Hot off the presses! Jul 10 Cell

The Jul 10 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(1):1, 3 (2009)
  
• Cell Biology Select
  - Cell 138(1):5, 7 (2009)
  From time immemorial, the process of aging has been a subject of fascination. Molecular understanding of the cellular determinants of life span has revealed that far from being an uncontrolled process of gradual breakdown, aging is regulated by specific cellular pathways. This Cell Biology Select highlights recent studies that examine the molecular consequences of aging and uncover regulatory mechanisms that may influence the pathways that modulate life span.
• Driving Biofuels from Field to Fuel Tank
  - Cell 138(1):9-12 (2009)
  Rising oil prices, fears of global warming, and instability in oil-producing countries have ignited the rush to produce biofuels from plants. The science is progressing rapidly, driven by favorable policies and generous financing, but many hurdles remain before cars and trucks run on "gasohol" or "grassoline."
• Teeing Up Transcription on CpG Islands
  - Cell 138(1):14-16 (2009)
  Eukaryotic cells use elaborate molecular mechanisms to rapidly activate signal-dependent gene expression. New work provides fresh insights into these mechanisms by demonstrating that CpG islands in promoters are nucleosome-destabilizing elements and can facilitate the establishment of an unusual poised transcriptional state ([Ramirez-Carrozzi et al., 2009] and [Hargreaves et al., 2009]).
• Disorder, Promiscuity, and Toxic Partnerships
  - Cell 138(1):16-18 (2009)
  Many genes are toxic when overexpressed, but general mechanisms for this toxicity have proven elusive. Vavouri et al. (2009) find that intrinsic protein disorder and promiscuous molecular interactions are strong determinants of dosage sensitivity, explaining in part the toxicity of dosage-sensitive oncogenes in mice and humans.
• Chromatin Places Metabolism Center Stage
  - Cell 138(1):18-20 (2009)
  Dynamic changes in histone and transcription factor acetylation modulate gene expression. A study in Science (Wellen et al., 2009) reports that changes in glucose metabolism alter the availability of acetyl-CoA, the essential cofactor for protein acetylation. These findings reveal a direct connection between central metabolism and mammalian gene expression.
• Breaking Up Just Got Easier to Do
  - Cell 138(1):20-22 (2009)
  The SLX4 protein functions as a platform for catalytic subunits of structure-specific endonucleases. Findings reported in Cell ([Fekairi et al., 2009] and [Svendsen et al., 2009]) and in Molecular Cell ([Andersen et al., 2009] and [Muñoz et al., 2009]) now identify the human SLX4 and show that in association with the SLX1 endonuclease it directs the symmetric cleavage and resolution of Holliday junctions.
• A Positive Spin on the Centromere
  - Cell 138(1):22-24 (2009)
  The properties of centromeric nucleosomes have been the subject of considerable debate and controversy. Furuyama and Henikoff (2009) now provide surprising evidence that centromeric nucleosomes wrap DNA in an orientation that is opposite to that of canonical nucleosomes.
• Getting to First Base in Proteasome Assembly
  - Cell 138(1):25-28 (2009)
  Assembly of complex structures such as the eukaryotic 26S proteasome requires intricate mechanisms that ensure precise subunit arrangements. Recent studies have shed light on the pathway for ordered assembly of the base of the 19S regulatory particle of the 26S proteasome by identifying new precursor complexes and four dedicated chaperones involved in its assembly.
• Redefining Chronic Viral Infection
  - Cell 138(1):30-50 (2009)
  Viruses that cause chronic infection constitute a stable but little-recognized part of our metagenome: our virome. Ongoing immune responses hold these chronic viruses at bay while avoiding immunopathologic damage to persistently infected tissues. The immunologic imprint generated by these responses to our virome defines the normal immune system. The resulting dynamic but metastable equilibrium between the virome and the host can be dangerous, benign, or even symbiotic. These concepts require that we reformulate how we assign etiologies for diseases, especially those with a chronic inflammatory component, as well as how we design and interpret genome-wide association studies, and how we vaccinate to limit or control our virome.
• WNT/TCF Signaling through LEF1 and HOXB9 Mediates Lung Adenocarcinoma Metastasis
  - Cell 138(1):51-62 (2009)
  Metastasis from lung adenocarcinoma can occur swiftly to multiple organs within months of diagnosis. The mechanisms that confer this rapid metastatic capacity to lung tumors are unknown. Activation of the canonical WNT/TCF pathway is identified here as a determinant of metastasis to brain and bone during lung adenocarcinoma progression. Gene expression signatures denoting WNT/TCF activation are associated with relapse to multiple organs in primary lung adenocarcinoma. Metastatic subpopulations isolated from independent lymph node-derived lung adenocarcinoma cell lines harbor a hyperactive WNT/TCF pathway. Reduction of TCF activity in these cells attenuates their ability to form brain and bone metastases in mice, independently of effects on tumor growth in the lungs. The WNT/TCF target genes HOXB9 and LEF1 are identified as mediators of chemotactic invasion and colony outgrowth. Thus, a distinct WNT/TCF signaling program through LEF1 and HOXB9 enhances the competence of! lung adenocarcinoma cells to colonize the bones and the brain.
• Mammalian BTBD12/SLX4 Assembles A Holliday Junction Resolvase and Is Required for DNA Repair
  - Cell 138(1):63-77 (2009)
  Structure-specific endonucleases mediate cleavage of DNA structures formed during repair of collapsed replication forks and double-strand breaks (DSBs). Here, we identify BTBD12 as the human ortholog of the budding yeast DNA repair factor Slx4p and D. melanogaster MUS312. Human SLX4 forms a multiprotein complex with the ERCC4(XPF)-ERCC1, MUS81-EME1, and SLX1 endonucleases and also associates with MSH2/MSH3 mismatch repair complex, telomere binding complex TERF2(TRF2)-TERF2IP(RAP1), the protein kinase PLK1 and the uncharacterized protein C20orf94. Depletion of SLX4 causes sensitivity to mitomycin C and camptothecin and reduces the efficiency of DSB repair in vivo. SLX4 complexes cleave 3′ flap, 5′ flap, and replication fork structures; yet unlike other endonucleases associated with SLX4, the SLX1-SLX4 module promotes symmetrical cleavage of static and migrating Holliday junctions (HJs), identifying SLX1-SLX4 as a HJ resolvase. Thus, SLX4 assembles a modular toolkit ! for repair of specific types of DNA lesions and is critical for cellular responses to replication fork failure.
• Human SLX4 Is a Holliday Junction Resolvase Subunit that Binds Multiple DNA Repair/Recombination Endonucleases
  - Cell 138(1):78-89 (2009)
  Structure-specific endonucleases resolve DNA secondary structures generated during DNA repair and recombination. The yeast 5′ flap endonuclease Slx1-Slx4 has received particular attention with the finding that Slx4 has Slx1-independent key functions in genome maintenance. Although Slx1 is a highly conserved protein in eukaryotes, no orthologs of Slx4 were reported other than in fungi. Here we report the identification of Slx4 orthologs in metazoa, including fly MUS312, essential for meiotic recombination, and human BTBD12, an ATM/ATR checkpoint kinase substrate. Human SLX1-SLX4 displays robust Holliday junction resolvase activity in addition to 5′ flap endonuclease activity. Depletion of SLX1 and SLX4 results in 53BP1 foci accumulation and H2AX phosphorylation as well as cellular hypersensitivity to MMS. Furthermore, we show that SLX4 binds the XPFERCC4 and MUS81 subunits of the XPF-ERCC1 and MUS81-EME1 endonucleases and is required for DNA interstrand crosslink re! pair. We propose that SLX4 acts as a docking platform for multiple structure-specific endonucleases.
• Mammalian Telomeres Resemble Fragile Sites and Require TRF1 for Efficient Replication
  - Cell 138(1):90-103 (2009)
  Telomeres protect chromosome ends through the interaction of telomeric repeats with shelterin, a protein complex that represses DNA damage signaling and DNA repair reactions. The telomeric repeats are maintained by telomerase, which solves the end replication problem. We report that the TTAGGG repeat arrays of mammalian telomeres pose a challenge to the DNA replication machinery, giving rise to replication-dependent defects that resemble those of aphidicolin-induced common fragile sites. Gene deletion experiments showed that efficient duplication of telomeres requires the shelterin component TRF1. Without TRF1, telomeres activate the ATR kinase in S phase and show a fragile-site phenotype in metaphase. Single-molecule analysis of replicating telomeres showed that TRF1 promotes efficient replication of TTAGGG repeats and prevents fork stalling. Two helicases implicated in the removal of G4 DNA structures, BLM and RTEL1, were required to repress the fragile-telomere phen! otype. These results identify a second telomere replication problem that is solved by the shelterin component TRF1.
• Centromeric Nucleosomes Induce Positive DNA Supercoils
  - Cell 138(1):104-113 (2009)
  Centromeres of higher eukaryotes are epigenetically maintained; however, the mechanism that underlies centromere inheritance is unknown. Centromere identity and inheritance require the assembly of nucleosomes containing the CenH3 histone variant in place of canonical H3. Although H3 nucleosomes wrap DNA in a left-handed manner and induce negative supercoils, we show here that CenH3 nucleosomes reconstituted from Drosophila histones induce positive supercoils. Furthermore, we show that CenH3 likewise induces positive supercoils in functional centromeres in vivo, using a budding yeast minichromosome system and temperature-sensitive mutations in kinetochore proteins. The right-handed wrapping of DNA around the histone core implied by positive supercoiling indicates that centromere nucleosomes are unlikely to be octameric and that the exposed surfaces holding the nucleosome together would be available for kinetochore protein recruitment. The mutual incompatibility of nucle! osomes with opposite topologies could explain how centromeres are efficiently maintained as unique loci on chromosomes.
• A Unifying Model for the Selective Regulation of Inducible Transcription by CpG Islands and Nucleosome Remodeling
  - Cell 138(1):114-128 (2009)
  We describe a broad mechanistic framework for the transcriptional induction of mammalian primary response genes by Toll-like receptors and other stimuli. One major class of primary response genes is characterized by CpG-island promoters, which facilitate promiscuous induction from constitutively active chromatin without a requirement for SWI/SNF nucleosome remodeling complexes. The low nucleosome occupancy at promoters in this class can be attributed to the assembly of CpG islands into unstable nucleosomes, which may lead to SWI/SNF independence. Another major class consists of non-CpG-island promoters that assemble into stable nucleosomes, resulting in SWI/SNF dependence and a requirement for transcription factors that promote selective nucleosome remodeling. Some stimuli, including serum and tumor necrosis factor-α, exhibit a strong bias toward activation of SWI/SNF-independent CpG-island genes. In contrast, interferon-β is strongly biased toward SWI/SNF-dependent ! non-CpG-island genes. By activating a diverse set of transcription factors, Toll-like receptors induce both classes and others for an optimal response to microbial pathogens.
• Control of Inducible Gene Expression by Signal-Dependent Transcriptional Elongation
  - Cell 138(1):129-145 (2009)
  Most inducible transcriptional programs consist of primary and secondary response genes (PRGs and SRGs) that differ in their kinetics of expression and in their requirements for new protein synthesis and chromatin remodeling. Here we show that many PRGs, in contrast to SRGs, have preassembled RNA polymerase II (Pol II) and positive histone modifications at their promoters in the basal state. Pol II at PRGs generates low levels of full-length unspliced transcripts but fails to make mature, protein-coding transcripts in the absence of stimulation. Induction of PRGs is controlled at the level of transcriptional elongation and mRNA processing, through the signal-dependent recruitment of P-TEFb. P-TEFb is in turn recruited by the bromodomain-containing protein Brd4, which detects H4K5/8/12Ac inducibly acquired at PRG promoters. Our findings suggest that the permissive structure of PRGs both stipulates their unique regulation in the basal state by corepressor complexes and e! nables their rapid induction in multiple cell types.
• CarD Is an Essential Regulator of rRNA Transcription Required for Mycobacterium tuberculosis Persistence
  - Cell 138(1):146-159 (2009)
  Mycobacterium tuberculosis is arguably the world's most successful infectious agent because of its ability to control its own cell growth within the host. Bacterial growth rate is closely coupled to rRNA transcription, which in E. coli is regulated through DksA and (p)ppGpp. The mechanisms of rRNA transcriptional control in mycobacteria, which lack DksA, are undefined. Here we identify CarD as an essential mycobacterial protein that controls rRNA transcription. Loss of CarD is lethal for mycobacteria in culture and during infection of mice. CarD depletion leads to sensitivity to killing by oxidative stress, starvation, and DNA damage, accompanied by failure to reduce rRNA transcription. CarD can functionally replace DksA for stringent control of rRNA transcription, even though CarD associates with a different site on RNA polymerase. These findings highlight a distinct molecular mechanism for regulating rRNA transcription in mycobacteria that is critical for M. tubercul! osis pathogenesis.
• A Systems-Level Analysis of Perfect Adaptation in Yeast Osmoregulation
  - Cell 138(1):160-171 (2009)
  Negative feedback can serve many different cellular functions, including noise reduction in transcriptional networks and the creation of circadian oscillations. However, only one special type of negative feedback ("integral feedback") ensures perfect adaptation, where steady-state output is independent of steady-state input. Here we quantitatively measure single-cell dynamics in the Saccharomyces cerevisiae hyperosmotic shock network, which regulates membrane turgor pressure. Importantly, we find that the nuclear enrichment of the MAP kinase Hog1 perfectly adapts to changes in external osmolarity, a feature robust to signaling fidelity and operating with very low noise. By monitoring multiple system quantities (e.g., cell volume, Hog1, glycerol) and using varied input waveforms (e.g., steps and ramps), we assess in a minimally invasive manner the network location of the mechanism responsible for perfect adaptation. We conclude that the system contains only one effe! ctive integrating mechanism, which requires Hog1 kinase activity and regulates glycerol synthesis but not leakage.
• Myelin Gene Regulatory Factor Is a Critical Transcriptional Regulator Required for CNS Myelination
  - Cell 138(1):172-185 (2009)
  The transcriptional control of CNS myelin gene expression is poorly understood. Here we identify gene model 98, which we have named myelin gene regulatory factor (MRF), as a transcriptional regulator required for CNS myelination. Within the CNS, MRF is specifically expressed by postmitotic oligodendrocytes. MRF is a nuclear protein containing an evolutionarily conserved DNA binding domain homologous to a yeast transcription factor. Knockdown of MRF in oligodendrocytes by RNA interference prevents expression of most CNS myelin genes; conversely, overexpression of MRF within cultured oligodendrocyte progenitors or the chick spinal cord promotes expression of myelin genes. In mice lacking MRF within the oligodendrocyte lineage, premyelinating oligodendrocytes are generated but display severe deficits in myelin gene expression and fail to myelinate. These mice display severe neurological abnormalities and die because of seizures during the third postnatal week. These findi! ngs establish MRF as a critical transcriptional regulator essential for oligodendrocyte maturation and CNS myelination.
• Evolution of Genetic Networks Underlying the Emergence of Thymopoiesis in Vertebrates
  - Cell 138(1):186-197 (2009)
  About 500 million years ago, a new type of adaptive immune defense emerged in basal jawed vertebrates, accompanied by morphological innovations, including the thymus. Did these evolutionary novelties arise de novo or from elaboration of ancient genetic networks? We reconstructed the genetic changes underlying thymopoiesis by comparative genome and expression analyses in chordates and basal vertebrates. The derived models of genetic networks were experimentally verified in bony fishes. Ancestral networks defining circumscribed regions of the pharyngeal epithelium of jawless vertebrates expanded in cartilaginous fishes to incorporate novel genes, notably those encoding chemokines. Correspondingly, novel networks evolved in lymphocytes of jawed vertebrates to control the expression of additional chemokine receptors. These complementary changes enabled unprecedented Delta/Notch signaling between pharyngeal epithelium and lymphoid cells that was exploited for specification ! to the T cell lineage. Our results provide a framework elucidating the evolution of key features of the adaptive immune system in jawed vertebrates.
• Intrinsic Protein Disorder and Interaction Promiscuity Are Widely Associated with Dosage Sensitivity
  - Cell 138(1):198-208 (2009)
  Why are genes harmful when they are overexpressed? By testing possible causes of overexpression phenotypes in yeast, we identify intrinsic protein disorder as an important determinant of dosage sensitivity. Disordered regions are prone to make promiscuous molecular interactions when their concentration is increased, and we demonstrate that this is the likely cause of pathology when genes are overexpressed. We validate our findings in two animals, Drosophila melanogaster and Caenorhabditis elegans. In mice and humans the same properties are strongly associated with dosage-sensitive oncogenes, such that mass-action-driven molecular interactions may be a frequent cause of cancer. Dosage-sensitive genes are tightly regulated at the transcriptional, RNA, and protein levels, which may serve to prevent harmful increases in protein concentration under physiological conditions. Mass-action-driven interaction promiscuity is a single theoretical framework that can be used to unde! rstand, predict, and possibly treat the effects of increased gene expression in evolution and disease.
• Hematopoietic Stem Cells Reversibly Switch from Dormancy to Self-Renewal during Homeostasis and Repair
  - Cell 138(1):209 (2009)
  
• SnapShot: Ca2+-Calcineurin-NFATSignaling
  - Cell 138(1):210-210.e1 (2009)