Early commitment and robust differentiation in colonic crypts
Tissue stem cells produce a constant flux of differentiated cells with distinct proportions. Here, we show that stem cells in colonic crypts differentiate early to form precisely 1:3 ratio of secretory to absorptive cells. This precision is surprising, as there are only eight stem cells making irreversible fate decisions, and so large stochastic effects of this small pool should have yielded much larger noise in cell proportions. We use single molecule FISH, lineage-tracing mice and simulations to identify the homeostatic mechanisms facilitating robust proportions. We find that Delta-Notch lateral inhibition operates in a ...
Source: Molecular Systems Biology - January 2, 2017 Category: Molecular Biology Authors: Toth, B., Ben-Moshe, S., Gavish, A., Barkai, N., Itzkovitz, S. Tags: Development & Differentiation, Quantitative Biology & Dynamical Systems, Stem Cells Articles Source Type: research
Subgenic Pol II interactomes identify region-specific transcription elongation regulators
Transcription, RNA processing, and chromatin-related factors all interact with RNA polymerase II (Pol II) to ensure proper timing and coordination of transcription and co-transcriptional processes. Many transcription elongation regulators must function simultaneously to coordinate these processes, yet few strategies exist to explore the complement of factors regulating specific stages of transcription. To this end, we developed a strategy to purify Pol II elongation complexes from subgenic regions of a single gene, namely the 5' and 3' regions, using sequences in the nascent RNA. Applying this strategy to Saccharomyces cer...
Source: Molecular Systems Biology - January 1, 2017 Category: Molecular Biology Authors: Harlen, K. M., Churchman, L. S. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Methods & Resources, Transcription Articles Source Type: research
Yeast GPCR signaling reflects the fraction of occupied receptors, not the number
According to receptor theory, the effect of a ligand depends on the amount of agonist–receptor complex. Therefore, changes in receptor abundance should have quantitative effects. However, the response to pheromone in Saccharomyces cerevisiae is robust (unaltered) to increases or reductions in the abundance of the G-protein-coupled receptor (GPCR), Ste2, responding instead to the fraction of occupied receptor. We found experimentally that this robustness originates during G-protein activation. We developed a complete mathematical model of this step, which suggested the ability to compute fractional occupancy depends o...
Source: Molecular Systems Biology - December 28, 2016 Category: Molecular Biology Authors: Bush, A., Vasen, G., Constantinou, A., Dunayevich, P., Patop, I. L., Blaustein, M., Colman-Lerner, A. Tags: Quantitative Biology & Dynamical Systems, Signal Transduction Articles Source Type: research
Model-guided combinatorial optimization of complex synthetic gene networks
Constructing gene circuits that satisfy quantitative performance criteria has been a long-standing challenge in synthetic biology. Here, we show a strategy for optimizing a complex three-gene circuit, a novel proportional miRNA biosensor, using predictive modeling to initiate a search in the phase space of sensor genetic composition. We generate a library of sensor circuits using diverse genetic building blocks in order to access favorable parameter combinations and uncover specific genetic compositions with greatly improved dynamic range. The combination of high-throughput screening data and the data obtained from detaile...
Source: Molecular Systems Biology - December 27, 2016 Category: Molecular Biology Authors: Schreiber, J., Arter, M., Lapique, N., Haefliger, B., Benenson, Y. Tags: Network Biology, Synthetic Biology & Biotechnology Articles Source Type: research
Frequency doubling in the cyanobacterial circadian clock
Organisms use circadian clocks to generate 24-h rhythms in gene expression. However, the clock can interact with other pathways to generate shorter period oscillations. It remains unclear how these different frequencies are generated. Here, we examine this problem by studying the coupling of the clock to the alternative sigma factor sigC in the cyanobacterium Synechococcus elongatus. Using single-cell microscopy, we find that psbAI, a key photosynthesis gene regulated by both sigC and the clock, is activated with two peaks of gene expression every circadian cycle under constant low light. This two-peak oscillation is depen...
Source: Molecular Systems Biology - December 21, 2016 Category: Molecular Biology Authors: Martins, B. M., Das, A. K., Antunes, L., Locke, J. C. Tags: Network Biology, Quantitative Biology & Dynamical Systems Articles Source Type: research
Proteomics reveals the effects of sustained weight loss on the human plasma proteome
Sustained weight loss is a preferred intervention in a wide range of metabolic conditions, but the effects on an individual's health state remain ill-defined. Here, we investigate the plasma proteomes of a cohort of 43 obese individuals that had undergone 8 weeks of 12% body weight loss followed by a year of weight maintenance. Using mass spectrometry-based plasma proteome profiling, we measured 1,294 plasma proteomes. Longitudinal monitoring of the cohort revealed individual-specific protein levels with wide-ranging effects of losing weight on the plasma proteome reflected in 93 significantly affected proteins. The a...
Source: Molecular Systems Biology - December 21, 2016 Category: Molecular Biology Authors: Geyer, P. E., Wewer Albrechtsen, N. J., Tyanova, S., Grassl, N., Iepsen, E. W., Lundgren, J., Madsbad, S., Holst, J. J., Torekov, S. S., Mann, M. Tags: Metabolism, Post-translational Modifications, Proteolysis & Proteomics, Systems Medicine Articles Source Type: research
Non-genetic diversity modulates population performance
Biological functions are typically performed by groups of cells that express predominantly the same genes, yet display a continuum of phenotypes. While it is known how one genotype can generate such non-genetic diversity, it remains unclear how different phenotypes contribute to the performance of biological function at the population level. We developed a microfluidic device to simultaneously measure the phenotype and chemotactic performance of tens of thousands of individual, freely swimming Escherichia coli as they climbed a gradient of attractant. We discovered that spatial structure spontaneously emerged from initiall...
Source: Molecular Systems Biology - December 18, 2016 Category: Molecular Biology Authors: Waite, A. J., Frankel, N. W., Dufour, Y. S., Johnston, J. F., Long, J., Emonet, T. Tags: Microbiology, Virology & Host Pathogen Interaction, Quantitative Biology & Dynamical Systems, Signal Transduction Articles Source Type: research
Diverse mechanisms of metaeffector activity in an intracellular bacterial pathogen, Legionella pneumophila
Pathogens deliver complex arsenals of translocated effector proteins to host cells during infection, but the extent to which these proteins are regulated once inside the eukaryotic cell remains poorly defined. Among all bacterial pathogens, Legionella pneumophila maintains the largest known set of translocated substrates, delivering over 300 proteins to the host cell via its Type IVB, Icm/Dot translocation system. Backed by a few notable examples of effector–effector regulation in L. pneumophila, we sought to define the extent of this phenomenon through a systematic analysis of effector–effector functional...
Source: Molecular Systems Biology - December 15, 2016 Category: Molecular Biology Authors: Urbanus, M. L., Quaile, A. T., Stogios, P. J., Morar, M., Rao, C., Di Leo, R., Evdokimova, E., Lam, M., Oatway, C., Cuff, M. E., Osipiuk, J., Michalska, K., Nocek, B. P., Taipale, M., Savchenko, A., Ensminger, A. W. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Genetics, Gene Therapy & Genetic Disease, Microbiology, Virology & Host Pathogen Interaction Articles Source Type: research
Disentangling genetic and epigenetic determinants of ultrafast adaptation
A major rationale for the advocacy of epigenetically mediated adaptive responses is that they facilitate faster adaptation to environmental challenges. This motivated us to develop a theoretical–experimental framework for disclosing the presence of such adaptation-speeding mechanisms in an experimental evolution setting circumventing the need for pursuing costly mutation–accumulation experiments. To this end, we exposed clonal populations of budding yeast to a whole range of stressors. By growth phenotyping, we found that almost complete adaptation to arsenic emerged after a few mitotic cell divisions without i...
Source: Molecular Systems Biology - December 14, 2016 Category: Molecular Biology Authors: Gjuvsland, A. B., Zörgö, E., Samy, J. K., Stenberg, S., Demirsoy, I. H., Roque, F., Maciaszczyk-Dziubinska, E., Migocka, M., Alonso-Perez, E., Zackrisson, M., Wysocki, R., Tamas, M. J., Jonassen, I., Omholt, S. W., Warringer, J. Tags: Evolution, Genome-Scale & Integrative Biology Reports Source Type: research
Distinct cellular states determine calcium signaling response
The heterogeneity in mammalian cells signaling response is largely a result of pre-existing cell-to-cell variability. It is unknown whether cell-to-cell variability rises from biochemical stochastic fluctuations or distinct cellular states. Here, we utilize calcium response to adenosine trisphosphate as a model for investigating the structure of heterogeneity within a population of cells and analyze whether distinct cellular response states coexist. We use a functional definition of cellular state that is based on a mechanistic dynamical systems model of calcium signaling. Using Bayesian parameter inference, we obtain high...
Source: Molecular Systems Biology - December 14, 2016 Category: Molecular Biology Authors: Yao, J., Pilko, A., Wollman, R. Tags: Quantitative Biology & Dynamical Systems, Signal Transduction Articles Source Type: research
Capturing native interactions: intrinsic methods to study chromatin conformation
The 3D organization of chromatin controls gene expression through spatial interactions between genomic loci. FISH and 3C-based methods that are commonly used to study chromatin organization utilize chemical crosslinking, a step that may introduce biases in detectable chromatin interactions. In their recent study, Papantonis and colleagues (Brant et al, 2016) developed alternative new methods of detecting chromatin contacts without the use of chemical crosslinking agents. These tools increase the resolution and confidence at which interactions can be identified, and may be informative for chromatin interaction dynamics...
Source: Molecular Systems Biology - December 8, 2016 Category: Molecular Biology Authors: Rowley, M. J., Corces, V. G. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Genome-Scale & Integrative Biology, Methods & Resources News [amp ] Views Source Type: research
Exploiting native forces to capture chromosome conformation in mammalian cell nuclei
Mammalian interphase chromosomes fold into a multitude of loops to fit the confines of cell nuclei, and looping is tightly linked to regulated function. Chromosome conformation capture (3C) technology has significantly advanced our understanding of this structure-to-function relationship. However, all 3C-based methods rely on chemical cross-linking to stabilize spatial interactions. This step remains a "black box" as regards the biases it may introduce, and some discrepancies between microscopy and 3C studies have now been reported. To address these concerns, we developed "i3C", a novel approach for capturing spatial inter...
Source: Molecular Systems Biology - December 8, 2016 Category: Molecular Biology Authors: Brant, L., Georgomanolis, T., Nikolic, M., Brackley, C. A., Kolovos, P., van Ijcken, W., Grosveld, F. G., Marenduzzo, D., Papantonis, A. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Genome-Scale & Integrative Biology, Methods & Resources Reports Source Type: research
Global analysis of regulatory divergence in the evolution of mouse alternative polyadenylation
Alternative polyadenylation (APA), which is regulated by both cis-elements and trans-factors, plays an important role in post-transcriptional regulation of eukaryotic gene expression. However, comparing to the extensively studied transcription and alternative splicing, the extent of APA divergence during evolution and the relative cis- and trans-contribution remain largely unexplored. To directly address these questions for the first time in mammals, by using deep sequencing-based methods, we measured APA divergence between C57BL/6J and SPRET/EiJ mouse strains as well as allele-specific APA pattern in their F1 hybrids. Amo...
Source: Molecular Systems Biology - December 7, 2016 Category: Molecular Biology Authors: Xiao, M.-S., Zhang, B., Li, Y.-S., Gao, Q., Sun, W., Chen, W. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Genome-Scale & Integrative Biology, Transcription Articles Source Type: research
An atlas of human kinase regulation
The coordinated regulation of protein kinases is a rapid mechanism that integrates diverse cues and swiftly determines appropriate cellular responses. However, our understanding of cellular decision-making has been limited by the small number of simultaneously monitored phospho-regulatory events. Here, we have estimated changes in activity in 215 human kinases in 399 conditions derived from a large compilation of phosphopeptide quantifications. This atlas identifies commonly regulated kinases as those that are central in the signaling network and defines the logic relationships between kinase pairs. Co-regulation along the...
Source: Molecular Systems Biology - November 30, 2016 Category: Molecular Biology Authors: Ochoa, D., Jonikas, M., Lawrence, R. T., El Debs, B., Selkrig, J., Typas, A., Villen, J., Santos, S. D., Beltrao, P. Tags: Genome-Scale & Integrative Biology, Post-translational Modifications, Proteolysis & Proteomics, Signal Transduction Articles Source Type: research
Single-cell sequencing maps gene expression to mutational phylogenies in PDGF- and EGF-driven gliomas
Glioblastoma multiforme (GBM) is the most common and aggressive type of primary brain tumor. Epidermal growth factor (EGF) and platelet-derived growth factor (PDGF) receptors are frequently amplified and/or possess gain-of-function mutations in GBM. However, clinical trials of tyrosine-kinase inhibitors have shown disappointing efficacy, in part due to intra-tumor heterogeneity. To assess the effect of clonal heterogeneity on gene expression, we derived an approach to map single-cell expression profiles to sequentially acquired mutations identified from exome sequencing. Using 288 single cells, we constructed hig...
Source: Molecular Systems Biology - November 24, 2016 Category: Molecular Biology Authors: Müller, S., Liu, S. J., Di Lullo, E., Malatesta, M., Pollen, A. A., Nowakowski, T. J., Kohanbash, G., Aghi, M., Kriegstein, A. R., Lim, D. A., Diaz, A. Tags: Cancer, Chromatin, Epigenetics, Genomics & Functional Genomics, Genome-Scale & Integrative Biology Articles Source Type: research
