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 cell populations. While gene network "rewiring" is known to accompany cellular adaptation to different environments, how PoV changes between environments and its underlying regulatory mechanisms are less understood. Here, we systematically explored context-dependent PoV among genes in human macrophages, utilizing different cytokines as natural perturbations of multiple molecular parameters that may influence PoV. Our single-cell, epigenomic, computational, and stochastic simulation analyses reveal that environmental adaptation can tune PoV to potentially shape cellular heterogeneity by changing parameters such as the degree of phosphorylation and transcription factor-chromatin interactions. This quantitative tuning of PoV may be a widespread, yet underexplored, property of cellular adaptation to distinct environments.
journal_name
Cell Systjournal_title
Cell systemsauthors
Martins AJ,Narayanan M,Prüstel T,Fixsen B,Park K,Gottschalk RA,Lu Y,Andrews-Pfannkoch C,Lau WW,Wendelsdorf KV,Tsang JSdoi
10.1016/j.cels.2017.03.002subject
Has Abstractpub_date
2017-04-26 00:00:00pages
379-392.e12issue
4eissn
2405-4712issn
2405-4720pii
S2405-4712(17)30087-Xjournal_volume
4pub_type
杂志文章相关文献
Cell Systems文献大全abstract：:Overlap of RNA and protein networks reveals glia cells as key players for the development of symptomatic Alzheimer's disease in humans. ...
journal_title：Cell systems
pub_type： 评论,杂志文章
doi：10.1016/j.cels.2017.02.006
更新日期：2017-02-22 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：:The tumor-suppressing transcription factor p53 is highly conserved at the protein level and plays a key role in the DNA damage response. One important aspect of p53 regulation is its dynamics in response to DNA damage, which include oscillations. Here, we observe that, while the qualitative oscillatory nature of p53 d...
journal_title：Cell systems
pub_type： 杂志文章
doi：10.1016/j.cels.2017.09.012
更新日期：2017-10-25 00:00:00
abstract：:We combine a genome-scale RNAi screen in mouse epiblast stem cells (EpiSCs) with genetic interaction, protein localization, and "protein-level dependency" studies-a systematic technique that uncovers post-transcriptional regulation-to delineate the network of factors that control the expression of Oct4, a key regulato...
journal_title：Cell systems
pub_type： 杂志文章
doi：10.1016/j.cels.2015.08.002
更新日期：2015-08-26 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：: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：: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：: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：: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：:Effective design of combination therapies requires understanding the changes in cell physiology that result from drug interactions. Here, we show that the genome-wide transcriptional response to combinations of two drugs, measured at a rigorously controlled growth rate, can predict higher-order antagonism with a third...
journal_title：Cell systems
pub_type： 杂志文章
doi：10.1016/j.cels.2019.10.004
更新日期：2019-11-27 00:00:00
abstract：:Cell-to-cell transcriptional variability in otherwise homogeneous cell populations plays an important role in tissue function and development. Single-cell RNA sequencing can characterize this variability in a transcriptome-wide manner. However, technical variation and the confounding between variability and mean expre...
journal_title：Cell systems
pub_type： 杂志文章
doi：10.1016/j.cels.2018.06.011
更新日期：2018-09-26 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：:Medically induced loss of consciousness (mLOC) during anesthesia is associated with a macroscale breakdown of brain connectivity, yet the neural microcircuit correlates of mLOC remain unknown. To explore this, we applied different analytical approaches (t-SNE/watershed segmentation, affinity propagation clustering, PC...
journal_title：Cell systems
pub_type： 杂志文章
doi：10.1016/j.cels.2019.03.007
更新日期：2019-05-22 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：:While decades of research have elucidated many steps of the alphavirus lifecycle, the earliest replication dynamics have remained unclear. This missing time window has obscured early replicase strand-synthesis behavior and prevented elucidation of how the first events of infection might influence subsequent viral comp...
journal_title：Cell systems
pub_type： 杂志文章
doi：10.1016/j.cels.2020.12.005
更新日期：2021-01-21 00:00:00
abstract：:Understanding the effects of genetic perturbations on the cellular state has been challenging using traditional pooled screens, which typically rely on the delivery of a single perturbation per cell and unidimensional phenotypic readouts. Here, we use barcoded open reading frame overexpression libraries coupled with s...
journal_title：Cell systems
pub_type： 杂志文章
doi：10.1016/j.cels.2018.10.008
更新日期：2018-11-28 00:00:00
abstract：:Ribosome profiling is a widespread tool for studying translational dynamics in human cells. Its central assumption is that ribosome footprint density on a transcript quantitatively reflects protein synthesis. Here, we test this assumption using pulsed-SILAC (pSILAC) high-accuracy targeted proteomics. We focus on multi...
journal_title：Cell systems
pub_type： 杂志文章
doi：10.1016/j.cels.2017.05.001
更新日期：2017-06-28 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：:Single-cell RNA-seq has emerged as a powerful tool in diverse applications, from determining the cell-type composition of tissues to uncovering regulators of developmental programs. A near-universal step in the analysis of single-cell RNA-seq data is to hypothesize the identity of each cell. Often, this is achieved by...
journal_title：Cell systems
pub_type： 杂志文章
doi：10.1016/j.cels.2019.06.004
更新日期：2019-08-28 00:00:00
abstract：:A new bioinformatics tool predicts natively disordered protein control elements that function in cis, opening the door to more systematic studies of this biomedically important class of protein modules. ...
journal_title：Cell systems
pub_type： 评论,杂志文章
doi：10.1016/j.cels.2016.02.011
更新日期：2016-02-24 00:00:00
abstract：:Studying autism genes in the context of the protein complexes to which they belong illustrates the potential of network-centric approaches for understanding complex genetic disease. ...
journal_title：Cell systems
pub_type： 杂志文章
doi：10.1016/j.cels.2015.11.004
更新日期：2015-11-25 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：:DNA shape adds specificity to sequence motifs but has not been explored systematically outside this context. We hypothesized that DNA-binding proteins (DBPs) preferentially occupy DNA with specific structures ("shape motifs") regardless of whether or not these correspond to high information content sequence motifs. We...
journal_title：Cell systems
pub_type： 杂志文章
doi：10.1016/j.cels.2018.12.001
更新日期：2019-01-23 00:00:00
abstract：:Hemizygous deletion of a gene in tumor cells frequently causes reduced expression of its encoded mRNA and protein, as well as reduced protein-but not mRNA-expression of other members in the same protein complex. ...
journal_title：Cell systems
pub_type： 评论,杂志文章
doi：10.1016/j.cels.2017.10.005
更新日期：2017-10-25 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：: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：:The recent increase of immunopeptidomics data, obtained by mass spectrometry or binding assays, opens up possibilities for investigating endogenous antigen presentation by the highly polymorphic human leukocyte antigen class I (HLA-I) protein. State-of-the-art methods predict with high accuracy presentation by HLA all...
journal_title：Cell systems
pub_type： 杂志文章
doi：10.1016/j.cels.2020.11.005
更新日期：2020-12-11 00:00:00
abstract：:This month: imaging the organelle interactome (Lippincott-Schwartz), big data immunology (Pulendran, Ginhoux), protein interactomes expand (Barna, Harper, Marcotte), and computation/engineering insights (Milinkovitch, Silver, and Sastry). ...
journal_title：Cell systems
pub_type： 杂志文章
doi：10.1016/j.cels.2017.06.010
更新日期：2017-06-28 00:00:00
abstract：:Establishing a quantitative connection between the population growth rate and the generation times of single cells is a prerequisite for understanding evolutionary dynamics of microbes. However, existing theories fail to account for the experimentally observed correlations between mother-daughter generation times that...
journal_title：Cell systems
pub_type： 杂志文章
doi：10.1016/j.cels.2017.08.015
更新日期：2017-10-25 00:00:00
abstract：:Clinically used RAF inhibitors are ineffective in RAS mutant tumors because they enhance homo- and heterodimerization of RAF kinases, leading to paradoxical activation of ERK signaling. Overcoming enhanced RAF dimerization and the resulting resistance is a challenge for drug design. Combining multiple inhibitors could...
journal_title：Cell systems
pub_type： 杂志文章
doi：10.1016/j.cels.2018.06.002
更新日期：2018-08-22 00:00:00
