scholarly journals Simultaneous quantification of mRNA and protein in single cells reveals post-transcriptional effects of genetic variation

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Christian Brion ◽  
Sheila M Lutz ◽  
Frank Wolfgang Albert
Keyword(s):  
Statistical Power ◽  
Single Cells ◽  
Live Cells ◽  
Kinase Gene ◽  
Fluorescent Reporters ◽  
Protein Levels ◽  
Simultaneous Quantification ◽  
Specific Effects ◽  
Recombinant Cells ◽  
Large Populations

Trans-acting DNA variants may specifically affect mRNA or protein levels of genes located throughout the genome. However, prior work compared trans-acting loci mapped in separate studies, many of which had limited statistical power. Here, we developed a CRISPR-based system for simultaneous quantification of mRNA and protein of a given gene via dual fluorescent reporters in single, live cells of the yeast Saccharomyces cerevisiae. In large populations of recombinant cells from a cross between two genetically divergent strains, we mapped 86 trans-acting loci affecting the expression of ten genes. Less than 20% of these loci had concordant effects on mRNA and protein of the same gene. Most loci influenced protein but not mRNA of a given gene. One locus harbored a premature stop variant in the YAK1 kinase gene that had specific effects on protein or mRNA of dozens of genes. These results demonstrate complex, post-transcriptional genetic effects on gene expression.

scholarly journals Simultaneous quantification of mRNA and protein in single cells reveals post-transcriptional effects of genetic variation

2020 ◽  
Author(s):  
Christian Brion ◽  
Sheila Lutz ◽  
Frank W. Albert
Keyword(s):  
Statistical Power ◽  
Single Cells ◽  
Live Cells ◽  
Kinase Gene ◽  
Protein Levels ◽  
Simultaneous Quantification ◽  
Specific Effects ◽  
Recombinant Cells ◽  
Dna Variants ◽  
Large Populations

AbstractTrans-acting DNA variants may specifically affect mRNA or protein levels of genes located throughout the genome. However, prior work compared trans-acting loci mapped in studies performed separately or with limited statistical power. Here, we developed a CRISPR-based system for simultaneous quantification of mRNA and protein of a given gene via dual fluorescent reporters in single, live cells of the yeast Saccharomyces cerevisiae. In large populations of recombinant cells from a cross between two genetically divergent strains, we mapped 86 trans-acting loci affecting the expression of ten genes. Less than 20% of these loci had concordant effects on mRNA and protein of the same gene. Most loci influenced protein but not mRNA of a given gene. One such locus harbored a premature stop variant in the YAK1 kinase gene that had specific effects on protein or mRNA of dozens of genes. These results demonstrate complex, post-transcriptional genetic effects on gene expression.One sentence summaryA CRISPR-based dual reporter assay enables genetic mapping of DNA variants that specifically affect mRNA or protein levels in trans.

scholarly journals Regulatory mechanisms are revealed by the distribution of transcription initiation times in single microbial cells

2017 ◽  
Author(s):  
Sandeep Choubey ◽  
Jane Kondev ◽  
Alvaro Sanchez
Keyword(s):  
Transcription Initiation ◽  
Single Cells ◽  
Quantitative Information ◽  
Rna Polymerases ◽  
Live Cells ◽  
Control Of Gene Expression ◽  
Fluorescent Reporters ◽  
Transcriptional Dynamics ◽  
General Stochastic Model ◽  
State Of Affairs

AbstractTranscription is the dominant point of control of gene expression. Biochemical studies have revealed key molecular components of transcription and their interactions, but the dynamics of transcription initiation in cells is still poorly understood. This state of affairs is being remedied with experiments that observe transcriptional dynamics in single cells using fluorescent reporters. Quantitative information about transcription initiation dynamics can also be extracted from experiments that use electron micrographs of RNA polymerases caught in the act of transcribing a gene (Miller spreads). Inspired by these data we analyze a general stochastic model of transcription initiation and elongation, and compute the distribution of transcription initiation times. We show that different mechanisms of initiation leave distinct signatures in the distribution of initiation times that can be compared to experiments. We analyze published micrographs of RNA polymerases transcribing ribosomal RNA genes inE.coliand compare the observed distributions of inter-polymerase distances with the predictions from previously hypothesized mechanisms for the regulation of these genes. Our analysis demonstrates the potential of measuring the distribution of time intervals between initiation events as a probe for dissecting mechanisms of transcription initiation in live cells.

scholarly journals ZipSeq : Barcoding for Real-time Mapping of Single Cell Transcriptomes

2020 ◽  
Author(s):  
Kenneth H. Hu ◽  
John P. Eichorst ◽  
Chris S. McGinnis ◽  
David M. Patterson ◽  
Eric D. Chow ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Real Time ◽  
Dimensional Space ◽  
Single Cells ◽  
Expression Patterns ◽  
Live Cells ◽  
Glass Substrates ◽  
Complete Mapping

ABSTRACTSpatial transcriptomics seeks to integrate single-cell transcriptomic data within the 3-dimensional space of multicellular biology. Current methods use glass substrates pre-seeded with matrices of barcodes or fluorescence hybridization of a limited number of probes. We developed an alternative approach, called ‘ZipSeq’, that uses patterned illumination and photocaged oligonucleotides to serially print barcodes (Zipcodes) onto live cells within intact tissues, in real-time and with on-the-fly selection of patterns. Using ZipSeq, we mapped gene expression in three settings: in-vitro wound healing, live lymph node sections and in a live tumor microenvironment (TME). In all cases, we discovered new gene expression patterns associated with histological structures. In the TME, this demonstrated a trajectory of myeloid and T cell differentiation, from periphery inward. A variation of ZipSeq efficiently scales to the level of single cells, providing a pathway for complete mapping of live tissues, subsequent to real-time imaging or perturbation.

scholarly journals Dynamic proteomics of HSV1 infection reveals molecular events that govern non-stochastic infection outcomes

2016 ◽  
Author(s):  
Nir Drayman ◽  
Omer Karin ◽  
Avi Mayo ◽  
Tamar Danon ◽  
Lev Shapira ◽  
...  
Keyword(s):  
Single Cells ◽  
Infection Process ◽  
Human Pathogen ◽  
Herpes Simplex Virus 1 ◽  
Host Interactions ◽  
Protein Levels ◽  
Molecular Events ◽  
Proteomics Approach ◽  
Infected Cells ◽  
Simplex Virus

AbstractViral infection is usually studied at the level of cell populations, averaging over hundreds of thousands of individual cells. Moreover, measurements are typically done by analyzing a few time points along the infection process. While informative, such measurements are limited in addressing how cell variability affects infection outcome. Here we employ dynamic proteomics to study virus-host interactions, using the human pathogen Herpes Simplex virus 1 as a model. We tracked >50,000 individual cells as they respond to HSV1 infection, allowing us to model infection kinetics and link infection outcome (productive or not) with the cell state at the time of initial infection. We find that single cells differ in their preexisting susceptibility to HSV1, and that this is partially mediated by their cell-cycle position. We also identify specific changes in protein levels and localization in infected cells, attesting to the power of the dynamic proteomics approach for studying virus-host interactions.

Potassium channel KCNJ15 is required for histamine-stimulated gastric acid secretion

2015 ◽  
Vol 309 (4) ◽  
pp. C264-C270 ◽  
Author(s):  
Jianye Yuan ◽  
Wensheng Liu ◽  
Serhan Karvar ◽  
Susan S. Baker ◽  
Wenjun He ◽  
...  
Keyword(s):  
Acid Secretion ◽  
Gastric Acid Secretion ◽  
Gastric Acid ◽  
Apical Membrane ◽  
Imaging System ◽  
Parietal Cells ◽  
Live Cells ◽  
Protein Levels ◽  
Endogenous Protein ◽  
Luminal Side

Gastric acid secretion is mediated by the K+-dependent proton pump (H+,K+-ATPase), which requires a continuous supply of K+ at the luminal side of the apical membrane. Several K+ channels are implicated in gastric acid secretion. However, the identity of the K+ channel(s) responsible for apical K+ supply is still elusive. Our previous studies have shown the translocation of KCNJ15 from cytoplasmic vesicles to the apical membrane on stimulation, indicating its involvement in gastric acid secretion. In this study, the stimulation associated trafficking of KCNJ15 was observed in a more native context with a live cell imaging system. KCNJ15 molecules in resting live cells were scattered in cytoplasm but exhibited apical localization after stimulation. Furthermore, knocking down KCNJ15 expression with a short hairpin RNA adenoviral construct abolished histamine-stimulated acid secretion in rabbit primary parietal cells. Moreover, KCNJ15, like H+,K+-ATPase, was detected in all of the parietal cells by immunofluorescence staining, whereas only about half of the parietal cells were positive for KCNQ1 under the same condition. Consistently, the endogenous protein levels of KCNJ15, analyzed by Western blotting, were higher than those of KCNQ1 in the gastric mucosa of human, mouse, and rabbit. These results provide evidence for a major role of KCNJ15 in apical K+ supply during stimulated acid secretion.

scholarly journals Simultaneous quantification of multiple endogenous biothiols in single living cells by plasmonic Raman probes

2017 ◽  
Vol 8 (11) ◽  
pp. 7582-7587 ◽  
Author(s):  
Shan-Shan Li ◽  
Qi-Yuan Guan ◽  
Mengmeng Zheng ◽  
Yu-Qi Wang ◽  
Deju Ye ◽  
...  
Keyword(s):  
Principal Component Analysis ◽  
Single Cells ◽  
Principal Component ◽  
Component Analysis ◽  
Living Cells ◽  
Simultaneous Quantification ◽  
Single Living Cells ◽  
Single Living

Three endogenous biothiols in single cells were simultaneously quantified by plasmonic Raman probes and quantitative principal component analysis (qPCA).

scholarly journals A new method for post-translationally labeling proteins in live cells for fluorescence imaging and tracking

2017 ◽  
Vol 30 (12) ◽  
pp. 771-780 ◽  
Author(s):  
M Hinrichsen ◽  
M Lenz ◽  
J M Edwards ◽  
O K Miller ◽  
S G J Mochrie ◽  
...  
Keyword(s):  
Fluorescent Protein ◽  
Single Cells ◽  
Covalent Bond ◽  
Subcellular Location ◽  
Turnover Time ◽  
Target Protein ◽  
Live Cells ◽  
General Applicability ◽  
Novel Approach ◽  
And Function

AbstractWe present a novel method to fluorescently label proteins, post-translationally, within live Saccharomycescerevisiae. The premise underlying this work is that fluorescent protein (FP) tags are less disruptive to normal processing and function when they are attached post-translationally, because target proteins are allowed to fold properly and reach their final subcellular location before being labeled. We accomplish this post-translational labeling by expressing the target protein fused to a short peptide tag (SpyTag), which is then covalently labeled in situ by controlled expression of an open isopeptide domain (SpyoIPD, a more stable derivative of the SpyCatcher protein) fused to an FP. The formation of a covalent bond between SpyTag and SpyoIPD attaches the FP to the target protein. We demonstrate the general applicability of this strategy by labeling several yeast proteins. Importantly, we show that labeling the membrane protein Pma1 in this manner avoids the mislocalization and growth impairment that occur when Pma1 is genetically fused to an FP. We also demonstrate that this strategy enables a novel approach to spatiotemporal tracking in single cells and we develop a Bayesian analysis to determine the protein’s turnover time from such data.

scholarly journals Fibronectin-Based Nanomechanical Biosensors to Map 3D Strains in Live Cells and Tissues

2020 ◽  
Author(s):  
Daniel J. Shiwarski ◽  
Joshua W. Tashman ◽  
Alkiviadis Tsamis ◽  
Jacqueline M. Bliley ◽  
Malachi A. Blundon ◽  
...  
Keyword(s):  
Spatial Resolution ◽  
Single Cells ◽  
Time Lapse ◽  
Confocal Imaging ◽  
Square Lattice ◽  
Live Cells ◽  
3D Analysis ◽  
Wide Range ◽  
And Function ◽  
Analysis Platform

AbstractMechanical forces are integral to a wide range of cellular processes including migration, differentiation and tissue morphogenesis; however, it has proved challenging to directly measure strain at high spatial resolution and with minimal tissue perturbation. Here, we fabricated, calibrated, and tested a fibronectin (FN)-based nanomechanical biosensor (NMBS) that can be applied to cells and tissues to measure the magnitude, direction, and dynamics of strain from subcellular to tissue length-scales. The NMBS is a fluorescently-labeled, ultrathin square lattice FN mesh with spatial resolution tailored by adjusting the width and spacing of the lattice fibers from 2-100 µm. Time-lapse 3D confocal imaging of the NMBS demonstrated strain tracking in 2D and 3D following mechanical deformation of known materials and was validated with finite element modeling. Imaging and 3D analysis of the NMBS applied to single cells, cell monolayers, and Drosophila ovarioles demonstrated the ability to dynamically track microscopic tensile and compressive strains in various biological applications with minimal tissue perturbation. This fabrication and analysis platform serves as a novel tool for studying cells, tissues, and more complex systems where forces guide structure and function.

scholarly journals Multiplexed dynamic imaging of genomic loci in single cells by combined CRISPR imaging and DNA sequential FISH

2017 ◽  
Author(s):  
Yodai Takei ◽  
Sheel Shah ◽  
Sho Harvey ◽  
Lei S. Qi ◽  
Long Cai
Keyword(s):  
Single Cells ◽  
Embryonic Stem ◽  
Dynamic Imaging ◽  
Live Cells ◽  
Chromosome Dynamics ◽  
Cellular Processes ◽  
Sequential Fish ◽  
Telomere Dynamics ◽  
Subtelomeric Regions

ABSTRACTVisualization of chromosome dynamics allows the investigation of spatiotemporal chromatin organization and its role in gene regulation and other cellular processes. However, current approaches to label multiple genomic loci in live cells have a fundamental limitation in the number of loci that can be labelled and uniquely identified. Here we describe an approach we call “track first and identify later” for multiplexed visualization of chromosome dynamics by combining two techniques: CRISPR labeling and DNA sequential fluorescence in situ hybridization (DNA seqFISH). Our approach first labels and tracks chromosomal loci in live cells with the CRISPR system, then barcodes those loci by DNA seqFISH in fixed cells and resolves their identities. We demonstrate our approach by tracking telomere dynamics, identifying 12 unique subtelomeric regions with variable detection efficiencies, and tracking back the telomere dynamics of respective chromosomes in mouse embryonic stem cells.

Sign in / Sign up

Export Citation Format

Share Document