Hot off the presses! Aug 07 Cell

The Aug 07 issue of the Cell is now up on Pubget (About 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:

• In This Issue
  - Cell 138(3):405, 407 (2009)
  
• Evolutionary Biology Select
  - Cell 138(3):409, 411 (2009)
  Life's ability to adapt to complex and changing environments is the subject of this issue's Evolutionary Biology Select. New findings suggest that microbes can prepare in advance for future changes in their environments and show that partial penetrance of a phenotype may be a stepping stone to dramatic evolutionary transitions. Other recent work links genetics and ecology, providing insight into the timing of flowering, disease susceptibility in nonhuman primates, and the impact of climate change on developmental plasticity in mammals.
• Biotech's Perfect Storm
  - Cell 138(3):413-415 (2009)
  The global financial crisis has hit biotech companies hard both in the US and Europe as venture capital dries up. Finding new sources of long-term financing for translating research into new therapeutics will be essential for maintaining innovation and new drug development by biotech companies.
• Learning Tolerance while Fighting Ignorance
  - Cell 138(3):416-420 (2009)
  Research on microbe-host interactions focuses principally on pathogens, yet our immune system must deal with the huge number of beneficial commensal bacteria in our gut. It is becoming clear that the host immune system must reach a delicate balance between destroying dangerous bacterial pathogens while preserving the beneficial gut microbiota.
• Developmental Biology Meets Ecology
  - Cell 138(3):421-422 (2009)
  
• MicroRNAs and Parallel Stem Cell Lives
  - Cell 138(3):423-424 (2009)
  A new study by Shimono et al. (2009) demonstrates that certain microRNAs that regulate the self-renewal factor BMI1 are downregulated in purified populations of normal mammary epithelial stem cells and breast tumor-initiating cells. These findings have important implications for the regulation of self-renewal and differentiation by microRNAs and suggest new ways of targeting cancer stem cells.
• Alpha Cells Beget Beta Cells
  - Cell 138(3):424-426 (2009)
  Understanding the origins of insulin-producing beta cells of the pancreas could lead to new treatments for diabetes. Collombat et al. (2009) now show that in response to injury, a population of pancreatic progenitor cells can give rise to glucagon-expressing alpha cells that then transdifferentiate into beta cells.
• Data Harvesting from Fields of Spindles
  - Cell 138(3):426-428 (2009)
  The mitotic spindle is essential for chromosome segregation and must be large enough to accommodate all of the chromatin in the dividing cell. In this issue, Dinarina et al. (2009) grow "fields" of spindles on coverslips to investigate the relationship between chromatin and spindle size as well as intrinsic mechanisms of spindle assembly.
• DNA Makes RNA Makes Innate Immunity
  - Cell 138(3):428-430 (2009)
  Microbial DNA in the cytosol induces production of interferon-β (IFN-β) and an innate immune response. Chiu et al. (2009) now implicate cytosolic DNA-dependent RNA polymerase III as the DNA sensor linking DNA release by pathogenic bacteria and viruses in the host cell cytosol to IFN-β production and innate immunity.
• Time's up: Bursting out of Transcription
  - Cell 138(3):430-432 (2009)
  Many inducible genes are transcribed in bursts. In this issue, Degenhardt et al. (2009) report computational models that predict and validate patterns of stochastic gene expression.
• Human Telomerase Caught in the Act
  - Cell 138(3):432-434 (2009)
  Based on prior work, it was expected that telomerase would preferentially elongate the shortest telomeres in a cell, extending the telomeric G-rich strand through a process that is coupled to the synthesis of the complementary strand. Contrary to this view, Zhao et al. (2009) now show that telomerase in human cancer cells extends most telomeres during every S phase and that complementary strand synthesis does not immediately follow telomerase action.
• Chromatin Architecture and the Generation of Antigen Receptor Diversity
  - Cell 138(3):435-448 (2009)
  The adaptive immune system generates a specific response to a vast spectrum of antigens. This remarkable property is achieved by lymphocytes that each express single and unique antigen receptors. During lymphocyte development, antigen receptor coding elements are assembled from widely dispersed gene segments. The assembly of antigen receptors is controlled at multiple levels, including epigenetic marking, nuclear location, and chromatin topology. Here, we review recently uncovered mechanisms that underpin long-range genomic interactions and the generation of antigen receptor diversity.
• The Ectopic Expression of Pax4 in the Mouse Pancreas Converts Progenitor Cells into α and Subsequently β Cells
  - Cell 138(3):449-462 (2009)
  We have previously reported that the loss of Arx and/or Pax4 gene activity leads to a shift in the fate of the different endocrine cell subtypes in the mouse pancreas, without affecting the total endocrine cell numbers. Here, we conditionally and ectopically express Pax4 using different cell-specific promoters and demonstrate that Pax4 forces endocrine precursor cells, as well as mature α cells, to adopt a β cell destiny. This results in a glucagon deficiency that provokes a compensatory and continuous glucagon+ cell neogenesis requiring the re-expression of the proendocrine gene Ngn3. However, the newly formed α cells fail to correct the hypoglucagonemia since they subsequently acquire a β cell phenotype upon Pax4 ectopic expression. Notably, this cycle of neogenesis and redifferentiation caused by ectopic expression of Pax4 in α cells is capable of restoring a functional β cell mass and curing diabetes in animals that have been chemically depleted of β cells.
• Telomere Extension Occurs at Most Chromosome Ends and Is Uncoupled from Fill-In in Human Cancer Cells
  - Cell 138(3):463-475 (2009)
  Telomeres are thought to be maintained by the preferential recruitment of telomerase to the shortest telomeres. The extension of the G-rich telomeric strand by telomerase is also believed to be coordinated with the complementary synthesis of the C strand by the conventional replication machinery. However, we show that under telomere length-maintenance conditions in cancer cells, human telomerase extends most chromosome ends during each S phase and is not preferentially recruited to the shortest telomeres. Telomerase rapidly extends the G-rich strand following telomere replication but fill-in of the C strand is delayed into late S phase. This late C-strand fill-in is not executed by conventional Okazaki fragment synthesis but by a mechanism using a series of small incremental steps. These findings highlight differences between telomerase actions during steady state versus nonequilibrium conditions and reveal steps in the human telomere maintenance pathway that may provi! de additional targets for the development of anti-telomerase therapeutics.
• Identification of a Physiologically Relevant Endogenous Ligand for PPARα in Liver
  - Cell 138(3):476-488 (2009)
  The nuclear receptor PPARα is activated by drugs to treat human disorders of lipid metabolism. Its endogenous ligand is unknown. PPARα-dependent gene expression is impaired with inactivation of fatty acid synthase (FAS), suggesting that FAS is involved in generation of a PPARα ligand. Here we demonstrate the FAS-dependent presence of a phospholipid bound to PPARα isolated from mouse liver. Binding was increased under conditions that induce FAS activity and displaced by systemic injection of a PPARα agonist. Mass spectrometry identified the species as 1-palmitoyl-2-oleoyl-sn-glycerol-3-phosphocholine (16:0/18:1-GPC). Knockdown of Cept1, required for phosphatidylcholine synthesis, suppressed PPARα-dependent gene expression. Interaction of 16:0/18:1-GPC with the PPARα ligand-binding domain and coactivator peptide motifs was comparable to PPARα agonists, but interactions with PPARδ were weak and none were detected with PPARγ. Portal vein infusion of 16:0/18:1-GPC! induced PPARα-dependent gene expression and decreased hepatic steatosis. These data suggest that 16:0/18:1-GPC is a physiologically relevant endogenous PPARα ligand.
• Population-Level Transcription Cycles Derive from Stochastic Timing of Single-Cell Transcription
  - Cell 138(3):489-501 (2009)
  Eukaryotic transcription is a dynamic process relying on a large number of proteins. By measuring the cycling expression of the pyruvate dehydrogenase kinase 4 gene in human cells, we constructed a detailed stochastic model for single-gene transcription at the molecular level using realistic kinetics for diffusion and protein complex dynamics. We observed that gene induction caused an approximate 60 min periodicity of several transcription related processes: first, the covalent histone modifications and presence of many regulatory proteins at the transcription start site; second, RNA polymerase II activity; third, chromatin loop formation; and fourth, mRNA accumulation. Our model can predict the precise timing of single-gene activity leading to transcriptional cycling on the cell population level when we take into account the sequential and irreversible multistep nature of transcriptional initiation. We propose that the cyclic nature of population gene expression is pr! imarily based on the intrinsic periodicity of the transcription process itself.
• Chromatin Shapes the Mitotic Spindle
  - Cell 138(3):502-513 (2009)
  In animal and plant cells, mitotic chromatin locally generates microtubules that self-organize into a mitotic spindle, and its dimensions and bipolar symmetry are essential for accurate chromosome segregation. By immobilizing microscopic chromatin-coated beads on slide surfaces using a microprinting technique, we have examined the effect of chromatin on the dimensions and symmetry of spindles in Xenopus laevis cytoplasmic extracts. While circular spots with diameters around 14–18 μm trigger bipolar spindle formation, larger spots generate an incorrect number of poles. We also examined lines of chromatin with various dimensions. Their length determined the number of poles that formed, with a 6 × 18 μm rectangular patch generating normal spindle morphology. Around longer lines, multiple poles formed and the structures were disorganized. While lines thinner than 10 μm generated symmetric structures, thicker lines induced the formation of asymmetric structures where ! all microtubules are on the same side of the line. Our results show that chromatin defines spindle shape and orientation. For a video summary of this article, see the PaperFlick file available with the online Supplemental Data.
• The Selectivity of Receptor Tyrosine Kinase Signaling Is Controlled by a Secondary SH2 Domain Binding Site
  - Cell 138(3):514-524 (2009)
  SH2 domain-mediated interactions represent a crucial step in transmembrane signaling by receptor tyrosine kinases. SH2 domains recognize phosphotyrosine (pY) in the context of particular sequence motifs in receptor phosphorylation sites. However, the modest binding affinity of SH2 domains to pY containing peptides may not account for and likely represents an oversimplified mechanism for regulation of selectivity of signaling pathways in living cells. Here we describe the crystal structure of the activated tyrosine kinase domain of FGFR1 in complex with a phospholipase Cγ fragment. The structural and biochemical data and experiments with cultured cells show that the selectivity of phospholipase Cγ binding and signaling via activated FGFR1 are determined by interactions between a secondary binding site on an SH2 domain and a region in FGFR1 kinase domain in a phosphorylation independent manner. These experiments reveal a mechanism for how SH2 domain selectivity is regu! lated in vivo to mediate a specific cellular process.
• Sites of Regulated Phosphorylation that Control K-Cl Cotransporter Activity
  - Cell 138(3):525-536 (2009)
  Modulation of intracellular chloride concentration ([Cl−]i) plays a fundamental role in cell volume regulation and neuronal response to GABA. Cl− exit via K-Cl cotransporters (KCCs) is a major determinant of [Cl−]I; however, mechanisms governing KCC activities are poorly understood. We identified two sites in KCC3 that are rapidly dephosphorylated in hypotonic conditions in cultured cells and human red blood cells in parallel with increased transport activity. Alanine substitutions at these sites result in constitutively active cotransport. These sites are highly phosphorylated in plasma membrane KCC3 in isotonic conditions, suggesting that dephosphorylation increases KCC3's intrinsic transport activity. Reduction of WNK1 expression via RNA interference reduces phosphorylation at these sites. Homologous sites are phosphorylated in all human KCCs. KCC2 is partially phosphorylated in neonatal mouse brain and dephosphorylated in parallel with KCC2 activation. These ! findings provide insight into regulation of [Cl−]i and have implications for control of cell volume and neuronal function.
• Myosin VI Undergoes Cargo-Mediated Dimerization
  - Cell 138(3):537-548 (2009)
  Myosin VI is the only known molecular motor that moves toward the minus ends of actin filaments; thus, it plays unique roles in diverse cellular processes. The processive walking of myosin VI on actin filaments requires dimerization of the motor, but the protein can also function as a nonprocessive monomer. The molecular mechanism governing the monomer-dimer conversion is not clear. We report the high-resolution NMR structure of the cargo-free myosin VI cargo-binding domain (CBD) and show that it is a stable monomer in solution. The myosin VI CBD binds to a fragment of the clathrin-coated vesicle adaptor Dab2 with a high affinity, and the X-ray structure of the myosin VI CBD in complex with Dab2 reveals that the motor undergoes a cargo-binding-mediated dimerization. The cargo-binding-induced dimerization may represent a general paradigm for the regulation of processivity for myosin VI as well as other myosins, including myosin VII and myosin X.
• A Class of Dynamin-like GTPases Involved in the Generation of the Tubular ER Network
  - Cell 138(3):549-561 (2009)
  The endoplasmic reticulum (ER) consists of tubules that are shaped by the reticulons and DP1/Yop1p, but how the tubules form an interconnected network is unknown. Here, we show that mammalian atlastins, which are dynamin-like, integral membrane GTPases, interact with the tubule-shaping proteins. The atlastins localize to the tubular ER and are required for proper network formation in vivo and in vitro. Depletion of the atlastins or overexpression of dominant-negative forms inhibits tubule interconnections. The Sey1p GTPase in S. cerevisiae is likely a functional ortholog of the atlastins; it shares the same signature motifs and membrane topology and interacts genetically and physically with the tubule-shaping proteins. Cells simultaneously lacking Sey1p and a tubule-shaping protein have ER morphology defects. These results indicate that formation of the tubular ER network depends on conserved dynamin-like GTPases. Since atlastin-1 mutations cause a common form of hered! itary spastic paraplegia, we suggest ER-shaping defects as a neuropathogenic mechanism.
• IRE1α Kinase Activation Modes Control Alternate Endoribonuclease Outputs to Determine Divergent Cell Fates
  - Cell 138(3):562-575 (2009)
  During endoplasmic reticulum (ER) stress, homeostatic signaling through the unfolded protein response (UPR) augments ER protein-folding capacity. If homeostasis is not restored, the UPR triggers apoptosis. We found that the ER transmembrane kinase/endoribonuclease (RNase) IRE1α is a key component of this apoptotic switch. ER stress induces IRE1α kinase autophosphorylation, activating the RNase to splice XBP1 mRNA and produce the homeostatic transcription factor XBP1s. Under ER stress—or forced autophosphorylation—IRE1α's RNase also causes endonucleolytic decay of many ER-localized mRNAs, including those encoding chaperones, as early events culminating in apoptosis. Using chemical genetics, we show that kinase inhibitors bypass autophosphorylation to activate the RNase by an alternate mode that enforces XBP1 splicing and averts mRNA decay and apoptosis. Alternate RNase activation by kinase-inhibited IRE1α can be reconstituted in vitro. We propose that divergent ! cell fates during ER stress hinge on a balance between IRE1α RNase outputs that can be tilted with kinase inhibitors to favor survival.
• RNA Polymerase III Detects Cytosolic DNA and Induces Type I Interferons through the RIG-I Pathway
  Chiu YH Macmillan JB Chen ZJ - Cell 138(3):576-591 (2009)
  Type I interferons (IFNs) are important for antiviral and autoimmune responses. Retinoic acid-induced gene I (RIG-I) and mitochondrial antiviral signaling (MAVS) proteins mediate IFN production in response to cytosolic double-stranded RNA or single-stranded RNA containing 5′-triphosphate (5′-ppp). Cytosolic B form double-stranded DNA, such as poly(dA-dT)•poly(dA-dT) [poly(dA-dT)], can also induce IFN-β, but the underlying mechanism is unknown. Here, we show that the cytosolic poly(dA-dT) DNA is converted into 5′-ppp RNA to induce IFN-β through the RIG-I pathway. Biochemical purification led to the identification of DNA-dependent RNA polymerase III (Pol-III) as the enzyme responsible for synthesizing 5′-ppp RNA from the poly(dA-dT) template. Inhibition of RNA Pol-III prevents IFN-β induction by transfection of DNA or infection with DNA viruses. Furthermore, Pol-III inhibition abrogates IFN-β induction by the intracellular bacterium Legionella pneumophila a! nd promotes the bacterial growth. These results suggest that RNA Pol-III is a cytosolic DNA sensor involved in innate immune responses.
• Downregulation of miRNA-200c Links Breast Cancer Stem Cells with Normal Stem Cells
  - Cell 138(3):592-603 (2009)
  Human breast tumors contain a breast cancer stem cell (BCSC) population with properties reminiscent of normal stem cells. We found 37 microRNAs that were differentially expressed between human BCSCs and nontumorigenic cancer cells. Three clusters, miR-200c-141, miR-200b-200a-429, and miR-183-96-182 were downregulated in human BCSCs, normal human and murine mammary stem/progenitor cells, and embryonal carcinoma cells. Expression of BMI1, a known regulator of stem cell self-renewal, was modulated by miR-200c. miR-200c inhibited the clonal expansion of breast cancer cells and suppressed the growth of embryonal carcinoma cells in vitro. Most importantly, miR-200c strongly suppressed the ability of normal mammary stem cells to form mammary ducts and tumor formation driven by human BCSCs in vivo. The coordinated downregulation of three microRNA clusters and the similar functional regulation of clonal expansion by miR-200c provide a molecular link that connects BCSCs with nor! mal stem cells.
• Mechanism for Activation of the EGF Receptor Catalytic Domain by the Juxtamembrane Segment
  - Cell 138(3):604 (2009)
  
• SnapShot: Effector and Memory T Cell Differentiation
  - Cell 138(3):606.e1-606.e2 (2009)