogenesis. This activity occurs downstream of known cytokinin receptors but through a branch of the cytokinin signaling pathway that does not involve transcriptional regulation. We show that cytokinin regulates endocytic recycling of the auxin efflux carrier PINFORMED1 (PIN1) by redirecting it for lytic degradation in vacuoles. Stimulation of the lytic PIN1 degradation is not a default effect for general downregulation of proteins from plasma membranes, but a specific mechanism to rapidly modulat! e the auxin distribution in cytokinin-mediated developmental processes.