Abstract：
:Isogenic cells in a common environment show substantial cell-to-cell variation in gene expression, often referred to as "expression noise." Here, we use multiple single-cell RNA-sequencing datasets to identify features associated with high or low expression noise in mouse embryonic stem cells. These include the core promoter architecture of a gene, with CpG island promoters and a TATA box associated with low and high noise, respectively. High noise is also associated with "conflicting" chromatin states-the absence of transcription-associated histone modifications or the presence of repressive ones in active genes. Genes regulated by pluripotency factors through super-enhancers show high and correlated expression variability, consistent with fluctuations in the pluripotent state. Together, our results provide an integrated view of how core promoters, chromatin, regulation, and pluripotency fluctuations contribute to the variability of gene expression across individual stem cells.
journal_name
Cell Systjournal_title
Cell systemsauthors
Faure AJ,Schmiedel JM,Lehner Bdoi
10.1016/j.cels.2017.10.003subject
Has Abstractpub_date
2017-11-22 00:00:00pages
471-484.e4issue
5eissn
2405-4712issn
2405-4720pii
S2405-4712(17)30440-4journal_volume
5pub_type
杂志文章相关文献
Cell Systems文献大全abstract：:Two studies show that noise is a key ingredient of new mechanisms for entraining the NF-κB system. ...
journal_title：Cell systems
pub_type： 杂志文章
doi：10.1016/j.cels.2016.12.008
更新日期：2016-12-21 00:00:00
abstract：:Racism and COVID-19 represent a pandemic on a pandemic for Blacks. The pandemics find themselves synergized to the detriment of Blacks and their health. The complexity of the combination of these pandemics are evident when examining the interplay between racist policing practices and health. ...
journal_title：Cell systems
pub_type： 杂志文章
doi：10.1016/j.cels.2020.07.002
更新日期：2020-07-22 00:00:00
abstract：:Signaling proteins display remarkable cell-to-cell heterogeneity in their dynamic responses to stimuli, but the consequences of this heterogeneity remain largely unknown. For instance, the contribution of the dynamics of the innate immune transcription factor nuclear factor κB (NF-κB) to gene expression output is disp...
journal_title：Cell systems
pub_type： 杂志文章
doi：10.1016/j.cels.2017.03.010
更新日期：2017-04-26 00:00:00
abstract：:The construction of complex gene-regulatory networks requires both inhibitory and upregulatory modules. However, the vast majority of RNA-based regulatory "parts" are inhibitory. Using a synthetic biology approach combined with SHAPE-seq, we explored the regulatory effect of RNA-binding protein (RBP)-RNA interactions ...
journal_title：Cell systems
pub_type： 杂志文章
doi：10.1016/j.cels.2019.04.007
更新日期：2019-07-24 00:00:00
abstract：:Understanding the complex interactions that occur between heterologous and native biochemical pathways represents a major challenge in metabolic engineering and synthetic biology. We present a workflow that integrates metabolomics, proteomics, and genome-scale models of Escherichia coli metabolism to study the effects...
journal_title：Cell systems
pub_type： 杂志文章
doi：10.1016/j.cels.2016.04.004
更新日期：2016-05-25 00:00:00
abstract：:Chinese hamster ovary (CHO) cells dominate biotherapeutic protein production and are widely used in mammalian cell line engineering research. To elucidate metabolic bottlenecks in protein production and to guide cell engineering and bioprocess optimization, we reconstructed the metabolic pathways in CHO and associated...
journal_title：Cell systems
pub_type： 杂志文章
doi：10.1016/j.cels.2016.10.020
更新日期：2016-11-23 00:00:00
abstract：:One snapshot of the peer review process for "Cytoplasmic Amplification of Transcriptional Noise Generates Substantial Cell-to-Cell Variability" (Hansen et al., 2018). ...
journal_title：Cell systems
pub_type： 评论,杂志文章
doi：10.1016/j.cels.2018.10.003
更新日期：2018-10-24 00:00:00
abstract：:Advances in biological engineering headline this month's Cell Systems call (Cell Systems 1, 307), alongside intriguing applications of modeling from the Elf, Goentoro, and Wolf groups. Check out our recent blogpost: http://crosstalk.cell.com/blog/a-call-for-papers-on-biological-engineering-and-synthetic-biology. ...
journal_title：Cell systems
pub_type： 杂志文章
doi：10.1016/j.cels.2016.08.006
更新日期：2016-08-01 00:00:00
abstract：:This month: selected work from the 2018 RECOMB meeting, organized by Ecole Polytechnique and held last April in Paris. ...
journal_title：Cell systems
pub_type： 杂志文章
doi：10.1016/j.cels.2018.08.005
更新日期：2018-08-22 00:00:00
abstract：:One snapshot of the peer review process for "Critical Roles of the Pentose Phosphate Pathway and GLN3 in Isobutanol-Specific Tolerance in Yeast" (Kuroda et al., 2019). ...
journal_title：Cell systems
pub_type： 评论,杂志文章
doi：10.1016/j.cels.2020.01.005
更新日期：2020-02-26 00:00:00
abstract：:Machine learning can be used to predict compounds acting synergistically, and this could greatly expand the universe of available potential treatments for diseases that are currently hidden in the dark chemical matter. ...
journal_title：Cell systems
pub_type： 杂志文章
doi：10.1016/j.cels.2015.12.005
更新日期：2015-12-23 00:00:00
abstract：:The field of systems immunology has grown extensively over the last few years, spurred by the generation of large datasets, new analytical tools, and modeling approaches. In this piece and its counterpart in Trends in Immunology [http://www.cell.com/trends/immunology/fulltext/S1471-4906(18)30013-9], eight authors disc...
journal_title：Cell systems
pub_type： 社论,面试
doi：10.1016/j.cels.2018.02.005
更新日期：2018-02-28 00:00:00
abstract：:Cell-to-cell variation in gene expression and the propagation of such variation (PoV or "noise propagation") from one gene to another in the gene network, as reflected by gene-gene correlation across single cells, are commonly observed in single-cell transcriptomic studies and can shape the phenotypic diversity of cel...
journal_title：Cell systems
pub_type： 杂志文章
doi：10.1016/j.cels.2017.03.002
更新日期：2017-04-26 00:00:00
abstract：:Recent advances in synthetic biology and biological system engineering have allowed the design and construction of engineered live biotherapeutics targeting a range of human clinical applications. In this review, we outline how systems approaches have been used to move from simple constitutive systems, where a single ...
journal_title：Cell systems
pub_type： 杂志文章,评审
doi：10.1016/j.cels.2018.06.008
更新日期：2018-07-25 00:00:00
abstract：:Three studies demonstrate the potential of state-of-the-art mass spectrometry-based proteomics for rapid, deep characterization of proteomes. ...
journal_title：Cell systems
pub_type： 评论,杂志文章
doi：10.1016/j.cels.2016.03.002
更新日期：2016-03-23 00:00:00
abstract：:Gram-negative bacteria are intrinsically resistant to drugs because of their double-membrane envelope structure that acts as a permeability barrier and as an anchor for efflux pumps. Antibiotics are blocked and expelled from cells and cannot reach high-enough intracellular concentrations to exert a therapeutic effect....
journal_title：Cell systems
pub_type： 杂志文章
doi：10.1016/j.cels.2019.03.008
更新日期：2019-04-24 00:00:00
abstract：:Recent mass spectrometry maps of the human interactome independently support the existence of a large multiprotein complex, dubbed "Commander." Broadly conserved across animals and ubiquitously expressed in nearly every human cell type examined thus far, Commander likely plays a fundamental cellular function, akin to ...
journal_title：Cell systems
pub_type： 杂志文章,评审
doi：10.1016/j.cels.2017.04.006
更新日期：2017-05-24 00:00:00
abstract：:Large-scale single-cell RNA sequencing (scRNA-seq) studies that profile hundreds of thousands of cells are becoming increasingly common, overwhelming existing analysis pipelines. Here, we describe how to enhance and accelerate single-cell data analysis by summarizing the transcriptomic heterogeneity within a dataset u...
journal_title：Cell systems
pub_type： 杂志文章
doi：10.1016/j.cels.2019.05.003
更新日期：2019-06-26 00:00:00
abstract：:Robust biological oscillators retain the critical ability to function in the presence of environmental perturbations. Although central architectures that support robust oscillations have been extensively studied, networks containing the same core vary drastically in their potential to oscillate, and it remains elusive...
journal_title：Cell systems
pub_type： 杂志文章
doi：10.1016/j.cels.2017.06.013
更新日期：2017-07-26 00:00:00
abstract：:Systematic assessment of tyrosine kinase-substrate relationships is fundamental to a better understanding of cellular signaling and its profound alterations in human diseases such as cancer. In human cells, such assessments are confounded by complex signaling networks, feedback loops, conditional activity, and intra-k...
journal_title：Cell systems
pub_type： 杂志文章
doi：10.1016/j.cels.2017.08.001
更新日期：2017-08-23 00:00:00
abstract：:Many data sets exhibit well-defined structure that can be exploited to design faster search tools, but it is not always clear when such acceleration is possible. Here we introduce a framework for similarity search based on characterizing a data set's entropy and fractal dimension. We prove that searching scales in tim...
journal_title：Cell systems
pub_type： 杂志文章
doi：10.1016/j.cels.2015.08.004
更新日期：2015-08-26 00:00:00
abstract：:Translation of mRNA into protein is a fundamental yet complex biological process with multiple factors that can potentially affect its efficiency. Here, we study a stochastic model describing the traffic flow of ribosomes along the mRNA and identify the key parameters that govern the overall rate of protein synthesis,...
journal_title：Cell systems
pub_type： 杂志文章
doi：10.1016/j.cels.2019.12.003
更新日期：2020-02-26 00:00:00
abstract：:A number of sequencing-based transcriptase drop-off assays have recently been developed to probe post-transcriptional dynamics of RNA-protein interaction, RNA structure, and RNA modification. Although these assays survey a diverse set of epitranscriptomic marks, we use the term toeprinting assays since they share meth...
journal_title：Cell systems
pub_type： 杂志文章
doi：10.1016/j.cels.2017.04.007
更新日期：2017-05-24 00:00:00
abstract：:Hi-C experiments study how genomes fold in 3D, generating contact maps containing features as small as 20 bp and as large as 200 Mb. Here we introduce Juicebox, a tool for exploring Hi-C and other contact map data. Juicebox allows users to zoom in and out of Hi-C maps interactively, just as a user of Google Earth migh...
journal_title：Cell systems
pub_type： 杂志文章
doi：10.1016/j.cels.2015.07.012
更新日期：2016-07-01 00:00:00
abstract：:An integrated approach unifies experimental observations and mathematical modeling to represent differentiation dynamics as discrete transition events underpinned by stochastic transitions between hidden states. ...
journal_title：Cell systems
pub_type： 评论,杂志文章
doi：10.1016/j.cels.2017.09.009
更新日期：2017-09-27 00:00:00
abstract：:Cancer evolution poses a central obstacle to cure, as resistant clones expand under therapeutic selection pressures. Genome sequencing of relapsed disease can nominate genomic alterations conferring resistance but sample collection lags behind, limiting therapeutic innovation. Genome-wide screens offer a complementary...
journal_title：Cell systems
pub_type： 杂志文章
doi：10.1016/j.cels.2019.10.002
更新日期：2020-01-22 00:00:00
abstract：:The Library of Integrated Network-Based Cellular Signatures (LINCS) is an NIH Common Fund program that catalogs how human cells globally respond to chemical, genetic, and disease perturbations. Resources generated by LINCS include experimental and computational methods, visualization tools, molecular and imaging data,...
journal_title：Cell systems
pub_type： 杂志文章,评审
doi：10.1016/j.cels.2017.11.001
更新日期：2018-01-24 00:00:00
abstract：:Despite improved methods for MHC affinity prediction, the vast majority of computationally predicted tumor neoantigens are not immunogenic experimentally, indicating that high-quality neoantigens are beyond current algorithms to discern. To enrich for neoantigens with the greatest likelihood of immunogenicity, we deve...
journal_title：Cell systems
pub_type： 杂志文章
doi：10.1016/j.cels.2019.08.009
更新日期：2019-10-23 00:00:00
abstract：:A principled approach to integrating metabolomics, proteomics, and genome-scale metabolic modeling facilitaties rational pathway engineering of E. coli. ...
journal_title：Cell systems
pub_type： 评论,杂志文章
doi：10.1016/j.cels.2016.05.005
更新日期：2016-06-22 00:00:00
abstract：:Accurately translating genotype to phenotype requires accounting for the functional impact of genetic variation at many biological scales. Here we present a strategy for genotype-phenotype reasoning based on existing knowledge of cellular subsystems. These subsystems and their hierarchical organization are defined by ...
journal_title：Cell systems
pub_type： 杂志文章
doi：10.1016/j.cels.2016.02.003
更新日期：2016-02-24 00:00:00
