Molecular transitions in early progenitors during human cord blood hematopoiesis
Hematopoietic stem cells (HSCs) give rise to diverse cell types in the blood system, yet our molecular understanding of the early trajectories that generate this enormous diversity in humans remains incomplete. Here, we leverage Drop-seq, a massively parallel single-cell RNA sequencing (scRNA-seq) approach, to individually profile 20,000 progenitor cells from human cord blood, without prior enrichment or depletion for individual lineages based on surface markers. Our data reveal a transcriptional compendium of progenitor states in human cord blood, representing four committed lineages downstream from HSC, alongside the tra...
Source: Molecular Systems Biology - March 15, 2018 Category: Molecular Biology Authors: Zheng, S., Papalexi, E., Butler, A., Stephenson, W., Satija, R. Tags: Development & Differentiation, Genome-Scale & Integrative Biology, Transcription Articles Source Type: research
Tuning dCas9's ability to block transcription enables robust, noiseless knockdown of bacterial genes
Over the past few years, tools that make use of the Cas9 nuclease have led to many breakthroughs, including in the control of gene expression. The catalytically dead variant of Cas9 known as dCas9 can be guided by small RNAs to block transcription of target genes, in a strategy also known as CRISPRi. Here, we reveal that the level of complementarity between the guide RNA and the target controls the rate at which RNA polymerase "kicks out" dCas9 from the target and completes transcription. We use this mechanism to precisely and robustly reduce gene expression by defined relative amounts. Alternatively, tuning repression by ...
Source: Molecular Systems Biology - March 8, 2018 Category: Molecular Biology Authors: Vigouroux, A., Oldewurtel, E., Cui, L., Bikard, D., van Teeffelen, S. Tags: Quantitative Biology & Dynamical Systems, Synthetic Biology & Biotechnology, Transcription Articles Source Type: research
Targeting CDK2 overcomes melanoma resistance against BRAF and Hsp90 inhibitors
Novel therapies are undergoing clinical trials, for example, the Hsp90 inhibitor, XL888, in combination with BRAF inhibitors for the treatment of therapy-resistant melanomas. Unfortunately, our data show that this combination elicits a heterogeneous response in a panel of melanoma cell lines including PDX-derived models. We sought to understand the mechanisms underlying the differential responses and suggest a patient stratification strategy. Thermal proteome profiling (TPP) identified the protein targets of XL888 in a pair of sensitive and unresponsive cell lines. Unbiased proteomics and phosphoproteomics analyses identif...
Source: Molecular Systems Biology - March 5, 2018 Category: Molecular Biology Authors: Azimi, A., Caramuta, S., Seashore-Ludlow, B., Boström, J., Robinson, J. L., Edfors, F., Tuominen, R., Kemper, K., Krijgsman, O., Peeper, D. S., Nielsen, J., Hansson, J., Egyhazi Brage, S., Altun, M., Uhlen, M., Maddalo, G. Tags: Cancer, Genome-Scale & Integrative Biology, Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research
Genomics of cellular proliferation in periodic environmental fluctuations
Living systems control cell growth dynamically by processing information from their environment. Although responses to a single environmental change have been intensively studied, little is known about how cells react to fluctuating conditions. Here, we address this question at the genomic scale by measuring the relative proliferation rate (fitness) of 3,568 yeast gene deletion mutants in out-of-equilibrium conditions: periodic oscillations between two environmental conditions. In periodic salt stress, fitness and its genetic variance largely depended on the oscillating period. Surprisingly, dozens of mutants displayed pro...
Source: Molecular Systems Biology - March 5, 2018 Category: Molecular Biology Authors: Salignon, J., Richard, M., Fulcrand, E., Duplus-Bottin, H., Yvert, G. Tags: Genome-Scale & Integrative Biology, Quantitative Biology & Dynamical Systems, Signal Transduction Articles Source Type: research
Photoperiodic control of the Arabidopsis proteome reveals a translational coincidence mechanism
Plants respond to seasonal cues such as the photoperiod, to adapt to current conditions and to prepare for environmental changes in the season to come. To assess photoperiodic responses at the protein level, we quantified the proteome of the model plant Arabidopsis thaliana by mass spectrometry across four photoperiods. This revealed coordinated changes of abundance in proteins of photosynthesis, primary and secondary metabolism, including pigment biosynthesis, consistent with higher metabolic activity in long photoperiods. Higher translation rates in the day than the night likely contribute to these changes, via an intera...
Source: Molecular Systems Biology - March 1, 2018 Category: Molecular Biology Authors: Seaton, D. D., Graf, A., Baerenfaller, K., Stitt, M., Millar, A. J., Gruissem, W. Tags: Plant Biology, Post-translational Modifications, Proteolysis & Proteomics, Quantitative Biology & Dynamical Systems Articles Source Type: research
Estrogen-dependent control and cell-to-cell variability of transcriptional bursting
Cellular decision-making and environmental adaptation are dependent upon a heterogeneous response of gene expression to external cues. Heterogeneity arises in transcription from random switching between transcriptionally active and inactive states, resulting in bursts of RNA synthesis. Furthermore, the cellular state influences the competency of transcription, thereby globally affecting gene expression in a cell-specific manner. We determined how external stimuli interplay with cellular state to modulate the kinetics of bursting. To this end, single-cell dynamics of nascent transcripts were monitored at the endogenous estr...
Source: Molecular Systems Biology - February 23, 2018 Category: Molecular Biology Authors: Fritzsch, C., Baumgärtner, S., Kuban, M., Steinshorn, D., Reid, G., Legewie, S. Tags: Quantitative Biology & Dynamical Systems, Transcription Articles Source Type: research
A unified approach for quantifying and interpreting DNA shape readout by transcription factors
Transcription factors (TFs) interpret DNA sequence by probing the chemical and structural properties of the nucleotide polymer. DNA shape is thought to enable a parsimonious representation of dependencies between nucleotide positions. Here, we propose a unified mathematical representation of the DNA sequence dependence of shape and TF binding, respectively, which simplifies and enhances analysis of shape readout. First, we demonstrate that linear models based on mononucleotide features alone account for 60–70% of the variance in minor groove width, roll, helix twist, and propeller twist. This explains why simple scor...
Source: Molecular Systems Biology - February 22, 2018 Category: Molecular Biology Authors: Rube, H. T., Rastogi, C., Kribelbauer, J. F., Bussemaker, H. J. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Methods & Resources, Transcription Source Type: research
Toward an integrated map of genetic interactions in cancer cells
Cancer genomes often harbor hundreds of molecular aberrations. Such genetic variants can be drivers or passengers of tumorigenesis and create vulnerabilities for potential therapeutic exploitation. To identify genotype-dependent vulnerabilities, forward genetic screens in different genetic backgrounds have been conducted. We devised MINGLE, a computational framework to integrate CRISPR/Cas9 screens originating from different libraries building on approaches pioneered for genetic network discovery in model organisms. We applied this method to integrate and analyze data from 85 CRISPR/Cas9 screens in human cancer cells combi...
Source: Molecular Systems Biology - February 21, 2018 Category: Molecular Biology Authors: Rauscher, B., Heigwer, F., Henkel, L., Hielscher, T., Voloshanenko, O., Boutros, M. Tags: Cancer, Computational Biology, Genome-Scale & Integrative Biology Articles Source Type: research
Antisense transcription-dependent chromatin signature modulates sense transcript dynamics
Antisense transcription is widespread in genomes. Despite large differences in gene size and architecture, we find that yeast and human genes share a unique, antisense transcription-associated chromatin signature. We asked whether this signature is related to a biological function for antisense transcription. Using quantitative RNA-FISH, we observed changes in sense transcript distributions in nuclei and cytoplasm as antisense transcript levels were altered. To determine the mechanistic differences underlying these distributions, we developed a mathematical framework describing transcription from initiation to transcript d...
Source: Molecular Systems Biology - February 12, 2018 Category: Molecular Biology Authors: Brown, T., Howe, F. S., Murray, S. C., Wouters, M., Lorenz, P., Seward, E., Rata, S., Angel, A., Mellor, J. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Genome-Scale & Integrative Biology, Transcription Articles Source Type: research
Modeling signaling-dependent pluripotency with Boolean logic to predict cell fate transitions
Pluripotent stem cells (PSCs) exist in multiple stable states, each with specific cellular properties and molecular signatures. The mechanisms that maintain pluripotency, or that cause its destabilization to initiate development, are complex and incompletely understood. We have developed a model to predict stabilized PSC gene regulatory network (GRN) states in response to input signals. Our strategy used random asynchronous Boolean simulations (R-ABS) to simulate single-cell fate transitions and strongly connected components (SCCs) strategy to represent population heterogeneity. This framework was applied to a reverse-engi...
Source: Molecular Systems Biology - January 29, 2018 Category: Molecular Biology Authors: Yachie-Kinoshita, A., Onishi, K., Ostblom, J., Langley, M. A., Posfai, E., Rossant, J., Zandstra, P. W. Tags: Development & Differentiation, Network Biology, Stem Cells Articles Source Type: research
Cell-specific responses to the cytokine TGF{beta} are determined by variability in protein levels
The cytokine TGFβ provides important information during embryonic development, adult tissue homeostasis, and regeneration. Alterations in the cellular response to TGFβ are involved in severe human diseases. To understand how cells encode the extracellular input and transmit its information to elicit appropriate responses, we acquired quantitative time-resolved measurements of pathway activation at the single-cell level. We established dynamic time warping to quantitatively compare signaling dynamics of thousands of individual cells and described heterogeneous single-cell responses by mathematical modeling. Our co...
Source: Molecular Systems Biology - January 25, 2018 Category: Molecular Biology Authors: Strasen, J., Sarma, U., Jentsch, M., Bohn, S., Sheng, C., Horbelt, D., Knaus, P., Legewie, S., Loewer, A. Tags: Quantitative Biology & Dynamical Systems, Signal Transduction Articles Source Type: research
Large-scale image-based profiling of single-cell phenotypes in arrayed CRISPR-Cas9 gene perturbation screens
High-content imaging using automated microscopy and computer vision allows multivariate profiling of single-cell phenotypes. Here, we present methods for the application of the CISPR-Cas9 system in large-scale, image-based, gene perturbation experiments. We show that CRISPR-Cas9-mediated gene perturbation can be achieved in human tissue culture cells in a timeframe that is compatible with image-based phenotyping. We developed a pipeline to construct a large-scale arrayed library of 2,281 sequence-verified CRISPR-Cas9 targeting plasmids and profiled this library for genes affecting cellular morphology and the subcellular lo...
Source: Molecular Systems Biology - January 23, 2018 Category: Molecular Biology Authors: de Groot, R., Lüthi, J., Lindsay, H., Holtackers, R., Pelkmans, L. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Genome-Scale & Integrative Biology, Methods & Resources Source Type: research
Assigning function to natural allelic variation via dynamic modeling of gene network induction
More and more natural DNA variants are being linked to physiological traits. Yet, understanding what differences they make on molecular regulations remains challenging. Important properties of gene regulatory networks can be captured by computational models. If model parameters can be "personalized" according to the genotype, their variation may then reveal how DNA variants operate in the network. Here, we combined experiments and computations to visualize natural alleles of the yeast GAL3 gene in a space of model parameters describing the galactose response network. Alleles altering the activation of Gal3p by galactose we...
Source: Molecular Systems Biology - January 15, 2018 Category: Molecular Biology Authors: Richard, M., Chuffart, F., Duplus-Bottin, H., Pouyet, F., Spichty, M., Fulcrand, E., Entrevan, M., Barthelaix, A., Springer, M., Jost, D., Yvert, G. Tags: Methods & Resources, Network Biology, Quantitative Biology & Dynamical Systems Articles Source Type: research
Non-genetic diversity modulates population performance
(Source: Molecular Systems Biology)
Source: Molecular Systems Biology - January 10, 2018 Category: Molecular Biology Authors: Waite, A. J., Frankel, N. W., Dufour, Y. S., Johnston, J. F., Long, J., Emonet, T. Tags: Corrigendum Source Type: research
A Sizer model for cell differentiation in Arabidopsis thaliana root growth
Plant roots grow due to cell division in the meristem and subsequent cell elongation and differentiation, a tightly coordinated process that ensures growth and adaptation to the changing environment. How the newly formed cells decide to stop elongating becoming fully differentiated is not yet understood. To address this question, we established a novel approach that combines the quantitative phenotypic variability of wild-type Arabidopsis roots with computational data from mathematical models. Our analyses reveal that primary root growth is consistent with a Sizer mechanism, in which cells sense their length and stop elong...
Source: Molecular Systems Biology - January 10, 2018 Category: Molecular Biology Authors: Pavelescu, I., Vilarrasa-Blasi, J., Planas-Riverola, A., Gonzalez-Garcia, M.-P., Cano-Delgado, A. I., Ibanes, M. Tags: Development & Differentiation, Plant Biology, Quantitative Biology & Dynamical Systems Articles Source Type: research
