All-in-One CRISPR-Cas9/FokI-dCas9 Vector-Mediated Multiplex Genome Engineering in Cultured Cells

2016 ◽  
pp. 41-56 ◽  
Author(s):  
Tetsushi Sakuma ◽  
Takuya Sakamoto ◽  
Takashi Yamamoto
Keyword(s):  
Genome Engineering ◽  
Cultured Cells

scholarly journals A genome engineering resource to uncover principles of cellular organization and tissue architecture by lipid signalling

2020 ◽  
Author(s):  
Deepti Trivedi ◽  
Vinitha CM ◽  
Karishma Bisht ◽  
Vishnu Janardan ◽  
Awadhesh Pandit ◽  
...  
Keyword(s):  
Human Disease ◽  
Genome Engineering ◽  
Cultured Cells ◽  
Cellular Organization ◽  
Cellular Processes ◽  
Lipid Signalling ◽  
Disease Biology ◽  
A Genome ◽  
Biochemical Analyses

SummaryPhosphoinositides (PI) are key regulators of cellular organization in eukaryotes and genes that tune PI signalling are implicated in human disease mechanisms. Biochemical analyses and studies in cultured cells have identified a large number of proteins that can mediate PI signalling. However, the role of such proteins in regulating cellular processes in vivo and development in metazoans remains to be understood. Here we describe a set of CRISPR based genome engineering tools that allow the manipulation of each of these proteins with spatial and temporal control during metazoan development. We demonstrate the use of these reagents to deplete a set of 103 proteins individually in the Drosophila eye and identify several new molecules that control eye development. Our work demonstrates the power of this resource in uncovering the molecular basis of tissue homeostasis during normal development and in human disease biology.

scholarly journals Precise genome engineering inDrosophilausing prime editing

2020 ◽  
Vol 118 (1) ◽  
pp. e2021996118
Author(s):  
Justin A. Bosch ◽  
Gabriel Birchak ◽  
Norbert Perrimon
Keyword(s):  
Gene Function ◽  
Mammalian Cells ◽  
Genome Engineering ◽  
Cultured Cells ◽  
Germ Line ◽  
Point Mutations ◽  
Model Organism ◽  
Model Organisms ◽  
Marker Genes ◽  
Germ Line Transmission

Precise genome editing is a valuable tool to study gene function in model organisms. Prime editing, a precise editing system developed in mammalian cells, does not require double-strand breaks or donor DNA and has low off-target effects. Here, we applied prime editing for the model organismDrosophila melanogasterand developed conditions for optimal editing. By expressing prime editing components in cultured cells or somatic cells of transgenic flies, we precisely introduce premature stop codons in three classical visible marker genes,ebony,white, andforked. Furthermore, by restricting editing to germ cells, we demonstrate efficient germ-line transmission of a precise edit inebonyto 36% of progeny. Our results suggest that prime editing is a useful system inDrosophilato study gene function, such as engineering precise point mutations, deletions, or epitope tags.

scholarly journals Microhomology-mediated end-joining-dependent integration of donor DNA in cells and animals using TALENs and CRISPR/Cas9

2014 ◽  
Vol 5 (1) ◽  
Author(s):  
Shota Nakade ◽  
Takuya Tsubota ◽  
Yuto Sakane ◽  
Satoshi Kume ◽  
Naoaki Sakamoto ◽  
...  
Keyword(s):  
Genome Engineering ◽  
Cultured Cells ◽  
Human Cells ◽  
Transcription Activator ◽  
End Joining ◽  
Precise Integration ◽  
Target Chromosome ◽  
Efficient Integration ◽  
Programmable Nucleases ◽  
Plasmid Backbone

Abstract Genome engineering using programmable nucleases enables homologous recombination (HR)-mediated gene knock-in. However, the labour used to construct targeting vectors containing homology arms and difficulties in inducing HR in some cell type and organisms represent technical hurdles for the application of HR-mediated knock-in technology. Here, we introduce an alternative strategy for gene knock-in using transcription activator-like effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) mediated by microhomology-mediated end-joining, termed the PITCh (Precise Integration into Target Chromosome) system. TALEN-mediated PITCh, termed TAL-PITCh, enables efficient integration of exogenous donor DNA in human cells and animals, including silkworms and frogs. We further demonstrate that CRISPR/Cas9-mediated PITCh, termed CRIS-PITCh, can be applied in human cells without carrying the plasmid backbone sequence. Thus, our PITCh-ing strategies will be useful for a variety of applications, not only in cultured cells, but also in various organisms, including invertebrates and vertebrates.

scholarly journals Precise genome engineering in Drosophila using prime editing

2020 ◽  
Author(s):  
Justin A. Bosch ◽  
Gabriel Birchak ◽  
Norbert Perrimon
Keyword(s):  
Gene Function ◽  
Mammalian Cells ◽  
Genome Engineering ◽  
Cultured Cells ◽  
Germ Line ◽  
Point Mutations ◽  
Model Organism ◽  
Model Organisms ◽  
Marker Genes ◽  
Germ Line Transmission

AbstractPrecise genome editing is a valuable tool to study gene function in model organisms. Prime editing, a precise editing system developed in mammalian cells, does not require double strand breaks or donor DNA and has low off-target effects. Here, we applied prime editing for the model organism Drosophila melanogaster and developed conditions for optimal editing. By expressing prime editing components in cultured cells or somatic cells of transgenic flies, we precisely installed premature stop codons in three classical visible marker genes, ebony, white, and forked. Furthermore, by restricting editing to germ cells, we demonstrate efficient germ line transmission of a precise edit in ebony to ~50% of progeny. Our results suggest that prime editing is a useful system in Drosophila to study gene function, such as engineering precise point mutations, deletions, or epitope tags.

scholarly journals A genome engineering resource to uncover principles of cellular organization and tissue architecture by lipid signaling

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Deepti Trivedi ◽  
Vinitha CM ◽  
Karishma Bisht ◽  
Vishnu Janardan ◽  
Awadhesh Pandit ◽  
...  
Keyword(s):  
Human Disease ◽  
Genome Engineering ◽  
Cultured Cells ◽  
Cellular Organization ◽  
Cellular Processes ◽  
Disease Biology ◽  
A Genome ◽  
Biochemical Analyses

Phosphoinositides (PI) are key regulators of cellular organization in eukaryotes and genes that tune PI signaling are implicated in human disease mechanisms. Biochemical analyses and studies in cultured cells have identified a large number of proteins that can mediate PI signaling. However, the role of such proteins in regulating cellular processes in vivo and development in metazoans remains to be understood. Here, we describe a set of CRISPR-based genome engineering tools that allow the manipulation of each of these proteins with spatial and temporal control during metazoan development. We demonstrate the use of these reagents to deplete a set of 103 proteins individually in the Drosophila eye and identify several new molecules that control eye development. Our work demonstrates the power of this resource in uncovering the molecular basis of tissue homeostasis during normal development and in human disease biology.

scholarly journals CRISPR delivery particles for developing therapeutic strategies in metabolic disease

2018 ◽  
Author(s):  
Yuefei Shen ◽  
Jessica L. Cohen ◽  
Sarah M. Nicoloro ◽  
Mark Kelly ◽  
Batuhan Yenilmez ◽  
...  
Keyword(s):  
Metabolic Disease ◽  
Therapeutic Strategy ◽  
Genome Engineering ◽  
Gene Deletion ◽  
Fluorescent Protein ◽  
Cultured Cells ◽  
Adaptive Immune System ◽  
Amphipathic Peptide ◽  
Cas9 Protein

ABSTRACTRNA-guided engineered nucleases derived from a prokaryotic adaptive immune system known as CRISPR-Cas represent a promising platform for gene deletion and editing. As a therapeutic approach, direct delivery of Cas9 protein and guide RNA could circumvent the safety problems associated with plasmid delivery and therefore represents an attractive tool for genome engineering. Gene deletion or editing in adipose tissue to enhance its energy expenditure, fat oxidation and secretion of bioactive factors through a “browning” process presents a potential therapeutic strategy to alleviate metabolic disease. Here, we developed novel CRISPR delivery particles, denoted CriPs, composed of nano-size complexes of Cas9 protein and single guide (sg)RNA, coated with an amphipathic peptide called Endo-Porter that mediates entry into cells. Efficient CRISPR-Cas9 mediated gene deletion of ectopically expressed Green fluorescent protein (GFP) by CriPs was achieved in multiple cell types including a macrophage cell line, primary macrophages and primary pre-adipocytes. Significant GFP loss was also observed in peritoneal exudate cells with minimum systemic toxicity in GFP expressing mice following intraperitoneal injection of CriPs containing sgRNA targeting Gfp. Furthermore, the disruption of the Nrip1 gene in white adipocytes by CriPs enhanced adipocyte “browning” with a marked increase of UCP1 expression. Deletion of Nrip1 by CriPs did not produce detectable off-target effects. Thus CriPs represent a novel CRISPR delivery system for Cas9 and sgRNA that is effective for ablating targeted gene products in cultured cells and in vivo, and provide a potential therapeutic strategy for metabolic disease.

Ultrastructural Correlations between Clonal Human Tumor Colonies and in Vivo Neoplasms

1982 ◽  
Vol 40 ◽  
pp. 210-211
Author(s):  
M.J. Murphy ◽  
R.R. Price ◽  
J.C. Sloman
Keyword(s):  
Cultured Cells ◽  
Human Tumor ◽  
Cell Type ◽  
Tumor Mass ◽  
Initial Cell ◽  
Cloning Assay ◽  
Human Tumor Cloning ◽  
The Relationship

The in vitro human tumor cloning assay originally described by Salmon and Hamburger has been applied recently to the investigation of differential anti-tumor drug sensitivities over a broad range of human neoplasms. A major problem in the acceptance of this technique has been the question of the relationship between the cultured cells and the original patient tumor, i.e., whether the colonies that develop derive from the neoplasm or from some other cell type within the initial cell population. A study of the ultrastructural morphology of the cultured cells vs. patient tumor has therefore been undertaken to resolve this question. Direct correlation was assured by division of a common tumor mass at surgical resection, one biopsy being fixed for TEM studies, the second being rapidly transported to the laboratory for culture.

Electron Probe Microanalysis of Frozen Hydrated Kidneys, Isolated Cells, and Cultured Cells

1982 ◽  
Vol 40 ◽  
pp. 402-403 ◽  
Author(s):  
Claude Lechene
Keyword(s):  
Liquid Nitrogen ◽  
Electron Probe Microanalysis ◽  
Electron Probe ◽  
Cultured Cells ◽  
Liquid Nitrogen Temperature ◽  
Elemental Content ◽  
Isolated Cells ◽  
Renal Tubular Cells ◽  
Diamond Saw ◽  
Saw Blade

Electron probe microanalysis of frozen hydrated kidneysThe goal of the method is to measure on the same preparation the chemical elemental content of the renal luminal tubular fluid and of the surrounding renal tubular cells. The following method has been developed. Rat kidneys are quenched in solid nitrogen. They are trimmed under liquid nitrogen and mounted in a copper holder using a conductive medium. Under liquid nitrogen, a flat surface is exposed by sawing with a diamond saw blade at constant speed and constant pressure using a custom-built cryosaw. Transfer into the electron probe column (Cameca, MBX) is made using a simple transfer device maintaining the sample under liquid nitrogen in an interlock chamber mounted on the electron probe column. After the liquid nitrogen is evaporated by creating a vacuum, the sample is pushed into the special stage of the instrument. The sample is maintained at close to liquid nitrogen temperature by circulation of liquid nitrogen in the special stage.

The Infection of Cells by Bullet-Shaped Viruses

1969 ◽  
Vol 27 ◽  
pp. 372-373
Author(s):  
Frederick A. Murphy ◽  
Alyne K. Harrison ◽  
Sylvia G. Whitfield
Keyword(s):  
Electron Microscopy ◽  
Physical Properties ◽  
Host Cell ◽  
Thin Section ◽  
Cultured Cells ◽  
Cell Infection ◽  
Thin Section Electron Microscopy ◽  
Section Electron ◽  
Section Electron Microscopy

The bullet-shaped viruses are currently classified together on the basis of similarities in virion morphology and physical properties. Biologically and ecologically the member viruses are extremely diverse. In searching for further bases for making comparisons of these agents, the nature of host cell infection, both in vivo and in cultured cells, has been explored by thin-section electron microscopy.

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