CD-tagging-MS2: detecting allelic expression of endogenous mRNAs and their protein products in single cells

Abstract Discriminating between the mRNA and protein outputs of each of the alleles of an endogenous gene in intact cells, is a difficult task. To examine endogenous transcripts originating from a specific allele, we applied Central Dogma tagging (CD-tagging), which is based on a tag insertion into an endogenous gene by creation of a new exon. Previously, CD-tagging was used to tag endogenous proteins. Here we developed a CD-tagging-MS2 approach in which two tags were inserted in tandem; a fluorescent protein tag in conjunction with the mRNA MS2 tag used for tagging mRNAs in cells. A cell clone library of CD-tagged-MS2 genes was generated, and protein and mRNA distributions were examined and characterized in single cells. Taking advantage of having one allele tagged, we demonstrate how the transcriptional activity of all alleles, tagged and untagged, can be identified using single molecule RNA fluorescence in situ hybridization (smFISH). Allele-specific mRNA expression and localization were quantified under normal and stress conditions. The latter generate cytoplasmic stress granules (SGs) that can store mRNAs, and the distribution of the mRNAs within and outside of the SGs was measured. Altogether, CD-tagging-MS2 is a robust and inexpensive approach for direct simultaneous detection of an endogenous mRNA and its translated protein product in the same cell.

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Visualization of class A GPCR oligomerization by image-based fluorescence fluctuation spectroscopy

10.1101/240903 ◽

2017 ◽

Cited By ~ 3

Author(s):

Ali Isbilir ◽

Jan Möller ◽

Andreas Bock ◽

Ulrike Zabel ◽

Paolo Annibale ◽

...

Keyword(s):

Single Molecule ◽

Metabotropic Glutamate Receptors ◽

Fluorescent Protein ◽

Methodological Approach ◽

Correlation Spectroscopy ◽

Membrane Receptors ◽

Image Correlation ◽

Intact Cells ◽

Class A ◽

Image Correlation Spectroscopy

AbstractG protein-coupled receptors (GPCRs) represent the largest class of cell surface receptors conveying extracellular information into intracellular signals. Many GPCRs have been shown to be able to oligomerize and it is firmly established that Class C GPCRs (e.g. metabotropic glutamate receptors) function as obligate dimers. However, the oligomerization capability of the larger Class A GPCRs (e.g. comprising the β-adrenergic receptors (β-ARs)) is still, despite decades of research, highly debated.Here we assess the oligomerization behavior of three prototypical Class A GPCRs, the β1-ARs, β2-ARs, and muscarinic M2Rs in single, intact cells. We combine two image correlation spectroscopy methods based on molecular brightness, i.e. the analysis of fluorescence fluctuations over space and over time, and thereby provide an assay able to robustly and precisely quantify the degree of oligomerization of GPCRs. In addition, we provide a comparison between two labelling strategies, namely C-terminally-attached fluorescent proteins and N-terminally-attached SNAP-tags, in order to rule out effects arising from potential fluorescent protein-driven oligomerization. The degree of GPCR oligomerization is expressed with respect to a set of previously reported as well as newly established monomeric or dimeric control constructs. Our data reveal that all three prototypical GPRCs studied display, under unstimulated conditions, a prevalently monomeric fingerprint. Only the β2-AR shows a slight degree of oligomerization.From a methodological point of view, our study suggests three key aspects. First, the combination of two image correlation spectroscopy methods allows addressing cells transiently expressing high concentrations of membrane receptors, far from the single molecule regime, at a density where the kinetic equilibrium should favor dimers and higher-order oligomers. Second, our methodological approach, allows to selectively target cell membrane regions devoid of artificial oligomerization hot-spots (such as vesicles). Third, our data suggest that the β1-AR appears to be a superior monomeric control than the widely used membrane protein CD86.Taken together, we suggest that our combined image correlation spectroscopy method is a powerful approach to assess the oligomerization behavior of GPCRs in intact cells at high expression levels.

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Multiplex labeling and manipulation of endogenous neuronal proteins using sequential CRISPR/Cas9 gene editing

10.1101/2022.01.02.474730 ◽

2022 ◽

Author(s):

Wouter J Droogers ◽

Jelmer Willems ◽

Harold D MacGillavry ◽

Arthur PH de Jong

Keyword(s):

Genome Editing ◽

Single Molecule ◽

Time Window ◽

Single Cells ◽

Synaptic Proteins ◽

Flp Recombinase ◽

Neuronal Proteins ◽

Endogenous Proteins ◽

Living Neurons ◽

High Degree

Recent advances in CRISPR/Cas9-mediated knock-in methods enable labeling of individual endogenous proteins with fluorophores, to determine their spatiotemporal expression in intact biological preparations. However, multiplex knock-in methods remain limited, particularly in postmitotic cells, due to a high degree of crosstalk between genome editing events. We present Conditional Activation of Knock-in Expression (CAKE), which delivers efficient, flexible and accurate multiplex genome editing in neurons. CAKE is based on sequential gRNA expression operated by a Cre- or Flp-recombinase to control the time window for genomic integration of each donor sequence, which diminishes crosstalk between genome editing events. Importantly, CAKE is compatible with multiple CRISPR/Cas9 strategies, and we show the utilization of CAKE for co-localization of various endogenous proteins, including synaptic scaffolds, ion channels and neurotransmitter receptor subunits. Knock-in efficacy was highly sensitive to DNA vector amount, while knock-in crosstalk was dependent on the rate of donor DNA integration and timing of Cre activation. We applied CAKE to study the co-distribution of endogenous synaptic proteins using dual-color single-molecule localization microscopy, and we introduced dimerization modules to acutely control synaptic receptor dynamics in living neurons. Taken together, CAKE is a versatile method for multiplex protein labeling, enabling accurate detection, precise localization and acute manipulation of endogenous proteins in single cells.

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Long-term Live Single Cell Quantification of Transcription Factor Dynamics

Blood ◽

10.1182/blood.v128.22.sci-4.sci-4 ◽

2016 ◽

Vol 128 (22) ◽

pp. SCI-4-SCI-4

Author(s):

Timm Schroeder

Keyword(s):

Transcription Factor ◽

Single Cell ◽

Cell Fate ◽

Fluorescent Protein ◽

Conflicts Of Interest ◽

Single Cells ◽

Molecular Control ◽

Endogenous Gene ◽

Stem And Progenitor Cells

Abstract Hematopoiesis is highly complex and dynamic, and consist of large numbers of different cells expressing many molecules. Despite intensive research, many long-standing questions in hematopoiesis research remain disputed. One major reason is the fact that we usually only analyze populations of cells - rather than individual cells - at very few time points of an experiment. Tracking of individual cells would be an extremely powerful approach to improve our understanding of molecular cell fate control. We are therefore developing imaging systems to follow the fate of single cells over many generations. We program new software to help recording and displaying the divisional history, position, properties, interaction, etc. of all individual cells over many generations. In addition, novel microfluidics devices are designed and produced to allow improved observation and manipulation of cells. Our technologies allow continuous long-term quantification of protein expression or activity in living cells. Among other approaches, we generate knock in models expressing transcription factor to fluorescent protein fusions from endogenous gene loci. This enables non-invasive long-term live quantification of transcription factor protein dynamics in single stem and progenitor cells throughout their differentiation. The resulting novel kind of continuous quantitative single cell data is used for the generation and falsification of models describing the molecular control of hematopoietic cell fates. Disclosures No relevant conflicts of interest to declare.

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Simultaneous detection of mRNA and protein in single cells using immunofluorescence-combined single-molecule RNA FISH

BioTechniques ◽

10.2144/000114340 ◽

2015 ◽

Vol 59 (4) ◽

Cited By ~ 23

Author(s):

Jakub Kochan ◽

Mateusz Wawro ◽

Aneta Kasza

Keyword(s):

Single Molecule ◽

Single Cells ◽

Simultaneous Detection ◽

Rna Fish

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Combining single-molecule super-resolved localization microscopy with fluorescence polarization imaging to study cellular processes

10.1101/2021.01.06.425576 ◽

2021 ◽

Author(s):

Jack W Shepherd ◽

Alex L Payne-Dwyer ◽

Mark C Leake

Keyword(s):

Single Molecule ◽

Fluorescence Polarization ◽

Fluorescent Protein ◽

Imaging Modality ◽

Simultaneous Detection ◽

Optical Resolution ◽

Biological Processes ◽

Localization Microscopy ◽

Cellular Processes ◽

Wide Range

AbstractSuper-resolution microscopy has enabled valuable insights into the subcellular, mechanistic details of many different biological processes across a wide range of cell types. Fluorescence polarization spectroscopy tools have also enabled important insights into cellular processes through identifying orientational changes of biological molecules typically at an ensemble level. Here, we combine these two biophysical methodologies in a single home-made instrument to enable the simultaneous detection of orthogonal fluorescence polarization signals from single fluorescent protein molecules used as common reporters on the localization on biomolecules in cellular processes, whose spatial location can be pinpointed to a super-resolved precision better than the diffraction-limited optical resolution. In this small innovation we have adapted a millisecond timescale “Slimfield” microscope used for single-molecule detection to enable spitting of the fluorescence polarization emissions into two separate imaging channels for s- and p- polarization signals that are imaged onto separate halves of the same high sensitivity back-illuminated CMOS camera detector. We applied this fluorescence polarization super-resolved imaging modality to a range of test fluorescent samples relevant to the study of biological processes, including purified monomeric green fluorescent protein (mGFP). Our findings are largely qualitative but demonstrate promise in showing how fluorescence polarization and Slimfield-mediated super-resolved localization microscopy can be combined on the same sample to enable new biological insights.

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Site-Specific Protein Covalent Attachment to Nanotubes and Its Electronic Impact on Single Molecule Function

10.26434/chemrxiv.7798973.v1 ◽

2019 ◽

Author(s):

Adam Beachey ◽

Harley Worthy ◽

William David Jamieson ◽

Suzanne Thomas ◽

Benjamin Bowen ◽

...

Keyword(s):

Single Molecule ◽

Fluorescent Protein ◽

Functional Integration ◽

Attachment Site ◽

Covalent Attachment ◽

Great Promise ◽

Functional Coupling ◽

Phenyl Azide ◽

Electronic Impact ◽

Protein Attachment

<p>Functional integration of proteins with carbon-based nanomaterials such as nanotubes holds great promise in emerging electronic and optoelectronic applications. Control over protein attachment poses a major challenge for consistent and useful device fabrication, especially when utilizing single/few molecule properties. Here, we exploit genetically encoded phenyl azide photochemistry to define the direct covalent attachment of three different proteins, including the fluorescent protein GFP, to carbon nanotube side walls. Single molecule fluorescence revealed that on attachment to SWCNTs GFP’s fluorescence changed in terms of intensity and improved resistance to photobleaching; essentially GFP is fluorescent for much longer on attachment. The site of attachment proved important in terms of electronic impact on GFP function, with the attachment site furthest from the functional center having the larger effect on fluorescence. Our approach provides a versatile and general method for generating intimate protein-CNT hybrid bioconjugates. It can be potentially applied easily to any protein of choice; attachment position and thus interface characteristics with the CNT can easily be changed by simply placing the phenyl azide chemistry at different residues by gene mutagenesis. Thus, our approach will allow consistent construction and modulate functional coupling through changing the protein attachment position.</p>

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Split-wrmScarlet and split-sfGFP: Tools for faster, easier fluorescent l abeling of endogenous proteins in Caenorhabditis elegans

Genetics ◽

10.1093/genetics/iyab014 ◽

2021 ◽

Author(s):

Jérôme Goudeau ◽

Catherine S Sharp ◽

Jonathan Paw ◽

Laura Savy ◽

Manuel D Leonetti ◽

...

Keyword(s):

Fluorescent Protein ◽

Fluorescent Proteins ◽

Fluorescent Labeling ◽

Large Fragment ◽

C Elegans ◽

High Affinity ◽

Red Fluorescent Proteins ◽

Invaluable Tool ◽

Endogenous Proteins ◽

Fluorescent Tags

Abstract We create and share a new red fluorophore, along with a set of strains, reagents and protocols, to make it faster and easier to label endogenous C. elegans proteins with fluorescent tags. CRISPR-mediated fluorescent labeling of C. elegans proteins is an invaluable tool, but it is much more difficult to insert fluorophore-size DNA segments than it is to make small gene edits. In principle, high-affinity asymmetrically split fluorescent proteins solve this problem in C. elegans: the small fragment can quickly and easily be fused to almost any protein of interest, and can be detected wherever the large fragment is expressed and complemented. However, there is currently only one available strain stably expressing the large fragment of a split fluorescent protein, restricting this solution to a single tissue (the germline) in the highly autofluorescent green channel. No available C. elegans lines express unbound large fragments of split red fluorescent proteins, and even state-of-the-art split red fluorescent proteins are dim compared to the canonical split-sfGFP protein. In this study, we engineer a bright, high-affinity new split red fluorophore, split-wrmScarlet. We generate transgenic C. elegans lines to allow easy single-color labeling in muscle or germline cells and dual-color labeling in somatic cells. We also describe a novel expression strategy for the germline, where traditional expression strategies struggle. We validate these strains by targeting split-wrmScarlet to several genes whose products label distinct organelles, and we provide a protocol for easy, cloning-free CRISPR/Cas9 editing. As the collection of split-FP strains for labeling in different tissues or organelles expands, we will post updates at doi.org/10.5281/zenodo.3993663

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SUGAR-seq enables simultaneous detection of glycans, epitopes, and the transcriptome in single cells

Science Advances ◽

10.1126/sciadv.abe3610 ◽

2021 ◽

Vol 7 (8) ◽

pp. eabe3610

Author(s):

Conor J. Kearney ◽

Stephin J. Vervoort ◽

Kelly M. Ramsbottom ◽

Izabela Todorovski ◽

Emily J. Lelliott ◽

...

Keyword(s):

Single Cell ◽

Posttranslational Modification ◽

Cellular Differentiation ◽

Single Cells ◽

Simultaneous Detection ◽

Surface Protein ◽

Rna Seq ◽

Cell Level ◽

Simultaneous Integration ◽

Unique Surface

Multimodal single-cell RNA sequencing enables the precise mapping of transcriptional and phenotypic features of cellular differentiation states but does not allow for simultaneous integration of critical posttranslational modification data. Here, we describe SUrface-protein Glycan And RNA-seq (SUGAR-seq), a method that enables detection and analysis of N-linked glycosylation, extracellular epitopes, and the transcriptome at the single-cell level. Integrated SUGAR-seq and glycoproteome analysis identified tumor-infiltrating T cells with unique surface glycan properties that report their epigenetic and functional state.

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