Hot off the presses! Aug 19 Cell

The Aug 19 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 146(4):489, 491 (2011)
  
• Remote Control: The Brain and Beyond
  - Cell 146(4):493, 495 (2011)
  Once the preserve of sci-fi movies and Internet conspiracy theorists, remote manipulation of brain activity is becoming an increasingly useful tool in our efforts to understand how neural circuits control behavior. In this issue's Select, we investigate recent work using optogenetics and related techniques to probe sleep, memory, addiction, and aggression and find a potential therapy for diabetes along the way.
• Transcription Factor Loading: Please Take My Place!
  - Cell 146(4):497-499 (2011)
  Interactions of transcription factors with chromatin are highly dynamic. Now Voss et al. (2011) demonstrate that two transcription factors with identical DNA-binding specificities do not compete for occupancy at a given DNA element, but instead, one factor can even facilitate the binding of another. This assisted loading probably involves chromatin-remodeling machines.
• Travel Notes from the Equatorial Circle
  - Cell 146(4):499-501 (2011)
  Accurate chromosome segregation during mitosis and meiosis is essential for cell viability. Two papers in this issue of Cell ([Kitajima et al., 2011] and [Magidson et al., 2011]) describe chromosome movements during cell division with unprecedented accuracy, revealing previously unrecognized features of chromosome spindle alignment and paving the way to quantitative phenotypic and mechanistic analyses of chromosome alignment during prometaphase.
• Elongated Membrane Zones Boost Interactions of Diffusing Proteins
  - Cell 146(4):501-503 (2011)
  Biological membranes are two dimensional, making the discovery of quasi-one-dimensional diffusion of membrane proteins puzzling. Jaqaman et al. (2011) now show that actomyosin and tubulin interact to establish long, thin diffusion corridors, thereby increasing the effective concentration of select membrane proteins to promote their interactions and modulate signaling.
• Meeting the (N-Terminal) End with Acetylation
  - Cell 146(4):503-505 (2011)
  Cell-fate decisions are tightly linked to cellular energy status. In this issue, Yi et al. (2011) introduce a mechanism by which Bcl-xL lowers the threshold for apoptosis by suppressing acetyl-CoA production, which, in turn, suppresses the N-alpha-acetylation important for activation of the proapoptotic protease caspase-2.
• Organizing Graduate Life Sciences Education around Nodes and Connections
  - Cell 146(4):506-509 (2011)
  Biomedical education is currently faced with a number of significant challenges, including the explosion of information and the need to train researchers who can work across traditional disciplinary boundaries. We propose a new integrated model for graduate education in the life sciences that addresses these issues.
• Mechanisms for the Inheritance of Chromatin States
  - Cell 146(4):510-518 (2011)
  Studies in eukaryotes ranging from yeast to mammals indicate that specific chromatin structures can be inherited following DNA replication via mechanisms acting in cis. Both the initial establishment of such chromatin structures and their inheritance require sequence-dependent specificity factors and changes in histone posttranslational modifications. Here I propose models for the maintenance of epigenetic information in which DNA silencers or nascent RNA scaffolds act as sensors that work cooperatively with parentally inherited histones to re-establish chromatin states following DNA replication.
• Reconstitution of the Mouse Germ Cell Specification Pathway in Culture by Pluripotent Stem Cells
  - Cell 146(4):519-532 (2011)
  The generation of properly functioning gametes in vitro requires reconstitution of the multistepped pathway of germ cell development. We demonstrate here the generation of primordial germ cell-like cells (PGCLCs) in mice with robust capacity for spermatogenesis. PGCLCs were generated from embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) through epiblast-like cells (EpiLCs), a cellular state highly similar to pregastrulating epiblasts but distinct from epiblast stem cells (EpiSCs). Reflecting epiblast development, EpiLC induction from ESCs/iPSCs is a progressive process, and EpiLCs highly competent for the PGC fate are a transient entity. The global transcription profiles, epigenetic reprogramming, and cellular dynamics during PGCLC induction from EpiLCs meticulously capture those associated with PGC specification from the epiblasts. Furthermore, we identify Integrin-β3 and SSEA1 as markers that allow the isolation of PGCLCs with spermatogenic cap! acity from tumorigenic undifferentiated cells. Our findings provide a paradigm for the first step of in vitro gametogenesis.
• Linking RNA Polymerase Backtracking to Genome Instability in E. coli
  - Cell 146(4):533-543 (2011)
  Frequent codirectional collisions between the replisome and RNA polymerase (RNAP) are inevitable because the rate of replication is much faster than that of transcription. Here we show that, in E. coli, the outcome of such collisions depends on the productive state of transcription elongation complexes (ECs). Codirectional collisions with backtracked (arrested) ECs lead to DNA double-strand breaks (DSBs), whereas head-on collisions do not. A mechanistic model is proposed to explain backtracking-mediated DSBs. We further show that bacteria employ various strategies to avoid replisome collisions with backtracked RNAP, the most general of which is translation that prevents RNAP backtracking. If translation is abrogated, DSBs are suppressed by elongation factors that either prevent backtracking or reactivate backtracked ECs. Finally, termination factors also contribute to genomic stability by removing arrested ECs. Our results establish RNAP backtracking as the intrinsic h! azard to chromosomal integrity and implicate active ribosomes and other anti-backtracking mechanisms in genome maintenance.
• Dynamic Exchange at Regulatory Elements during Chromatin Remodeling Underlies Assisted Loading Mechanism
  - Cell 146(4):544-554 (2011)
  The glucocorticoid receptor (GR), like other eukaryotic transcription factors, regulates gene expression by interacting with chromatinized DNA response elements. Photobleaching experiments in living cells indicate that receptors transiently interact with DNA on the time scale of seconds and predict that the response elements may be sparsely occupied on average. Here, we show that the binding of one receptor at the glucocorticoid response element (GRE) does not reduce the steady-state binding of another receptor variant to the same GRE. Mathematical simulations reproduce this noncompetitive state using short GR/GRE residency times and relatively long times between DNA binding events. At many genomic sites where GR binding causes increased chromatin accessibility, concurrent steady-state binding levels for the variant receptor are actually increased, a phenomenon termed assisted loading. Temporally sparse transcription factor-DNA interactions induce local chromatin reorg! anization, resulting in transient access for binding of secondary regulatory factors. PaperClip To listen to this audio, enable JavaScript on your browser. However, you can download and play the audio by clicking on the icon below Download this Audio (2855 K)
• The Spatial Arrangement of Chromosomes during Prometaphase Facilitates Spindle Assembly
  - Cell 146(4):555-567 (2011)
  Error-free chromosome segregation requires stable attachment of sister kinetochores to the opposite spindle poles (amphitelic attachment). Exactly how amphitelic attachments are achieved during spindle assembly remains elusive. We employed photoactivatable GFP and high-resolution live-cell confocal microscopy to visualize complete 3D movements of individual kinetochores throughout mitosis in nontransformed human cells. Combined with electron microscopy, molecular perturbations, and immunofluorescence analyses, this approach reveals unexpected details of chromosome behavior. Our data demonstrate that unstable lateral interactions between kinetochores and microtubules dominate during early prometaphase. These transient interactions lead to the reproducible arrangement of chromosomes in an equatorial ring on the surface of the nascent spindle. A computational model predicts that this toroidal distribution of chromosomes exposes kinetochores to a high density of microtubul! es which facilitates subsequent formation of amphitelic attachments. Thus, spindle formation involves a previously overlooked stage of chromosome prepositioning which promotes formation of amphitelic attachments.
• Complete Kinetochore Tracking Reveals Error-Prone Homologous Chromosome Biorientation in Mammalian Oocytes
  - Cell 146(4):568-581 (2011)
  Chromosomes must establish stable biorientation prior to anaphase to achieve faithful segregation during cell division. The detailed process by which chromosomes are bioriented and how biorientation is coordinated with spindle assembly and chromosome congression remain unclear. Here, we provide complete 3D kinetochore-tracking datasets throughout cell division by high-resolution imaging of meiosis I in live mouse oocytes. We show that in acentrosomal oocytes, chromosome congression forms an intermediate chromosome configuration, the prometaphase belt, which precedes biorientation. Chromosomes then invade the elongating spindle center to form the metaphase plate and start biorienting. Close to 90% of all chromosomes undergo one or more rounds of error correction of their kinetochore-microtubule attachments before achieving correct biorientation. This process depends on Aurora kinase activity. Our analysis reveals the error-prone nature of homologous chromosome biorienta! tion, providing a possible explanation for the high incidence of aneuploid eggs observed in mammals, including humans.
• Rapid Microtubule Self-Assembly Kinetics
  - Cell 146(4):582-592 (2011)
  Microtubule assembly is vital for many fundamental cellular processes. Current models for microtubule assembly kinetics assume that the subunit dissociation rate from a microtubule tip is independent of free subunit concentration. Total-Internal-Reflection-Fluorescence (TIRF) microscopy experiments and data from a laser tweezers assay that measures in vitro microtubule assembly with nanometer resolution, provides evidence that the subunit dissociation rate from a microtubule tip increases as the free subunit concentration increases. These data are consistent with a two-dimensional model for microtubule assembly, and are explained by a shift in microtubule tip structure from a relatively blunt shape at low free concentrations to relatively tapered at high free concentrations. We find that because both the association and the dissociation rates increase at higher free subunit concentrations, the kinetics of microtubule assembly are an order-of-magnitude higher than curre! ntly estimated in the literature.
• Cytoskeletal Control of CD36 Diffusion Promotes Its Receptor and Signaling Function
  - Cell 146(4):593-606 (2011)
  The mechanisms that govern receptor coalescence into functional clusters—often a critical step in their stimulation by ligand—are poorly understood. We used single-molecule tracking to investigate the dynamics of CD36, a clustering-responsive receptor that mediates oxidized LDL uptake by macrophages. We found that CD36 motion in the membrane was spatially structured by the cortical cytoskeleton. A subpopulation of receptors diffused within linear confinement regions whose unique geometry simultaneously facilitated freedom of movement along one axis while increasing the effective receptor density. Co-confinement within troughs enhanced the probability of collisions between unligated receptors and promoted their clustering. Cytoskeleton perturbations that inhibited diffusion in linear confinement regions reduced receptor clustering in the absence of ligand and, following ligand addition, suppressed CD36-mediated signaling and internalization. These observations demon! strate a role for the cytoskeleton in controlling signal transduction by structuring receptor diffusion within membrane regions that increase their collision frequency.
• Metabolic Regulation of Protein N-Alpha-Acetylation by Bcl-xL Promotes Cell Survival
  - Cell 146(4):607-620 (2011)
  Previous experiments suggest a connection between the N-alpha-acetylation of proteins and sensitivity of cells to apoptotic signals. Here, we describe a biochemical assay to detect the acetylation status of proteins and demonstrate that protein N-alpha-acetylation is regulated by the availability of acetyl-CoA. Because the antiapoptotic protein Bcl-xL is known to influence mitochondrial metabolism, we reasoned that Bcl-xL may provide a link between protein N-alpha-acetylation and apoptosis. Indeed, Bcl-xL overexpression leads to a reduction in levels of acetyl-CoA and N-alpha-acetylated proteins in the cell. This effect is independent of Bax and Bak, the known binding partners of Bcl-xL. Increasing cellular levels of acetyl-CoA by addition of acetate or citrate restores protein N-alpha-acetylation in Bcl-xL-expressing cells and confers sensitivity to apoptotic stimuli. We propose that acetyl-CoA serves as a signaling molecule that couples apoptotic sensitivity to metab! olism by regulating protein N-alpha-acetylation.
• Structural Linkage between Ligand Discrimination and Receptor Activation by Type I Interferons
  - Cell 146(4):621-632 (2011)
  Type I Interferons (IFNs) are important cytokines for innate immunity against viruses and cancer. Sixteen human type I IFN variants signal through the same cell-surface receptors, IFNAR1 and IFNAR2, yet they can evoke markedly different physiological effects. The crystal structures of two human type I IFN ternary signaling complexes containing IFNα2 and IFNω reveal recognition modes and heterotrimeric architectures that are unique among the cytokine receptor superfamily but conserved between different type I IFNs. Receptor-ligand cross-reactivity is enabled by conserved receptor-ligand "anchor points" interspersed among ligand-specific interactions that "tune" the relative IFN-binding affinities, in an apparent extracellular "ligand proofreading" mechanism that modulates biological activity. Functional differences between IFNs are linked to their respective receptor recognition chemistries, in concert with a ligand-induced conformational change in IFNAR1,! that collectively control signal initiation and complex stability, ultimately regulating differential STAT phosphorylation profiles, receptor internalization rates, and downstream gene expression patterns. PaperFlick To view the video inline, enable JavaScript on your browser. However, you can download and view the video by clicking on the icon below Download this Video (19002 K)
• Stochastic State Transitions Give Rise to Phenotypic Equilibrium in Populations of Cancer Cells
  - Cell 146(4):633-644 (2011)
  Cancer cells within individual tumors often exist in distinct phenotypic states that differ in functional attributes. While cancer cell populations typically display distinctive equilibria in the proportion of cells in various states, the mechanisms by which this occurs are poorly understood. Here, we study the dynamics of phenotypic proportions in human breast cancer cell lines. We show that subpopulations of cells purified for a given phenotypic state return towards equilibrium proportions over time. These observations can be explained by a Markov model in which cells transition stochastically between states. A prediction of this model is that, given certain conditions, any subpopulation of cells will return to equilibrium phenotypic proportions over time. A second prediction is that breast cancer stem-like cells arise de novo from non-stem-like cells. These findings contribute to our understanding of cancer heterogeneity and reveal how stochasticity in single-cell b! ehaviors promotes phenotypic equilibrium in populations of cancer cells.
• The Human Mitochondrial Transcriptome
  - Cell 146(4):645-658 (2011)
  The human mitochondrial genome comprises a distinct genetic system transcribed as precursor polycistronic transcripts that are subsequently cleaved to generate individual mRNAs, tRNAs, and rRNAs. Here, we provide a comprehensive analysis of the human mitochondrial transcriptome across multiple cell lines and tissues. Using directional deep sequencing and parallel analysis of RNA ends, we demonstrate wide variation in mitochondrial transcript abundance and precisely resolve transcript processing and maturation events. We identify previously undescribed transcripts, including small RNAs, and observe the enrichment of several nuclear RNAs in mitochondria. Using high-throughput in vivo DNaseI footprinting, we establish the global profile of DNA-binding protein occupancy across the mitochondrial genome at single-nucleotide resolution, revealing regulatory features at mitochondrial transcription initiation sites and functional insights into disease-associated variants. This ! integrated analysis of the mitochondrial transcriptome reveals unexpected complexity in the regulation, expression, and processing of mitochondrial RNA and provides a resource for future studies of mitochondrial function (accessed at http://mitochondria.matticklab.com).
• Generation of Isogenic Pluripotent Stem Cells Differing Exclusively at Two Early Onset Parkinson Point Mutations
  - Cell 146(4):659 (2011)
  
• SnapShot: Dendritic Cells
  - Cell 146(4):660-660.e2 (2011)