CRISPR-mediated live imaging of genome editing and transcription

Science ◽  
2019 ◽  
Vol 365 (6459) ◽  
pp. 1301-1305 ◽  
Author(s):  
Haifeng Wang ◽  
Muneaki Nakamura ◽  
Timothy R. Abbott ◽  
Dehua Zhao ◽  
Kaiwen Luo ◽  
...  
Keyword(s):  
Real Time ◽  
Genome Editing ◽  
Single Cells ◽  
Cell Types ◽  
Live Imaging ◽  
Dna Double Strand Breaks ◽  
Chromosomal Disorders ◽  
Dna And Rna ◽  
Multiple Loci ◽  
Patau Syndrome

We report a robust, versatile approach called CRISPR live-cell fluorescent in situ hybridization (LiveFISH) using fluorescent oligonucleotides for genome tracking in a broad range of cell types, including primary cells. An intrinsic stability switch of CRISPR guide RNAs enables LiveFISH to accurately detect chromosomal disorders such as Patau syndrome in prenatal amniotic fluid cells and track multiple loci in human T lymphocytes. In addition, LiveFISH tracks the real-time movement of DNA double-strand breaks induced by CRISPR-Cas9–mediated editing and consequent chromosome translocations. Finally, by combining Cas9 and Cas13 systems, LiveFISH allows for simultaneous visualization of genomic DNA and RNA transcripts in living cells. The LiveFISH approach enables real-time live imaging of DNA and RNA during genome editing, transcription, and rearrangements in single cells.

scholarly journals Temporal-Spatial Visualization of Endogenous Chromosome Rearrangements in Living Cells

2019 ◽  
Author(s):  
Haifeng Wang ◽  
Muneaki Nakamura ◽  
Dehua Zhao ◽  
Cindy M Nguyen ◽  
Cordelia Yu ◽  
...  
Keyword(s):  
Real Time ◽  
Gene Editing ◽  
Genome Rearrangement ◽  
Cell Types ◽  
Living Cells ◽  
Primary Cells ◽  
Chromosomal Disorders ◽  
Time Dynamics ◽  
Chromosome Translocations ◽  
Patau Syndrome

AbstractVisualizing the real-time dynamics of genome rearrangement in single living cells is core to studying genomics and diagnostics. Here, we report a robust, versatile approach named CRISPR Live-cell fluorescent in situhybridization (LiveFISH) for multi-locus genome tracking and cytogenetic detection in a broad variety of cell types including primary cells. LiveFISH utilizes an intrinsic stability switch of CRISPR guide RNAs, which enables efficient and accurate detection of chromosomal disorders such as Patau Syndrome in prenatal amniotic fluid cells and allows multi-locus tracking in human T lymphocytes. Using LiveFISH, we are able to detect and track real-time spatiotemporal dynamics of non-homologous endogenous chromosome translocations induced by gene editing. This new approach enables FISH imaging in living primary cells, which can provide useful insights into the spatiotemporal changes of genome organization and rearrangements in normal and diseased primary cells and will enable fast cytogenetic visualization of various gene-editing associated chromosomal translocations.

scholarly journals Multi-omic profiling of transcriptome and DNA methylome in single nuclei with molecular partitioning

2018 ◽  
Author(s):  
Chongyuan Luo ◽  
Hanqing Liu ◽  
Bang-An Wang ◽  
Anna Bartlett ◽  
Angeline Rivkin ◽  
...  
Keyword(s):  
Single Cell ◽  
Single Cells ◽  
Cell Types ◽  
Cell Type ◽  
Data Types ◽  
Rna Molecules ◽  
Dna And Rna ◽  
Multiple Data ◽  
Mammalian Tissues ◽  
Single Nucleus

AbstractSingle-cell transcriptomic and epigenomic analyses provide powerful strategies for unbiased determination of cell types in mammalian tissues. Although previous studies have identified cell types using individual molecular signatures, the generation of consensus cell type classification requires the integration of multiple data types. Most existing single-cell techniques can only make one type of molecular measurement. Here we describe single-nucleus methylcytosine and transcriptome sequencing (snmCT-seq), a multi-omic method that requires no physical separation of DNA and RNA molecules. We demonstrated that snmCT-seq profiles generated from single cells or nuclei robustly distinguish human cell types and accurately measures cytosine DNA methylation and gene expression signatures of each cell type.

Live imaging of cellular dynamics using a multi-imaging vector in single cells

2014 ◽  
Vol 50 (73) ◽  
pp. 10734-10736 ◽  
Author(s):  
Kyoungsook Park ◽  
Jinyoung Jeong ◽  
Bong Hyun Chung
Keyword(s):  
Real Time ◽  
Single Cells ◽  
Live Imaging ◽  
Vector System ◽  
Real Time Monitoring ◽  
Cellular Dynamics

A multi-imaging vector system based on 2A peptides is developed for real-time monitoring of cellular dynamics.

Novel Innate Immune Functions Revealed by Dynamic, Real-Time Live Imaging of Bacterial Infections

2010 ◽  
Vol 30 (2) ◽  
pp. 107-117 ◽  
Author(s):  
Keira Melican ◽  
Jorrit Boekel ◽  
Monica Ryden-Aulin ◽  
Agneta Richter-Dahlfors
Keyword(s):  
Real Time ◽  
Bacterial Infections ◽  
Live Imaging ◽  
Innate Immune ◽  
Immune Functions

scholarly journals The landscape of alternative polyadenylation in single cells of the developing mouse embryo

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Vikram Agarwal ◽  
Sereno Lopez-Darwin ◽  
David R. Kelley ◽  
Jay Shendure
Keyword(s):  
Rna Binding ◽  
Developmental Stages ◽  
Single Cells ◽  
Neuronal Cell ◽  
Alternative Polyadenylation ◽  
Cell Types ◽  
Untranslated Regions ◽  
Mammalian Development ◽  
Translation Rate ◽  
Dynamic Landscape

Abstract3′ untranslated regions (3′ UTRs) post-transcriptionally regulate mRNA stability, localization, and translation rate. While 3′-UTR isoforms have been globally quantified in limited cell types using bulk measurements, their differential usage among cell types during mammalian development remains poorly characterized. In this study, we examine a dataset comprising ~2 million nuclei spanning E9.5–E13.5 of mouse embryonic development to quantify transcriptome-wide changes in alternative polyadenylation (APA). We observe a global lengthening of 3′ UTRs across embryonic stages in all cell types, although we detect shorter 3′ UTRs in hematopoietic lineages and longer 3′ UTRs in neuronal cell types within each stage. An analysis of RNA-binding protein (RBP) dynamics identifies ELAV-like family members, which are concomitantly induced in neuronal lineages and developmental stages experiencing 3′-UTR lengthening, as putative regulators of APA. By measuring 3′-UTR isoforms in an expansive single cell dataset, our work provides a transcriptome-wide and organism-wide map of the dynamic landscape of alternative polyadenylation during mammalian organogenesis.

scholarly journals Dramatic nucleolar dispersion in the salivary gland of Schwenkfeldina sp. (Diptera: Sciaridae)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
José Mariano Amabis ◽  
Eduardo Gorab
Keyword(s):  
Salivary Gland ◽  
Transcriptional Activity ◽  
Relative Proportion ◽  
Extreme Case ◽  
Cell Types ◽  
Chromosome Length ◽  
Chromosomal Distribution ◽  
Dna And Rna ◽  
Polytene Nuclei ◽  
Chromosome Regions

AbstractMicronucleoli are among the structures composing the peculiar scenario of the nucleolus in salivary gland nuclei of dipterans representative of Sciaridae. Micronucleolar bodies contain ribosomal DNA and RNA, are transcriptionally active and may appear free in the nucleoplasm or associated with specific chromosome regions in salivary gland nuclei. This report deals with an extreme case of nucleolar fragmentation/dispersion detected in the salivary gland of Schwenkfeldina sp. Such a phenomenon in this species was found to be restricted to cell types undergoing polyteny and seems to be differentially controlled according to the cell type. Furthermore, transcriptional activity was detected in virtually all the micronucleolar bodies generated in the salivary gland. The relative proportion of the rDNA in polytene and diploid tissues showed that rDNA under-replication did not occur in polytene nuclei suggesting that the nucleolar and concomitant rDNA dispersion in Schwenkfeldina sp. may reflect a previously hypothesised process in order to counterbalance the rDNA loss due to the under-replication. The chromosomal distribution of epigenetic markers for the heterochromatin agreed with early cytological observations in this species suggesting that heterochromatin is spread throughout the chromosome length of Schwenkfeldina sp. A comparison made with results from another sciarid species argues for a role played by the heterochromatin in the establishment of the rDNA topology in polytene nuclei of Sciaridae.

Metabolic modulation of hexokinase association with mitochondria in living smooth muscle cells

1996 ◽  
Vol 270 (2) ◽  
pp. C488-C499 ◽  
Author(s):  
R. M. Lynch ◽  
W. Carrington ◽  
K. E. Fogarty ◽  
F. S. Fay
Keyword(s):  
Smooth Muscle ◽  
Smooth Muscle Cells ◽  
Energy State ◽  
Single Cells ◽  
Inverse Correlation ◽  
Muscle Cells ◽  
Cell Types ◽  
Differential Sensitivity ◽  
Similar Distribution ◽  
Apparent Difference

Hexokinase isoform I binds to mitochondria of many cell types. It has been hypothesized that this association is regulated by changes in the concentrations of specific cellular metabolites. To study the distribution of hexokinase in living cells, fluorophore-labeled functional hexokinase I was prepared. After microinjection into A7r5 smooth muscle cells, hexokinase localized to distinct structures identified as mitochondria. The endogenous hexokinase demonstrated a similar distribution with the use of immunocytochemistry. 2-Deoxyglucose elicited an increase in glucose 6-phosphate (G-6-P) and a decrease in ATP levels and diminished hexokinase binding to mitochondria in single cells. 3-O-methylglucose elicited slowly developing decreases in all three parameters. In contrast, cyanide elicited a rapid decrease in both ATP and hexokinase binding. Analyses of changes in metabolite levels and hexokinase binding indicate a positive correlation between binding and cell energy state as monitored by ATP. On the other hand, only in the presence of 2-deoxyglucose was the predicted inverse correlation between binding and G-6-P observed. Unlike the relatively large changes in distribution observed with the fluorescent-injected hexokinase, cyanide caused only a small decrease in the localization of endogenous hexokinase with mitochondria. These findings suggest that changes in the concentrations of specific metabolites can alter the binding of hexokinase I to specific sites on mitochondria. Moreover, the apparent difference in sensitivity of injected and endogenous hexokinase to changes in metabolites may reflect the presence of at least two classes of binding mechanisms for hexokinase, with differential sensitivity to metabolites.

scholarly journals CRISPR-Cas9 delivery to hard-to-transfect cells via membrane deformation

2015 ◽  
Vol 1 (7) ◽  
pp. e1500454 ◽  
Author(s):  
Xin Han ◽  
Zongbin Liu ◽  
Myeong chan Jo ◽  
Kai Zhang ◽  
Ying Li ◽  
...  
Keyword(s):  
Genome Editing ◽  
Function Analysis ◽  
Embryonic Stem ◽  
Cell Types ◽  
Disease Genes ◽  
Deformation Method ◽  
Targeting Therapy ◽  
Membrane Deformation ◽  
Guide Rna ◽  
Different Cell Types

The CRISPR (clustered regularly interspaced short palindromic repeats)–Cas (CRISPR-associated) nuclease system represents an efficient tool for genome editing and gene function analysis. It consists of two components: single-guide RNA (sgRNA) and the enzyme Cas9. Typical sgRNA and Cas9 intracellular delivery techniques are limited by their reliance on cell type and exogenous materials as well as their toxic effects on cells (for example, electroporation). We introduce and optimize a microfluidic membrane deformation method to deliver sgRNA and Cas9 into different cell types and achieve successful genome editing. This approach uses rapid cell mechanical deformation to generate transient membrane holes to enable delivery of biomaterials in the medium. We achieved high delivery efficiency of different macromolecules into different cell types, including hard-to-transfect lymphoma cells and embryonic stem cells, while maintaining high cell viability. With the advantages of broad applicability across different cell types, particularly hard-to-transfect cells, and flexibility of application, this method could potentially enable new avenues of biomedical research and gene targeting therapy such as mutation correction of disease genes through combination of the CRISPR-Cas9–mediated knockin system.

scholarly journals HiCImpute: A Bayesian Hierarchical Model for Identifying Structural Zeros and Enhancing Single Cell Hi-C Data.

2021 ◽  
Author(s):  
Qing Xie ◽  
Chengong Han ◽  
Victor Jin ◽  
Shili Lin
Keyword(s):  
Quality Improvement ◽  
Data Quality ◽  
Single Cell ◽  
Single Cells ◽  
High Sensitivity ◽  
Real Data ◽  
Cell Types ◽  
Sequencing Depth ◽  
2D Data ◽  
Structural Zeros

Single cell Hi-C techniques enable one to study cell to cell variability in chromatin interactions. However, single cell Hi-C (scHi-C) data suffer severely from sparsity, that is, the existence of excess zeros due to insufficient sequencing depth. Complicate things further is the fact that not all zeros are created equal, as some are due to loci truly not interacting because of the underlying biological mechanism (structural zeros), whereas others are indeed due to insufficient sequencing depth (sampling zeros), especially for loci that interact infrequently. Differentiating between structural zeros and sampling zeros is important since correct inference would improve downstream analyses such as clustering and discovery of subtypes. Nevertheless, distinguishing between these two types of zeros has received little attention in the single cell Hi-C literature, where the issue of sparsity has been addressed mainly as a data quality improvement problem. To fill this gap, in this paper, we propose HiCImpute, a Bayesian hierarchy model that goes beyond data quality improvement by also identifying observed zeros that are in fact structural zeros. HiCImpute takes spatial dependencies of scHi-C 2D data structure into account while also borrowing information from similar single cells and bulk data, when such are available. Through an extensive set of analyses of synthetic and real data, we demonstrate the ability of HiCImpute for identifying structural zeros with high sensitivity, and for accurate imputation of dropout values in sampling zeros. Downstream analyses using data improved from HiCImpute yielded much more accurate clustering of cell types compared to using observed data or data improved by several comparison methods. Most significantly, HiCImpute-improved data has led to the identification of subtypes within each of the excitatory neuronal cells of L4 and L5 in the prefrontal cortex.

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