scholarly journals Development of a CRISPR-SaCas9 system for projection- and function-specific gene editing in the rat brain

2020 ◽  
Vol 6 (12) ◽  
pp. eaay6687 ◽  
Author(s):  
Haojie Sun ◽  
Su Fu ◽  
Shuang Cui ◽  
Xiangsha Yin ◽  
Xiaoyan Sun ◽  
...  
Keyword(s):  
Rat Brain ◽  
Gene Editing ◽  
High Efficiency ◽  
Protein A ◽  
Cell Types ◽  
Cell Labeling ◽  
Specific Gene ◽  
Creb Binding Protein ◽  
A Genome ◽  
And Function

A genome editing technique based on the clustered regularly interspaced short palindromic repeats (CRISPR)–associated endonuclease Cas9 enables efficient modification of genes in various cell types, including neurons. However, neuronal ensembles even in the same brain region are not anatomically or functionally uniform but divide into distinct subpopulations. Such heterogeneity requires gene editing in specific neuronal populations. We developed a CRISPR-SaCas9 system–based technique, and its combined application with anterograde/retrograde AAV vectors and activity-dependent cell-labeling techniques achieved projection- and function-specific gene editing in the rat brain. As a proof-of-principle application, we knocked down the cbp (CREB-binding protein), a sample target gene, in specific neuronal subpopulations in the medial prefrontal cortex, and demonstrated the significance of the projection- and function-specific CRISPR-SaCas9 system in revealing neuronal and circuit basis of memory. The high efficiency and specificity of our projection- and function-specific CRISPR-SaCas9 system could be widely applied in neural circuitry studies.

scholarly journals FLAMs: A self-replicating ex vivo model of alveolar macrophages for functional genetic studies

2021 ◽  
Author(s):  
Sean Thomas ◽  
Kathryn Wierenga ◽  
James Pestka ◽  
Andrew Olive
Keyword(s):  
Alveolar Macrophages ◽  
Ex Vivo ◽  
Fetal Liver ◽  
Expression Profiles ◽  
Surface Expression ◽  
Specific Gene ◽  
Ex Vivo Model ◽  
A Genome ◽  
Underlying Mechanisms ◽  
And Function

Alveolar macrophages (AMs) are tissue resident cells in the lungs derived from the fetal liver that maintain lung homeostasis and respond to inhaled stimuli. While the importance of AMs is undisputed, they remain refractory to standard experimental approaches and high-throughput functional genetics as they are challenging to isolate and rapidly lose AM properties in standard culture. This limitation hinders our understanding of key regulatory mechanisms that control AM maintenance and function. Here, we describe the development of a new model, fetal liver-derived alveolar-like macrophages (FLAMs), which maintains cellular morphologies, expression profiles, and functional mechanisms similar to murine AMs. FLAMs combine treatment with two key cytokines for AM maintenance, GM-CSF and TGFβ. We leveraged the long-term stability of FLAMs to develop functional genetic tools using CRISPR-Cas9-mediated gene editing. Targeted editing confirmed the role of AM-specific gene Marco and the IL-1 receptor Il1r1 in modulating the AM response to crystalline silica. Furthermore, a genome-wide knockout library using FLAMs identified novel genes required for surface expression of the AM marker Siglec-F, most notably those related to the peroxisome. Taken together, our results suggest that FLAMs are a stable, self-replicating model of AM function that enables previously impossible global genetic approaches to define the underlying mechanisms of AM maintenance and function.

scholarly journals Integrated computational and experimental identification of p53, KRAS and VHL mutant selection associated with CRISPR-Cas9 editing

2018 ◽  
Author(s):  
Sanju Sinha ◽  
Karina Barbosa Guerra ◽  
Kuoyuan Cheng ◽  
Mark DM Leiserson ◽  
David M Wilson ◽  
...  
Keyword(s):  
Gene Editing ◽  
Mutant Cell ◽  
Cell Types ◽  
Driver Mutations ◽  
Mutant Selection ◽  
Cancer Driver ◽  
Genome Wide ◽  
A Genome ◽  
Induced Changes ◽  
Different Cell Types

AbstractRecent studies have reported that CRISPR-Cas9 gene editing induces a p53-dependent DNA damage response in primary cells, which may select for cells with oncogenic p53 mutations11,12. It is unclear whether these CRISPR-induced changes are applicable to different cell types, and whether CRISPR gene editing may select for other oncogenic mutations. Addressing these questions, we analyzed genome-wide CRISPR and RNAi screens to systematically chart the mutation selection potential of CRISPR knockouts across the whole exome. Our analysis suggests that CRISPR gene editing can select for mutants of KRAS and VHL, at a level comparable to that reported for p53. These predictions were further validated in a genome-wide manner by analyzing independent CRISPR screens and patients’ tumor data. Finally, we performed a new set of pooled and arrayed CRISPR screens to evaluate the competition between CRISPR-edited isogenic p53 WT and mutant cell lines, which further validated our predictions. In summary, our study systematically charts and points to the potential selection of specific cancer driver mutations during CRISPR-Cas9 gene editing.

scholarly journals Thoc1 Deficiency Compromises Gene Expression Necessary for Normal Testis Development in the Mouse

2009 ◽  
Vol 29 (10) ◽  
pp. 2794-2803 ◽  
Author(s):  
Xiaoling Wang ◽  
Meenalakshmi Chinnam ◽  
Jianmin Wang ◽  
Yanqing Wang ◽  
Xiaojing Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Polymerase Ii ◽  
Rna Processing ◽  
Cell Types ◽  
Specific Gene ◽  
Mammalian Development ◽  
Expression Of Genes ◽  
Normal Differentiation ◽  
And Function

ABSTRACT Accumulating evidence suggests that regulation of RNA processing through an RNP-driven mechanism is important for coordinated gene expression. This hypothesis predicts that defects in RNP biogenesis will adversely affect the elaboration of specific gene expression programs. To explore the role of RNP biogenesis on mammalian development, we have characterized the phenotype of mice hypomorphic for Thoc1. Thoc1 encodes an essential component of the evolutionarily conserved TREX complex. TREX accompanies the elongating RNA polymerase II and facilitates RNP assembly and recruitment of RNA processing factors. Hypomorphic Thoc1 mice are viable despite significantly reduced Thoc1 expression in the tissues examined. While most tissues of Thoc1-deficient mice appear to develop and function normally, gametogenesis is severely compromised. Male infertility is associated with a loss in spermatocyte viability and abnormal endocrine signaling. We suggest that loss of spermatocyte viability is a consequence of defects in the expression of genes required for normal differentiation of cell types within the testes. A number of the genes affected appear to be direct targets for regulation by Thoc1. These findings support the notion that Thoc1-mediated RNP assembly contributes to the coordinated expression of genes necessary for normal differentiation and development in vivo.

scholarly journals Natural variation in stochastic photoreceptor specification and color preference in Drosophila

2017 ◽  
Author(s):  
Caitlin Anderson ◽  
India Reiss ◽  
Cyrus Zhou ◽  
Annie Cho ◽  
Haziq Siddiqi ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Natural Variation ◽  
Genome Wide Association Study ◽  
Vision System ◽  
Cell Types ◽  
Color Preference ◽  
A Genome ◽  
Stochastic Expression ◽  
Fly Eye ◽  
And Function

AbstractEach individual perceives the world in a unique way, but little is known about the genetic basis of variation in sensory perception. Here we investigated natural variation in the development and function of the color vision system of Drosophila. In the fly eye, the random mosaic of color-detecting R7 photoreceptor subtypes is determined by stochastic expression of the transcription factor Spineless (Ss). Individual R7s randomly choose between SsON or SsOFF fates at a ratio of 65:35, resulting in unique patterns but consistent proportions of cell types across genetically identical retinas. In a genome wide association study, we identified a naturally occurring insertion in a regulatory DNA element in the ss gene that lowers the ratio of SsON to SsOFF cells. This change in photoreceptor fates shifts the innate color preference of flies from green to blue. The genetic variant increases the binding affinity for Klumpfuss (Klu), a zinc finger transcriptional repressor that regulates ss expression. Klu is expressed at intermediate levels to determine the normal ratio of SsON to SsOFF cells. Thus, binding site affinity and transcription factor levels are finely tuned to regulate stochastic on/off gene expression, setting the ratio of alternative cell fates and ultimately determining color preference.

scholarly journals A common haplotype lowers PU.1 expression in myeloid cells and delays onset of Alzheimer’s disease

2017 ◽  
Author(s):  
Kuan-lin Huang ◽  
Edoardo Marcora ◽  
Anna A Pimenova ◽  
Antonio F Di Narzo ◽  
Manav Kapoor ◽  
...  
Keyword(s):  
Gene Expression ◽  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Cell Function ◽  
Age At Onset ◽  
Myeloid Cell ◽  
Cell Types ◽  
A Genome ◽  
Monocytes And Macrophages ◽  
And Function

AbstractA genome-wide survival analysis of 14,406 Alzheimer’s disease (AD) cases and 25,849 controls identified eight previously reported AD risk loci and fourteen novel loci associated with age at onset. LD score regression of 220 cell types implicated regulation of myeloid gene expression in AD risk. In particular, the minor allele of rs1057233 (G), within the previously reported CELF1 AD risk locus, showed association with delayed AD onset and lower expression of SPI1 in monocytes and macrophages. SPI1 encodes PU.1, a transcription factor critical for myeloid cell development and function. AD heritability is enriched within the PU.1 cistrome, implicating a myeloid PU.1 target gene network in AD. Finally, experimentally altered PU.1 levels affect the expression of mouse orthologs of many AD risk genes and the phagocytic activity of mouse microglial cells. Our results suggest that lower SPI1 expression reduces AD risk by regulating myeloid gene expression and cell function.

scholarly journals Recent advancements on use of CRISPR /Cas9 in maize yield and quality improvement

2021 ◽  
Vol 49 (3) ◽  
pp. 12459
Author(s):  
Syed F.A. GILLANI ◽  
Adnan RASHEED ◽  
Yasir MAJEED ◽  
Huma TARIQ ◽  
Peng YUNLING
Keyword(s):  
Quality Improvement ◽  
Gene Editing ◽  
Human Life ◽  
Crop Improvement ◽  
Maize Yield ◽  
Specific Gene ◽  
Crop Species ◽  
Current Application ◽  
Crop Quality ◽  
A Genome

CRISPR/Cas is a genome editing technique, permits accurate improvement of fiscally significant yield species by transgenic and non-transgenic strategies. We have reviewed CRISPR/Cas9 with or without DNA solution design in both maize as samples to redesign tolerance against dry season obstruction, improving seed’s oil contents production, and a gift of herbicide strength. Fundamentally, by exploiting the technologies of CRISPR/Cas9, development with late advances in plant tissue culture can be brought directly into monetarily significant genotypes. The various crop species are major agricultural products and play an indispensable role in sustaining human life. Over a long period, breeders strove to increase crop yield and improve quality through traditional breeding strategies. Today, many breeders have achieved remarkable results using modern molecular technologies. Recently, a new gene-editing system named the clustered regularly interspaced short palindromic repeats CRISPR/Cas9 technology has also improved crop quality. It has become the most popular tool for crop improvement due to its versatility. It has accelerated crop breeding progress by its precision in specific gene editing. This review summarizes the current application of CRISPR/Cas9 technology in crop quality improvement. It includes the modulation in appearance, palatability, nutritional components, and other preferred traits of various crops. Assortment created through such CRISPR/Cas9 engaged advanced raising procedures can be muddled from the regularly happening assortment and appropriately should be quickly open for commercialization.

scholarly journals CRISPR/Cas in genome defense and gene editing

2016 ◽  
Vol 9 (1) ◽  
pp. 68-74
Author(s):  
Svetlana Kryštofová
Keyword(s):  
Gene Editing ◽  
Defense Mechanism ◽  
Cell Types ◽  
Eukaryotic Cells ◽  
Specific Gene ◽  
Gene Expressions ◽  
Site Specific ◽  
Genome Defense ◽  
Engineered Nucleases ◽  
Foreign Dna

AbstractTargeted genome editing using engineered nucleases such as ZFNs and TALENs has been rapidly replaced by the CRISPR/Cas9 (clustered, regulatory interspaced, short palindromic/ CRISPR-associated nuclease) system. CRISPR/Cas9 technology represents a significant improvement enabling a new level of targeting, efficiency and simplicity. Gene editing mediated by CRISPR/Cas9 has been recently used not only in bacteria but in many eukaryotic cells and organisms, from yeasts to mammals. Other modifications of the CRISPR-Cas9 system have been used to introduce heterologous domains to regulate gene expressions or label specific loci in various cell types. The review focuses not only on native CRISPR/Cas systems which evolved in prokaryotes as an endogenous adaptive defense mechanism against foreign DNA attacks, but also on the CRISPR/Cas9 adoption as a powerful tool for site-specific gene modifications in fungi, plants and mammals.

scholarly journals Alteration of STIM1/Orai1-Mediated SOCE in Skeletal Muscle: Impact in Genetic Muscle Diseases and Beyond

Cells ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 2722
Author(s):  
Elena Conte ◽  
Paola Imbrici ◽  
Paola Mantuano ◽  
Maria Coppola ◽  
Giulia Maria Camerino ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Muscle Function ◽  
Molecular Mechanisms ◽  
Therapeutic Potential ◽  
Critical Role ◽  
Protein A ◽  
Cell Types ◽  
Muscle Diseases ◽  
Cellular Processes ◽  
And Function

Intracellular Ca2+ ions represent a signaling mediator that plays a critical role in regulating different muscular cellular processes. Ca2+ homeostasis preservation is essential for maintaining skeletal muscle structure and function. Store-operated Ca2+ entry (SOCE), a Ca2+-entry process activated by depletion of intracellular stores contributing to the regulation of various function in many cell types, is pivotal to ensure a proper Ca2+ homeostasis in muscle fibers. It is coordinated by STIM1, the main Ca2+ sensor located in the sarcoplasmic reticulum, and ORAI1 protein, a Ca2+-permeable channel located on transverse tubules. It is commonly accepted that Ca2+ entry via SOCE has the crucial role in short- and long-term muscle function, regulating and adapting many cellular processes including muscle contractility, postnatal development, myofiber phenotype and plasticity. Lack or mutations of STIM1 and/or Orai1 and the consequent SOCE alteration have been associated with serious consequences for muscle function. Importantly, evidence suggests that SOCE alteration can trigger a change of intracellular Ca2+ signaling in skeletal muscle, participating in the pathogenesis of different progressive muscle diseases such as tubular aggregate myopathy, muscular dystrophy, cachexia, and sarcopenia. This review provides a brief overview of the molecular mechanisms underlying STIM1/Orai1-dependent SOCE in skeletal muscle, focusing on how SOCE alteration could contribute to skeletal muscle wasting disorders and on how SOCE components could represent pharmacological targets with high therapeutic potential.

scholarly journals Genome-wide comparative analysis reveals human- mouse regulatory landscape and evolution

2014 ◽  
Author(s):  
Olgert Denas ◽  
Richard Sandstrom ◽  
Yong Cheng ◽  
Kathryn Beal ◽  
Javier Herrero ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Cell Types ◽  
Regulatory Elements ◽  
The Other ◽  
Specific Gene ◽  
Regulatory Sequence ◽  
Regulatory Sequences ◽  
Species Specific ◽  
And Function ◽  
Human And Mouse

Background: Because species-specific gene expression is driven by species-specific regulation, understanding the relationship between sequence and function of the regulatory regions in different species will help elucidate how differences among species arise. Despite active experimental and computational research, the relationships among sequence, conservation, and function are still poorly understood. Results: We compared transcription factor occupied segments (TFos) for 116 human and 35 mouse TFs in 546 human and 125 mouse cell types and tissues from the Human and the Mouse ENCODE projects. We based the map between human and mouse TFos on a one-to-one nucleotide cross-species mapper, bnMapper, that utilizes whole genome alignments (WGA). Our analysis shows that TFos are under evolutionary constraint, but a substantial portion (25.1% of mouse and 25.85% of human on average) of the TFos does not have a homologous sequence on the other species; this portion varies among cell types and TFs. Furthermore, 47.67% and 57.01% of the homologous TFos sequence shows binding activity on the other species for human and mouse respectively. However, 79.87% and 69.22% is repurposed such that it binds the same TF in different cells or different TFs in the same cells. Remarkably, within the set of TFos not showing conservation of occupancy, the corresponding genome regions in the other species are preferred locations of novel TFos. These events suggest that a substantial amount of functional regulatory sequences is exapted from other biochemically active genomic material. Despite substantial repurposing of TFos, we did not find substantial changes in their predicted target genes, suggesting that CRMs buffer evolutionary events allowing little or no change in the TF – target gene associations. Thus, the small portion of TFos with strictly conserved occupancy underestimates the degree of conservation of regulatory interactions. Conclusion: We mapped regulatory sequences from an extensive number of TFs and cell types between human and mouse. A comparative analysis of this correspondence unveiled the extent of the shared regulatory sequence across TFs and cell types under study. Importantly, a large part of the shared regulatory sequence repurposed on the other species. This sequence, fueled by turnover events, provides a strong case for exaptation in regulatory elements.

Role of PKC isozymes in water transport in toad urinary bladder

1991 ◽  
Vol 49 ◽  
pp. 302-303
Author(s):  
A.J. Mia ◽  
L.X. Oakford ◽  
T. Yorio
Keyword(s):  
Urinary Bladder ◽  
Apical Membrane ◽  
Membrane Surface ◽  
Protein A ◽  
Cell Types ◽  
Leukemic Cells ◽  
Toad Urinary Bladder ◽  
Pkc Isozymes ◽  
Antibody Labeling

Protein kinase C (PKC) isozymes, when activated, are translocated to particulate membrane fractions for transport to the apical membrane surface in a variety of cell types. Evidence of PKC translocation was demonstrated in human megakaryoblastic leukemic cells, and in cardiac myocytes and fibroblasts, using FTTC immunofluorescent antibody labeling techniques. Recently, we reported immunogold localizations of PKC subtypes I and II in toad urinary bladder epithelia, following 60 min stimulation with Mezerein (MZ), a PKC activator, or antidiuretic hormone (ADH). Localization of isozyme subtypes I and n was carried out in separate grids using specific monoclonal antibodies with subsequent labeling with 20nm protein A-gold probes. Each PKC subtype was found to be distributed singularly and in discrete isolated patches in the cytosol as well as in the apical membrane domains. To determine if the PKC isozymes co-localized within the cell, a double immunogold labeling technique using single grids was utilized.

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