Cell

Critical Role of Amyloid-like Oligomers of Drosophila Orb2 in the Persistence of Memory.

Publication Date: 2012 Jan 24 PMID: 22284910
Authors: Majumdar, A. - Cesario, W. C. - White-Grindley, E. - Jiang, H. - Ren, F. - Khan, M. R. - Li, L. - Choi, E. M. - Kannan, K. - Guo, F. - Unruh, J. - Slaughter, B. - Si, K.
Journal: Cell

A long-standing question in the study of long-term memory is how a memory trace persists for years when the proteins that initiated the process turn over and disappear within days. Previously, we postulated that self-sustaining amyloidogenic oligomers of cytoplasmic polyadenylation element-binding protein (CPEB) provide a mechanism for the maintenance of activity-dependent synaptic changes and, thus, the persistence of memory. Here, we found that the Drosophila CPEB Orb2 forms amyloid-like oligomers, and oligomers are enriched in the synaptic membrane fraction. Of the two protein isoforms of Orb2, the amyloid-like oligomer formation is dependent on the Orb2A form. A point mutation in the prion-like domain of Orb2A, which reduced amyloid-like oligomerization of Orb2, did not interfere with learning or memory persisting up to 24 hr. However the mutant flies failed to stabilize memory beyond 48 hr. These results support the idea that amyloid-like oligomers of neuronal CPEB are critical for the persistence of long-term memory.

post to: CiteULike

Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome.

Publication Date: 2012 Jan 18 PMID: 22265598
Authors: Sexton, T. - Yaffe, E. - Kenigsberg, E. - Bantignies, F. - Leblanc, B. - Hoichman, M. - Parrinello, H. - Tanay, A. - Cavalli, G.
Journal: Cell

Chromosomes are the physical realization of genetic information and thus form the basis for its readout and propagation. Here we present a high-resolution chromosomal contact map derived from a modified genome-wide chromosome conformation capture approach applied to Drosophila embryonic nuclei. The data show that the entire genome is linearly partitioned into well-demarcated physical domains that overlap extensively with active and repressive epigenetic marks. Chromosomal contacts are hierarchically organized between domains. Global modeling of contact density and clustering of domains show that inactive domains are condensed and confined to their chromosomal territories, whereas active domains reach out of the territory to form remote intra- and interchromosomal contacts. Moreover, we systematically identify specific long-range intrachromosomal contacts between Polycomb-repressed domains. Together, these observations allow for quantitative prediction of the Drosophila chromosomal contact map, laying the foundation for detailed studies of chromosome structure and function in a genetically tractable system.

post to: CiteULike

SnapShot: Bioactive Lysophospholipids.

Publication Date: 2012 Jan 20 PMID: 22265422
Authors: Moolenaar, W. H. - Hla, T.
Journal: Cell

post to: CiteULike

Computational modeling of pancreatic cancer reveals kinetics of metastasis suggesting optimum treatment strategies.

Publication Date: 2012 Jan 20 PMID: 22265421
Authors: Haeno, H. - Gonen, M. - Davis, M. B. - Herman, J. M. - Iacobuzio-Donahue, C. A. - Michor, F.
Journal: Cell

Pancreatic cancer is a leading cause of cancer-related death, largely due to metastatic dissemination. We investigated pancreatic cancer progression by utilizing a mathematical framework of metastasis formation together with comprehensive data of 228 patients, 101 of whom had autopsies. We found that pancreatic cancer growth is initially exponential. After estimating the rates of pancreatic cancer growth and dissemination, we determined that patients likely harbor metastases at diagnosis and predicted the number and size distribution of metastases as well as patient survival. These findings were validated in an independent database. Finally, we analyzed the effects of different treatment modalities, finding that therapies that efficiently reduce the growth rate of cells earlier in the course of treatment appear to be superior to upfront tumor resection. These predictions can be validated in the clinic. Our interdisciplinary approach provides insights into the dynamics of pancreatic cancer metastasis and identifies optimum therapeutic interventions.

post to: CiteULike

EMT and Dissemination Precede Pancreatic Tumor Formation.

Publication Date: 2012 Jan 20 PMID: 22265420
Authors: Rhim, A. D. - Mirek, E. T. - Aiello, N. M. - Maitra, A. - Bailey, J. M. - McAllister, F. - Reichert, M. - Beatty, G. L. - Rustgi, A. K. - Vonderheide, R. H. - Leach, S. D. - Stanger, B. Z.
Journal: Cell

Metastasis is the leading cause of cancer-associated death but has been difficult to study because it involves a series of rare, stochastic events. To capture these events, we developed a sensitive method to tag and track pancreatic epithelial cells in a mouse model of pancreatic cancer. Tagged cells invaded and entered the bloodstream unexpectedly early, before frank malignancy could be detected by rigorous histologic analysis; this behavior was widely associated with epithelial-to-mesenchymal transition (EMT). Circulating pancreatic cells maintained a mesenchymal phenotype, exhibited stem cell properties, and seeded the liver. EMT and invasiveness were most abundant at inflammatory foci, and induction of pancreatitis increased the number of circulating pancreatic cells. Conversely, treatment with the immunosuppressive agent dexamethasone abolished dissemination. These results provide insight into the earliest events of cellular invasion in situ and suggest that inflammation enhances cancer progression in part by facilitating EMT and entry into the circulation.

post to: CiteULike

HSF-1 Regulators DDL-1/2 Link Insulin-like Signaling to Heat-Shock Responses and Modulation of Longevity.

Publication Date: 2012 Jan 20 PMID: 22265419
Authors: Chiang, W. C. - Ching, T. T. - Lee, H. C. - Mousigian, C. - Hsu, A. L.
Journal: Cell

Extended longevity is often correlated with increased resistance against various stressors. Insulin/IGF-1-like signaling (IIS) is known to have a conserved role in aging and cellular mechanisms against stress. In C. elegans, genetic studies suggest that heat-shock transcription factor HSF-1 is required for IIS to modulate longevity. Here, we report that the activity of HSF-1 is regulated by IIS. This regulation occurs at an early step of HSF-1 activation via two HSF-1 regulators, DDL-1 and DDL-2. Inhibition of DDL-1/2 increases longevity and thermotolerance in an hsf-1-dependent manner. Furthermore, biochemical analyses suggest that DDL-1/2 negatively regulate HSF-1 activity by forming a protein complex with HSF-1. The formation of this complex (DHIC) is affected by the phosphorylation status of DDL-1. Both the formation of DHIC and the phosphorylation of DDL-1 are controlled by IIS. Our findings point to DDL-1/2 as a link between IIS and the HSF-1 pathway.

post to: CiteULike

Local zones of endoplasmic reticulum complexity confine cargo in neuronal dendrites.

Publication Date: 2012 Jan 20 PMID: 22265418
Authors: Cui-Wang, T. - Hanus, C. - Cui, T. - Helton, T. - Bourne, J. - Watson, D. - Harris, K. M. - Ehlers, M. D.
Journal: Cell

Following synthesis, integral membrane proteins dwell in the endoplasmic reticulum (ER) for variable periods that are typically rate limiting for plasma membrane delivery. In neurons, the ER extends for hundreds of microns as an anastomosing network throughout highly branched dendrites. However, little is known about the mobility, spatial scales, or dynamic regulation of cargo in the dendritic ER. Here, we show that membrane proteins, including AMPA-type glutamate receptors, rapidly diffuse within the continuous network of dendritic ER but are confined by increased ER complexity at dendritic branch points and near dendritic spines. The spatial range of receptor mobility is rapidly restricted by type I mGluR signaling through a mechanism involving protein kinase C (PKC) and the ER protein CLIMP63. Moreover, local zones of ER complexity compartmentalize ER export and correspond to sites of new dendritic branches. Thus, local control of ER complexity spatially scales secretory trafficking within elaborate dendritic arbors.

post to: CiteULike

Mutation of a U2 snRNA Gene Causes Global Disruption of Alternative Splicing and Neurodegeneration.

Publication Date: 2012 Jan 20 PMID: 22265417
Authors: Jia, Y. - Mu, J. C. - Ackerman, S. L.
Journal: Cell

Although uridine-rich small nuclear RNAs (U-snRNAs) are essential for pre-mRNA splicing, little is known regarding their function in the regulation of alternative splicing or of the biological consequences of their dysfunction in mammals. Here, we demonstrate that mutation of Rnu2-8, one of the mouse multicopy U2 snRNA genes, causes ataxia and neurodegeneration. Coincident with the observed pathology, the level of mutant U2 RNAs was highest in the cerebellum and increased after granule neuron maturation. Furthermore, neuron loss was strongly dependent on the dosage of mutant and wild-type snRNA genes. Comprehensive transcriptome analysis identified a group of alternative splicing events, including the splicing of small introns, which were disrupted in the mutant cerebellum. Our results suggest that the expression of mammalian U2 snRNA genes, previously presumed to be ubiquitous, is spatially and temporally regulated, and dysfunction of a single U2 snRNA causes neuron degeneration through distortion of pre-mRNA splicing.

post to: CiteULike

Gene regulatory logic for reading the sonic hedgehog signaling gradient in the vertebrate neural tube.

Publication Date: 2012 Jan 20 PMID: 22265416
Authors: Balaskas, N. - Ribeiro, A. - Panovska, J. - Dessaud, E. - Sasai, N. - Page, K. M. - Briscoe, J. - Ribes, V.
Journal: Cell

Secreted signals, known as morphogens, provide the positional information that organizes gene expression and cellular differentiation in many developing tissues. In the vertebrate neural tube, Sonic Hedgehog (Shh) acts as a morphogen to control the pattern of neuronal subtype specification. Using an in vivo reporter of Shh signaling, mouse genetics, and systems modeling, we show that a spatially and temporally changing gradient of Shh signaling is interpreted by the regulatory logic of a downstream transcriptional network. The design of the network, which links three transcription factors to Shh signaling, is responsible for differential spatial and temporal gene expression. In addition, the network renders cells insensitive to fluctuations in signaling and confers hysteresis-memory of the signal. Our findings reveal that morphogen interpretation is an emergent property of the architecture of a transcriptional network that provides robustness and reliability to tissue patterning.

post to: CiteULike

Mutant p53 Disrupts Mammary Tissue Architecture via the Mevalonate Pathway.

Publication Date: 2012 Jan 20 PMID: 22265415
Authors: Freed-Pastor, W. A. - Mizuno, H. - Zhao, X. - Langerod, A. - Moon, S. H. - Rodriguez-Barrueco, R. - Barsotti, A. - Chicas, A. - Li, W. - Polotskaia, A. - Bissell, M. J. - Osborne, T. F. - Tian, B. - Lowe, S. W. - Silva, J. M. - Borresen-Dale, A. L. - Levine, A. J. - Bargonetti, J. - Prives, C.
Journal: Cell

p53 is a frequent target for mutation in human tumors, and mutant p53 proteins can actively contribute to tumorigenesis. We employed a three-dimensional culture model in which nonmalignant breast epithelial cells form spheroids reminiscent of acinar structures found in vivo, whereas breast cancer cells display highly disorganized morphology. We found that mutant p53 depletion is sufficient to phenotypically revert breast cancer cells to a more acinar-like morphology. Genome-wide expression analysis identified the mevalonate pathway as significantly upregulated by mutant p53. Statins and sterol biosynthesis intermediates reveal that this pathway is both necessary and sufficient for the phenotypic effects of mutant p53 on breast tissue architecture. Mutant p53 associates with sterol gene promoters at least partly via SREBP transcription factors. Finally, p53 mutation correlates with highly expressed sterol biosynthesis genes in human breast tumors. These findings implicate the mevalonate pathway as a therapeutic target for tumors bearing mutations in p53.

post to: CiteULike

The Mitochondrial Phosphatase PGAM5 Functions at the Convergence Point of Multiple Necrotic Death Pathways.

Publication Date: 2012 Jan 20 PMID: 22265414
Authors: Wang, Z. - Jiang, H. - Chen, S. - Du, F. - Wang, X.
Journal: Cell

The programmed necrosis induced by TNF-alpha requires the activities of the receptor-interacting serine-threonine kinases RIP1 and RIP3 and their interaction with the mixed lineage kinase domain-like protein MLKL. We report the identification of RIP1- and RIP3-containing protein complexes that form specifically in response to necrosis induction. One component of these complexes is the mitochondrial protein phosphatase PGAM5, which presents as two splice variants, PGAM5L (long form) and PGAM5S (short form). Knockdown of either form attenuated necrosis induced by TNF-alpha as well as reactive oxygen species (ROS) and calcium ionophore, whereas knockdown of RIP3 and MLKL blocked only TNF-alpha-mediated necrosis. Upon necrosis induction, PGAM5S recruited the mitochondrial fission factor Drp1 and activated its GTPase activity by dephosphorylating the serine 637 site of Drp1. Drp1 activation caused mitochondrial fragmentation, an early and obligatory step for necrosis execution. These data defined PGAM5 as the convergent point for multiple necrosis pathways.

post to: CiteULike

Mixed Lineage Kinase Domain-like Protein Mediates Necrosis Signaling Downstream of RIP3 Kinase.

Publication Date: 2012 Jan 20 PMID: 22265413
Authors: Sun, L. - Wang, H. - Wang, Z. - He, S. - Chen, S. - Liao, D. - Wang, L. - Yan, J. - Liu, W. - Lei, X. - Wang, X.
Journal: Cell

The receptor-interacting serine-threonine kinase 3 (RIP3) is a key signaling molecule in the programmed necrosis (necroptosis) pathway. This pathway plays important roles in a variety of physiological and pathological conditions, including development, tissue damage response, and antiviral immunity. Here, we report the identification of a small molecule called (E)-N-(4-(N-(3-methoxypyrazin-2-yl)sulfamoyl)phenyl)-3-(5-nitrothiophene-2 -yl)acrylamide-hereafter referred to as necrosulfonamide-that specifically blocks necrosis downstream of RIP3 activation. An affinity probe derived from necrosulfonamide and coimmunoprecipitation using anti-RIP3 antibodies both identified the mixed lineage kinase domain-like protein (MLKL) as the interacting target. MLKL was phosphorylated by RIP3 at the threonine 357 and serine 358 residues, and these phosphorylation events were critical for necrosis. Treating cells with necrosulfonamide or knocking down MLKL expression arrested necrosis at a specific step at which RIP3 formed discrete punctae in cells. These findings implicate MLKL as a key mediator of necrosis signaling downstream of the kinase RIP3.

post to: CiteULike

Endoplasmic Reticulum PI(3)P Lipid Binding Targets Malaria Proteins to the Host Cell.

Publication Date: 2012 Jan 20 PMID: 22265412
Authors: Bhattacharjee, S. - Stahelin, R. V. - Speicher, K. D. - Speicher, D. W. - Haldar, K.
Journal: Cell

Hundreds of effector proteins of the human malaria parasite Plasmodium falciparum constitute a "secretome" carrying a host-targeting (HT) signal, which predicts their export from the intracellular pathogen into the surrounding erythrocyte. Cleavage of the HT signal by a parasite endoplasmic reticulum (ER) protease, plasmepsin V, is the proposed export mechanism. Here, we show that the HT signal facilitates export by recognition of the lipid phosphatidylinositol-3-phosphate (PI(3)P) in the ER, prior to and independent of protease action. Secretome HT signals, including those of major virulence determinants, bind PI(3)P with nanomolar affinity and amino acid specificities displayed by HT-mediated export. PI(3)P-enriched regions are detected within the parasite's ER and colocalize with endogenous HT signal on ER precursors, which also display high-affinity binding to PI(3)P. A related pathogenic oomycete's HT signal export is dependent on PI(3)P binding, without cleavage by plasmepsin V. Thus, PI(3)P in the ER functions in mechanisms of secretion and pathogenesis.

post to: CiteULike

Coordinated Ciliary Beating Requires Odf2-Mediated Polarization of Basal Bodies via Basal Feet.

Publication Date: 2012 Jan 20 PMID: 22265411
Authors: Kunimoto, K. - Yamazaki, Y. - Nishida, T. - Shinohara, K. - Ishikawa, H. - Hasegawa, T. - Okanoue, T. - Hamada, H. - Noda, T. - Tamura, A. - Tsukita, S. - Tsukita, S.
Journal: Cell

Coordinated beating of cilia in the trachea generates a directional flow of mucus required to clear the airways. Each cilium originates from a barrel-shaped basal body, from the side of which protrudes a structure known as the basal foot. We generated mice in which exons 6 and 7 of Odf2, encoding a basal body and centrosome-associated protein Odf2/cenexin, are disrupted. Although Odf2(DeltaEx6,7/DeltaEx6,7) mice form cilia, ciliary beating is uncoordinated, and the mice display a coughing/sneezing phenotype. Whereas residual expression of the C-terminal region of Odf2 in these mice is sufficient for ciliogenesis, the resulting basal bodies lack basal feet. Loss of basal feet in ciliated epithelia disrupted the polarized organization of apical microtubule lattice without affecting planar cell polarity. The requirement for Odf2 in basal foot formation, therefore, reveals a crucial role of this structure in the polarized alignment of basal bodies and coordinated ciliary beating.

post to: CiteULike

Membrane Tension Maintains Cell Polarity by Confining Signals to the Leading Edge during Neutrophil Migration.

Publication Date: 2012 Jan 20 PMID: 22265410
Authors: Houk, A. R. - Jilkine, A. - Mejean, C. O. - Boltyanskiy, R. - Dufresne, E. R. - Angenent, S. B. - Altschuler, S. J. - Wu, L. F. - Weiner, O. D.
Journal: Cell

Little is known about how neutrophils and other cells establish a single zone of actin assembly during migration. A widespread assumption is that the leading edge prevents formation of additional fronts by generating long-range diffusible inhibitors or by sequestering essential polarity components. We use morphological perturbations, cell-severing experiments, and computational simulations to show that diffusion-based mechanisms are not sufficient for long-range inhibition by the pseudopod. Instead, plasma membrane tension could serve as a long-range inhibitor in neutrophils. We find that membrane tension doubles during leading-edge protrusion, and increasing tension is sufficient for long-range inhibition of actin assembly and Rac activation. Furthermore, reducing membrane tension causes uniform actin assembly. We suggest that tension, rather than diffusible molecules generated or sequestered at the leading edge, is the dominant source of long-range inhibition that constrains the spread of the existing front and prevents the formation of secondary fronts. VIDEO ABSTRACT:

post to: CiteULike

Requirements for Efficient Correction of DeltaF508 CFTR Revealed by Analyses of Evolved Sequences.

Publication Date: 2012 Jan 20 PMID: 22265409
Authors: Mendoza, J. L. - Schmidt, A. - Li, Q. - Nuvaga, E. - Barrett, T. - Bridges, R. J. - Feranchak, A. P. - Brautigam, C. A. - Thomas, P. J.
Journal: Cell

Misfolding of DeltaF508 cystic fibrosis (CF) transmembrane conductance regulator (CFTR) underlies pathology in most CF patients. F508 resides in the first nucleotide-binding domain (NBD1) of CFTR near a predicted interface with the fourth intracellular loop (ICL4). Efforts to identify small molecules that restore function by correcting the folding defect have revealed an apparent efficacy ceiling. To understand the mechanistic basis of this obstacle, positions statistically coupled to 508, in evolved sequences, were identified and assessed for their impact on both NBD1 and CFTR folding. The results indicate that both NBD1 folding and interaction with ICL4 are altered by the DeltaF508 mutation and that correction of either individual process is only partially effective. By contrast, combination of mutations that counteract both defects restores DeltaF508 maturation and function to wild-type levels. These results provide a mechanistic rationale for the limited efficacy of extant corrector compounds and suggest approaches for identifying compounds that correct both defective steps.

post to: CiteULike

Correction of Both NBD1 Energetics and Domain Interface Is Required to Restore DeltaF508 CFTR Folding and Function.

Publication Date: 2012 Jan 20 PMID: 22265408
Authors: Rabeh, W. M. - Bossard, F. - Xu, H. - Okiyoneda, T. - Bagdany, M. - Mulvihill, C. M. - Du, K. - di Bernardo, S. - Liu, Y. - Konermann, L. - Roldan, A. - Lukacs, G. L.
Journal: Cell

The folding and misfolding mechanism of multidomain proteins remains poorly understood. Although thermodynamic instability of the first nucleotide-binding domain (NBD1) of DeltaF508 CFTR (cystic fibrosis transmembrane conductance regulator) partly accounts for the mutant channel degradation in the endoplasmic reticulum and is considered as a drug target in cystic fibrosis, the link between NBD1 and CFTR misfolding remains unclear. Here, we show that DeltaF508 destabilizes NBD1 both thermodynamically and kinetically, but correction of either defect alone is insufficient to restore DeltaF508 CFTR biogenesis. Instead, both DeltaF508-NBD1 energetic and the NBD1-MSD2 (membrane-spanning domain 2) interface stabilization are required for wild-type-like folding, processing, and transport function, suggesting a synergistic role of NBD1 energetics and topology in CFTR-coupled domain assembly. Identification of distinct structural deficiencies may explain the limited success of DeltaF508 CFTR corrector molecules and suggests structure-based combination corrector therapies. These results may serve as a framework for understanding the mechanism of interface mutation in multidomain membrane proteins.

post to: CiteULike

A Recently Evolved Transcriptional Network Controls Biofilm Development in Candida albicans.

Publication Date: 2012 Jan 20 PMID: 22265407
Authors: Nobile, C. J. - Fox, E. P. - Nett, J. E. - Sorrells, T. R. - Mitrovich, Q. M. - Hernday, A. D. - Tuch, B. B. - Andes, D. R. - Johnson, A. D.
Journal: Cell

A biofilm is an organized, resilient group of microbes in which individual cells acquire properties, such as drug resistance, that are distinct from those observed in suspension cultures. Here, we describe and analyze the transcriptional network controlling biofilm formation in the pathogenic yeast Candida albicans, whose biofilms are a major source of medical device-associated infections. We have combined genetic screens, genome-wide approaches, and two in vivo animal models to describe a master circuit controlling biofilm formation, composed of six transcription regulators that form a tightly woven network with approximately 1,000 target genes. Evolutionary analysis indicates that the biofilm network has rapidly evolved: genes in the biofilm circuit are significantly weighted toward genes that arose relatively recently with ancient genes being underrepresented. This circuit provides a framework for understanding many aspects of biofilm formation by C. albicans in a mammalian host. It also provides insights into how complex cell behaviors can arise from the evolution of transcription circuits.

post to: CiteULike

A subpopulation of adult skeletal muscle stem cells retains all template DNA strands after cell division.

Publication Date: 2012 Jan 20 PMID: 22265406
Authors: Rocheteau, P. - Gayraud-Morel, B. - Siegl-Cachedenier, I. - Blasco, M. A. - Tajbakhsh, S.
Journal: Cell

Satellite cells are adult skeletal muscle stem cells that are quiescent and constitute a poorly defined heterogeneous population. Using transgenic Tg:Pax7-nGFP mice, we show that Pax7-nGFP(Hi) cells are less primed for commitment and have a lower metabolic status and delayed first mitosis compared to Pax7-nGFP(Lo) cells. Pax7-nGFP(Hi) can give rise to Pax7-nGFP(Lo) cells after serial transplantations. Proliferating Pax7-nGFP(Hi) cells exhibit lower metabolic activity, and the majority performs asymmetric DNA segregation during cell division, wherein daughter cells retaining template DNA strands express stem cell markers. Using chromosome orientation-fluorescence in situ hybridization, we demonstrate that all chromatids segregate asymmetrically, whereas Pax7-nGFP(Lo) cells perform random DNA segregation. Therefore, quiescent Pax7-nGFP(Hi) cells represent a reversible dormant stem cell state, and during muscle regeneration, Pax7-nGFP(Hi) cells generate distinct daughter cell fates by asymmetrically segregating template DNA strands to the stem cell. These findings provide major insights into the biology of stem cells that segregate DNA asymmetrically.

post to: CiteULike

Forkhead Transcription Factors Establish Origin Timing and Long-Range Clustering in S. cerevisiae.

Publication Date: 2012 Jan 20 PMID: 22265405
Authors: Knott, S. R. - Peace, J. M. - Ostrow, A. Z. - Gan, Y. - Rex, A. E. - Viggiani, C. J. - Tavare, S. - Aparicio, O. M.
Journal: Cell

The replication of eukaryotic chromosomes is organized temporally and spatially within the nucleus through epigenetic regulation of replication origin function. The characteristic initiation timing of specific origins is thought to reflect their chromatin environment or sub-nuclear positioning, however the mechanism remains obscure. Here we show that the yeast Forkhead transcription factors, Fkh1 and Fkh2, are global determinants of replication origin timing. Forkhead regulation of origin timing is independent of local levels or changes of transcription. Instead, we show that Fkh1 and Fkh2 are required for the clustering of early origins and their association with the key initiation factor Cdc45 in G1 phase, suggesting that Fkh1 and Fkh2 selectively recruit origins to emergent replication factories. Fkh1 and Fkh2 bind Fkh-activated origins, and interact physically with ORC, providing a plausible mechanism to cluster origins. These findings add a new dimension to our understanding of the epigenetic basis for differential origin regulation and its connection to chromosomal domain organization.

post to: CiteULike

Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation.

Publication Date: 2012 Jan 20 PMID: 22265404
Authors: Li, G. - Ruan, X. - Auerbach, R. K. - Sandhu, K. S. - Zheng, M. - Wang, P. - Poh, H. M. - Goh, Y. - Lim, J. - Zhang, J. - Sim, H. S. - Peh, S. Q. - Mulawadi, F. H. - Ong, C. T. - Orlov, Y. L. - Hong, S. - Zhang, Z. - Landt, S. - Raha, D. - Euskirchen, G. - Wei, C. L. - Ge, W. - Wang, H. - Davis, C. - Fisher-Aylor, K. I. - Mortazavi, A. - Gerstein, M. - Gingeras, T. - Wold, B. - Sun, Y. - Fullwood, M. J. - Cheung, E. - Liu, E. - Sung, W. K. - Snyder, M. - Ruan, Y.
Journal: Cell

Higher-order chromosomal organization for transcription regulation is poorly understood in eukaryotes. Using genome-wide Chromatin Interaction Analysis with Paired-End-Tag sequencing (ChIA-PET), we mapped long-range chromatin interactions associated with RNA polymerase II in human cells and uncovered widespread promoter-centered intragenic, extragenic, and intergenic interactions. These interactions further aggregated into higher-order clusters, wherein proximal and distal genes were engaged through promoter-promoter interactions. Most genes with promoter-promoter interactions were active and transcribed cooperatively, and some interacting promoters could influence each other implying combinatorial complexity of transcriptional controls. Comparative analyses of different cell lines showed that cell-specific chromatin interactions could provide structural frameworks for cell-specific transcription, and suggested significant enrichment of enhancer-promoter interactions for cell-specific functions. Furthermore, genetically-identified disease-associated noncoding elements were found to be spatially engaged with corresponding genes through long-range interactions. Overall, our study provides insights into transcription regulation by three-dimensional chromatin interactions for both housekeeping and cell-specific genes in human cells.

post to: CiteULike

Foxa1 and foxa2 are essential for sexual dimorphism in liver cancer.

Publication Date: 2012 Jan 20 PMID: 22265403
Authors: Li, Z. - Tuteja, G. - Schug, J. - Kaestner, K. H.
Journal: Cell

Hepatocellular carcinoma (HCC) is sexually dimorphic in both rodents and humans, with significantly higher incidence in males, an effect that is dependent on sex hormones. The molecular mechanisms by which estrogens prevent and androgens promote liver cancer remain unclear. Here, we discover that sexually dimorphic HCC is completely reversed in Foxa1- and Foxa2-deficient mice after diethylnitrosamine-induced hepatocarcinogenesis. Coregulation of target genes by Foxa1/a2 and either the estrogen receptor (ERalpha) or the androgen receptor (AR) was increased during hepatocarcinogenesis in normal female or male mice, respectively, but was lost in Foxa1/2-deficient mice. Thus, both estrogen-dependent resistance to and androgen-mediated facilitation of HCC depend on Foxa1/2. Strikingly, single nucleotide polymorphisms at FOXA2 binding sites reduce binding of both FOXA2 and ERalpha to their targets in human liver and correlate with HCC development in women. Thus, Foxa factors and their targets are central for the sexual dimorphism of HCC.

post to: CiteULike

Genome Sequencing of Pediatric Medulloblastoma Links Catastrophic DNA Rearrangements with TP53 Mutations.

Publication Date: 2012 Jan 20 PMID: 22265402
Authors: Rausch, T. - Jones, D. T. - Zapatka, M. - Stutz, A. M. - Zichner, T. - Weischenfeldt, J. - Jager, N. - Remke, M. - Shih, D. - Northcott, P. A. - Pfaff, E. - Tica, J. - Wang, Q. - Massimi, L. - Witt, H. - Bender, S. - Pleier, S. - Cin, H. - Hawkins, C. - Beck, C. - von Deimling, A. - Hans, V. - Brors, B. - Eils, R. - Scheurlen, W. - Blake, J. - Benes, V. - Kulozik, A. E. - Witt, O. - Martin, D. - Zhang, C. - Porat, R. - Merino, D. M. - Wasserman, J. - Jabado, N. - Fontebasso, A. - Bullinger, L. - Rucker, F. G. - Dohner, K. - Dohner, H. - Koster, J. - Molenaar, J. J. - Versteeg, R. - Kool, M. - Tabori, U. - Malkin, D. - Korshunov, A. - Taylor, M. D. - Lichter, P. - Pfister, S. M. - Korbel, J. O.
Journal: Cell

Genomic rearrangements are thought to occur progressively during tumor development. Recent findings, however, suggest an alternative mechanism, involving massive chromosome rearrangements in a one-step catastrophic event termed chromothripsis. We report the whole-genome sequencing-based analysis of a Sonic-Hedgehog medulloblastoma (SHH-MB) brain tumor from a patient with a germline TP53 mutation (Li-Fraumeni syndrome), uncovering massive, complex chromosome rearrangements. Integrating TP53 status with microarray and deep sequencing-based DNA rearrangement data in additional patients reveals a striking association between TP53 mutation and chromothripsis in SHH-MBs. Analysis of additional tumor entities substantiates a link between TP53 mutation and chromothripsis, and indicates a context-specific role for p53 in catastrophic DNA rearrangements. Among these, we observed a strong association between somatic TP53 mutations and chromothripsis in acute myeloid leukemia. These findings connect p53 status and chromothripsis in specific tumor types, providing a genetic basis for understanding particularly aggressive subtypes of cancer.

post to: CiteULike

Aging, rejuvenation, and epigenetic reprogramming: resetting the aging clock.

Publication Date: 2012 Jan 20 PMID: 22265401
Authors: Rando, T. A. - Chang, H. Y.
Journal: Cell

The underlying cause of aging remains one of the central mysteries of biology. Recent studies in several different systems suggest that not only may the rate of aging be modified by environmental and genetic factors, but also that the aging clock can be reversed, restoring characteristics of youthfulness to aged cells and tissues. This Review focuses on the emerging biology of rejuvenation through the lens of epigenetic reprogramming. By defining youthfulness and senescence as epigenetic states, a framework for asking new questions about the aging process emerges.

post to: CiteULike

Lineage tracing.

Publication Date: 2012 Jan 20 PMID: 22265400
Authors: Kretzschmar, K. - Watt, F. M.
Journal: Cell

Lineage tracing is the identification of all progeny of a single cell. Although its origins date back to developmental biology of invertebrates in the 19(th) century, lineage tracing is now an essential tool for studying stem cell properties in adult mammalian tissues. Lineage tracing provides a powerful means of understanding tissue development, homeostasis, and disease, especially when it is combined with experimental manipulation of signals regulating cell-fate decisions. Recently, the combination of inducible recombinases, multicolor reporter constructs, and live-cell imaging has provided unprecedented insights into stem cell biology. Here we discuss the different experimental strategies currently available for lineage tracing, their associated caveats, and new opportunities to integrate lineage tracing with the monitoring of intracellular signaling pathways.

post to: CiteULike

Chromothripsis and human disease: piecing together the shattering process.

Publication Date: 2012 Jan 20 PMID: 22265399
Authors: Maher, C. A. - Wilson, R. K.
Journal: Cell

The unprecedented resolution of high-throughput genomics has enabled the recent discovery of a phenomenon by which specific regions of the genome are shattered and then stitched together via a single devastating event, referred to as chromothripsis. Potential mechanisms governing this process are now emerging, with implications for our understanding of the role of genomic rearrangements in development and disease.

post to: CiteULike

Connecting threads: epigenetics and metabolism.

Publication Date: 2012 Jan 20 PMID: 22265398
Authors: Katada, S. - Imhof, A. - Sassone-Corsi, P.
Journal: Cell

Chromatin-modifying enzymes have long been proposed to be the authors of an epigenetic language, but the origin and meaning of the messages they write in chromatin are still mysterious. Recent studies suggesting that the effects of diet can be passed on epigenetically to offspring add weight to the idea that histones act as metabolic sensors, converting changes in metabolism into stable patterns of gene expression. The challenge will now be to understand how localized fluctuations in levels of metabolites control chromatin modifiers in space and time, translating a dynamic metabolic state into a histone map.

post to: CiteULike

Understanding metastasis in pancreatic cancer: a call for new clinical approaches.

Publication Date: 2012 Jan 20 PMID: 22265397
Authors: Tuveson, D. A. - Neoptolemos, J. P.
Journal: Cell

Although metastasis is a major cause of morbidity and mortality in patients with pancreatic cancer, the requisite events are currently unknown. In this issue of Cell, Haeno et al. and Rhim et al. propose that metastasis occurs much earlier than previously anticipated, with clear implications for improving patient care.

post to: CiteULike

RIP3 Finds Partners in Crime.

Publication Date: 2012 Jan 20 PMID: 22265396
Authors: Chan, F. K. - Baehrecke, E. H.
Journal: Cell

Programmed necrosis has long been recognized as a crucial component of animal development; however, the signaling pathway beyond the protein kinases RIP1 and RIP3 remains largely unknown. Sun et al. and Wang et al. now identify critical factors downstream of RIP1 and RIP3 in programmed necrosis, extending our understanding of this form of cell death.

post to: CiteULike

Funding in 2012: "great recession" starts to bite.

Publication Date: 2012 Jan 20 PMID: 22265395
Authors: Macilwain, C.
Journal: Cell

Biomedical research budgets are frozen or falling in developed countries. Can expansion in developing nations continue as economic contagion spreads?

post to: CiteULike

Bursting with Exciting Biology.

Publication Date: 2012 Jan 20 PMID: 22265394
Authors: Emilie - Elena - Robert - Karen - Lara - Faby - Michaeleen - Niki - Kara, C. - Kara, L. - Rosy
Journal: Cell

post to: CiteULike

Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages.

Publication Date: 2012 Jan 20 PMID: 22244452
Authors: Schmidt, D. - Schwalie, P. C. - Wilson, M. D. - Ballester, B. - Goncalves, A. - Kutter, C. - Brown, G. D. - Marshall, A. - Flicek, P. - Odom, D. T.
Journal: Cell

CTCF-binding locations represent regulatory sequences that are highly constrained over the course of evolution. To gain insight into how these DNA elements are conserved and spread through the genome, we defined the full spectrum of CTCF-binding sites, including a 33/34-mer motif, and identified over five thousand highly conserved, robust, and tissue-independent CTCF-binding locations by comparing ChIP-seq data from six mammals. Our data indicate that activation of retroelements has produced species-specific expansions of CTCF binding in rodents, dogs, and opossum, which often functionally serve as chromatin and transcriptional insulators. We discovered fossilized repeat elements flanking deeply conserved CTCF-binding regions, indicating that similar retrotransposon expansions occurred hundreds of millions of years ago. Repeat-driven dispersal of CTCF binding is a fundamental, ancient, and still highly active mechanism of genome evolution in mammalian lineages. PAPERCLIP:

post to: CiteULike

Generation of chimeric rhesus monkeys.

Publication Date: 2012 Jan 20 PMID: 22225614
Authors: Tachibana, M. - Sparman, M. - Ramsey, C. - Ma, H. - Lee, H. S. - Penedo, M. C. - Mitalipov, S.
Journal: Cell

Totipotent cells in early embryos are progenitors of all stem cells and are capable of developing into a whole organism, including extraembryonic tissues such as placenta. Pluripotent cells in the inner cell mass (ICM) are the descendants of totipotent cells and can differentiate into any cell type of a body except extraembryonic tissues. The ability to contribute to chimeric animals upon reintroduction into host embryos is the key feature of murine totipotent and pluripotent cells. Here, we demonstrate that rhesus monkey embryonic stem cells (ESCs) and isolated ICMs fail to incorporate into host embryos and develop into chimeras. However, chimeric offspring were produced following aggregation of totipotent cells of the four-cell embryos. These results provide insights into the species-specific nature of primate embryos and suggest that a chimera assay using pluripotent cells may not be feasible.

post to: CiteULike

Chimeric primates: embryonic stem cells need not apply.

Publication Date: 2012 Jan 20 PMID: 22225613
Authors: Trounson, A. - Grieshammer, U.
Journal: Cell

In this issue, Tachibana et al. report the generation of the first chimeras from a nonhuman primate, the rhesus monkey. Unlike mice, rhesus chimeras fail to form when embryonic stem cells are injected into blastocysts. Instead, chimera formation is achieved by aggregation of several four-cell embryos.

post to: CiteULike

Glycine decarboxylase activity drives non-small cell lung cancer tumor-initiating cells and tumorigenesis.

Publication Date: 2012 Jan 20 PMID: 22225612
Authors: Zhang, W. C. - Shyh-Chang, N. - Yang, H. - Rai, A. - Umashankar, S. - Ma, S. - Soh, B. S. - Sun, L. L. - Tai, B. C. - Nga, M. E. - Bhakoo, K. K. - Jayapal, S. R. - Nichane, M. - Yu, Q. - Ahmed, D. A. - Tan, C. - Sing, W. P. - Tam, J. - Thirugananam, A. - Noghabi, M. S. - Huei Pang, Y. - Ang, H. S. - Robson, P. - Kaldis, P. - Soo, R. A. - Swarup, S. - Lim, E. H. - Lim, B.
Journal: Cell

Identification of the factors critical to the tumor-initiating cell (TIC) state may open new avenues in cancer therapy. Here we show that the metabolic enzyme glycine decarboxylase (GLDC) is critical for TICs in non-small cell lung cancer (NSCLC). TICs from primary NSCLC tumors express high levels of the oncogenic stem cell factor LIN28B and GLDC, which are both required for TIC growth and tumorigenesis. Overexpression of GLDC and other glycine/serine enzymes, but not catalytically inactive GLDC, promotes cellular transformation and tumorigenesis. We found that GLDC induces dramatic changes in glycolysis and glycine/serine metabolism, leading to changes in pyrimidine metabolism to regulate cancer cell proliferation. In the clinic, aberrant activation of GLDC correlates with poorer survival in lung cancer patients, and aberrant GLDC expression is observed in multiple cancer types. This link between glycine metabolism and tumorigenesis may provide novel targets for advancing anticancer therapy.

post to: CiteULike

RNA dynamics in aging bacterial spores.

Publication Date: 2012 Jan 20 PMID: 22209493
Authors: Segev, E. - Smith, Y. - Ben-Yehuda, S.
Journal: Cell

Upon starvation, the bacterium Bacillus subtilis enters the process of sporulation, lasting several hours and culminating in formation of a spore, the most resilient cell type known. We show that a few days following sporulation, the RNA profile of spores is highly dynamic. In aging spores incubated at high temperatures, RNA content is globally decreased by degradation over several days. This degradation might be a strategy utilized by the spore to facilitate its dormancy. However, spores kept at low temperature exhibit a different RNA profile with evidence supporting transcription. Further, we demonstrate that germination is affected by spore age, incubation temperature, and RNA state, implying that spores can acquire dissimilar characteristics at a time they are considered dormant. We propose that, in contrast to current thinking, entering dormancy lasts a few days, during which spores are affected by the environment and undergo corresponding molecular changes influencing their emergence from quiescence.

post to: CiteULike