In vivo and in vitro knockout system labelled using fluorescent protein via microhomology-mediated end joining

Gene knockout is important for understanding gene function and genetic disorders. The CRISPR/Cas9 system has great potential to achieve this purpose. However, we cannot distinguish visually whether a gene is knocked out and in how many cells it is knocked out among a population of cells. Here, we developed a new system that enables the labelling of knockout cells with fluorescent protein through microhomology-mediated end joining–based knock-in. Using a combination with recombinant adeno-associated virus, we delivered our system into the retina, where the expression of Staphylococcus aureus Cas9 was driven by a retina ganglion cell (RGC)–specific promoter, and knocked out carnitine acetyltransferase (CAT). We evaluated RGCs and revealed that CAT is required for RGC survival. Furthermore, we applied our system to Keap1 and confirmed that Keap1 is not expressed in fluorescently labelled cells. Our system provides a promising framework for cell type–specific genome editing and fluorescent labelling of gene knockout based on knock-in.

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Btbd11 is an inhibitory interneuron specific synaptic scaffolding protein that supports excitatory synapse structure and function

10.1101/2021.11.01.466782 ◽

2021 ◽

Author(s):

Alexei M. Bygrave ◽

Ayesha Sengupta ◽

Ella P. Jackert ◽

Mehroz Ahmed ◽

Beloved Adenuga ◽

...

Keyword(s):

Inhibitory Interneuron ◽

Nmda Receptor Antagonist ◽

Specific Protein ◽

Network Activity ◽

Scaffolding Protein ◽

Inhibitory Interneurons ◽

Cell Type ◽

Cell Type Specific

Synapses in the brain exhibit cell–type–specific differences in basal synaptic transmission and plasticity. Here, we evaluated cell–type–specific differences in the composition of glutamatergic synapses, identifying Btbd11, as an inhibitory interneuron–specific synapse–enriched protein. Btbd11 is highly conserved across species and binds to core postsynaptic proteins including Psd–95. Intriguingly, we show that Btbd11 can undergo liquid–liquid phase separation when expressed with Psd–95, supporting the idea that the glutamatergic post synaptic density in synapses in inhibitory and excitatory neurons exist in a phase separated state. Knockout of Btbd11 from inhibitory interneurons decreased glutamatergic signaling onto parvalbumin–positive interneurons. Further, both in vitro and in vivo, we find that Btbd11 knockout disrupts network activity. At the behavioral level, Btbd11 knockout from interneurons sensitizes mice to pharmacologically induced hyperactivity following NMDA receptor antagonist challenge. Our findings identify a cell–type–specific protein that supports glutamatergic synapse function in inhibitory interneurons–with implication for circuit function and animal behavior.

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Revisiting the role of IRF3 in inflammation and immunity by conditional and specifically targeted gene ablation in mice

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1803936115 ◽

2018 ◽

Vol 115 (20) ◽

pp. 5253-5258 ◽

Cited By ~ 19

Author(s):

Hideyuki Yanai ◽

Shiho Chiba ◽

Sho Hangai ◽

Kohei Kometani ◽

Asuka Inoue ◽

...

Keyword(s):

Immune Cell ◽

Cell Types ◽

Type I ◽

Type I Ifn ◽

Cell Type ◽

Gene Ablation ◽

Cell Type Specific

IFN regulatory factor 3 (IRF3) is a transcription regulator of cellular responses in many cell types that is known to be essential for innate immunity. To confirm IRF3’s broad role in immunity and to more fully discern its role in various cellular subsets, we engineered Irf3-floxed mice to allow for the cell type-specific ablation of Irf3. Analysis of these mice confirmed the general requirement of IRF3 for the evocation of type I IFN responses in vitro and in vivo. Furthermore, immune cell ontogeny and frequencies of immune cell types were unaffected when Irf3 was selectively inactivated in either T cells or B cells in the mice. Interestingly, in a model of lipopolysaccharide-induced septic shock, selective Irf3 deficiency in myeloid cells led to reduced levels of type I IFN in the sera and increased survival of these mice, indicating the myeloid-specific, pathogenic role of the Toll-like receptor 4–IRF3 type I IFN axis in this model of sepsis. Thus, Irf3-floxed mice can serve as useful tool for further exploring the cell type-specific functions of this transcription factor.

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Efficient transduction of green fluorescent protein in spinal cord neurons using adeno-associated virus vectors containing cell type-specific promoters

Gene Therapy ◽

10.1038/sj.gt.3300358 ◽

1997 ◽

Vol 4 (1) ◽

pp. 16-24 ◽

Cited By ~ 212

Author(s):

AL Peel ◽

S Zolotukhin ◽

GW Schrimsher ◽

N Muzyczka ◽

PJ Reier

Keyword(s):

Spinal Cord ◽

Green Fluorescent Protein ◽

Fluorescent Protein ◽

Cell Type ◽

Adeno Associated Virus ◽

Spinal Cord Neurons ◽

Virus Vectors ◽

Cell Type Specific ◽

Green Fluorescent

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The contribution of astrocyte and neuronal Panx1 to seizures is model and brain region dependent

10.1101/2021.01.12.426355 ◽

2021 ◽

Author(s):

Price Obot ◽

Libor Velíšek ◽

Jana Velíšková ◽

Eliana Scemes

Keyword(s):

Brain Region ◽

Power Spectra ◽

Cortical Region ◽

Cell Type ◽

Epileptiform Discharges ◽

Seizure Models ◽

Cell Type Specific ◽

Specific Deletion

AbstractPannexin1 (Panx1) is an ATP release channel expressed in neurons and astrocytes that plays important roles in CNS physiology and pathology. Evidence for the involvement of Panx1 in seizures includes the reduction of epileptiform activity and ictal discharges following Panx1 channel blockade or deletion. However, very little is known about the relative contribution of astrocyte and neuronal Panx1 channels to hyperexcitability. To this end, mice with global and cell type specific deletion of Panx1 were used in one in vivo and two in vitro seizure models. In the low-Mg2+in vitro model, global deletion but not cell-type specific deletion of Panx1 reduced the frequency of epileptiform discharges. This reduced frequency of discharges did not impact the overall power spectra obtained from local field potentials. In the in vitro KA model, in contrast, global or cell type specific deletion of Panx1 did not affect the frequency of discharges, but reduced the overall power spectra. EEG recordings following KA-injection in vivo revealed that although global deletion of Panx1 did not affect the onset of status epilepticus (SE), SE onset was delayed in mice lacking neuronal Panx1 and accelerated in mice lacking astrocyte Panx1. EEG power spectral analysis disclosed a Panx1-dependent cortical region effect; while in the occipital region, overall spectral power was reduced in all three Panx1 genotypes; in the frontal cortex, the overall power was not affected by deletion of Panx1. Together, our results show that the contribution of Panx1 to ictal activity is model, cell-type and brain region dependent.

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DeepG4: A deep learning approach to predict cell-type specific active G-quadruplex regions

PLoS Computational Biology ◽

10.1371/journal.pcbi.1009308 ◽

2021 ◽

Vol 17 (8) ◽

pp. e1009308

Author(s):

Vincent Rocher ◽

Matthieu Genais ◽

Elissar Nassereddine ◽

Raphael Mourad

Keyword(s):

Deep Learning ◽

Double Helix ◽

Complex Molecule ◽

Cell Types ◽

Sequence Motif ◽

Cell Type ◽

G Quadruplex ◽

Cell Type Specific

DNA is a complex molecule carrying the instructions an organism needs to develop, live and reproduce. In 1953, Watson and Crick discovered that DNA is composed of two chains forming a double-helix. Later on, other structures of DNA were discovered and shown to play important roles in the cell, in particular G-quadruplex (G4). Following genome sequencing, several bioinformatic algorithms were developed to map G4s in vitro based on a canonical sequence motif, G-richness and G-skewness or alternatively sequence features including k-mers, and more recently machine/deep learning. Recently, new sequencing techniques were developed to map G4s in vitro (G4-seq) and G4s in vivo (G4 ChIP-seq) at few hundred base resolution. Here, we propose a novel convolutional neural network (DeepG4) to map cell-type specific active G4 regions (e.g. regions within which G4s form both in vitro and in vivo). DeepG4 is very accurate to predict active G4 regions in different cell types. Moreover, DeepG4 identifies key DNA motifs that are predictive of G4 region activity. We found that such motifs do not follow a very flexible sequence pattern as current algorithms seek for. Instead, active G4 regions are determined by numerous specific motifs. Moreover, among those motifs, we identified known transcription factors (TFs) which could play important roles in G4 activity by contributing either directly to G4 structures themselves or indirectly by participating in G4 formation in the vicinity. In addition, we used DeepG4 to predict active G4 regions in a large number of tissues and cancers, thereby providing a comprehensive resource for researchers. Availability: https://github.com/morphos30/DeepG4.

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Induction of Golli-MBP Expression in CNS Macrophages During Acute LPS-Induced CNS Inflammation and Experimental Autoimmune Encephalomyelitis (EAE)

The Scientific World JOURNAL ◽

10.1100/tsw.2007.251 ◽

2007 ◽

Vol 7 ◽

pp. 112-120 ◽

Cited By ~ 4

Author(s):

Tracey L. Papenfuss ◽

J. Cameron Thrash ◽

Patricia E. Danielson ◽

Pamela E. Foye ◽

Brian S. Hllbrush ◽

...

Keyword(s):

Experimental Autoimmune Encephalomyelitis ◽

Cell Type ◽

Autoimmune Encephalomyelitis ◽

Cns Inflammation ◽

Cell Type Specific ◽

Candidate Molecule ◽

Experimental Autoimmune

Microglia are the tissue macrophages of the CNS. Microglial activation coupled with macrophage infiltration is a common feature of many classic neurodegenerative disorders. The absence of cell-type specific markers has confounded and complicated the analysis of cell-type specific contributions toward the onset, progression, and remission of neurodegeneration. Molecular screens comparing gene expression in cultured microglia and macrophages identified Golli-myelin basic protein (MBP) as a candidate molecule enriched in peripheral macrophages.In situhybridization analysis of LPS/IFNg and experimental autoimmune encephalomyelitis (EAE)–induced CNS inflammation revealed that only a subset of CNS macrophages express Golli-MBP. Interestingly, the location and morphology of Golli-MBP+ CNS macrophages differs between these two models of CNS inflammation. These data demonstrate the difficulties of extendingin vitroobservations toin vivobiology and concretely illustrate the complex heterogeneity of macrophage activation states present in region- and stage-specific phases of CNS inflammation. Taken altogether, these are consistent with the emerging picture that the phenotype of CNS macrophages is actively defined by their molecular interactions with the CNS microenvironment.

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Cell-type–specific, multicolor labeling of endogenous proteins with split fluorescent protein tags in Drosophila

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2024690118 ◽

2021 ◽

Vol 118 (23) ◽

pp. e2024690118

Author(s):

Rie Kamiyama ◽

Kota Banzai ◽

Peiwei Liu ◽

Abhijit Marar ◽

Ryo Tamura ◽

...

Keyword(s):

Tandem Repeats ◽

Fluorescent Protein ◽

Protein Localization ◽

Fluorescence Signal ◽

Cell Type ◽

Genomic Locus ◽

Cell Type Specific ◽

Endogenous Proteins ◽

The Impact

The impact of the Drosophila experimental system on studies of modern biology cannot be understated. The ability to tag endogenously expressed proteins is essential to maximize the use of this model organism. Here, we describe a method for labeling endogenous proteins with self-complementing split fluorescent proteins (split FPs) in a cell-type–specific manner in Drosophila. A short fragment of an FP coding sequence is inserted into a specific genomic locus while the remainder of the FP is expressed using an available GAL4 driver line. In consequence, complementation fluorescence allows examination of protein localization in particular cells. Besides, when inserting tandem repeats of the short FP fragment at the same genomic locus, we can substantially enhance the fluorescence signal. The enhanced signal is of great value in live-cell imaging at the subcellular level. We can also accomplish a multicolor labeling system with orthogonal split FPs. However, other orthogonal split FPs do not function for in vivo imaging besides split GFP. Through protein engineering and in vivo functional studies, we report a red split FP that we can use for duplexed visualization of endogenous proteins in intricate Drosophila tissues. Using the two orthogonal split FP systems, we have simultaneously imaged proteins that reside in distinct subsynaptic compartments. Our approach allows us to study the proximity between and localization of multiple proteins endogenously expressed in essentially any cell type in Drosophila.

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Self-complementarity in adeno-associated virus enhances transduction and gene expression in mouse cochlear tissues

PLoS ONE ◽

10.1371/journal.pone.0242599 ◽

2020 ◽

Vol 15 (11) ◽

pp. e0242599

Author(s):

Graham Casey ◽

Charles Askew ◽

Mark A. Brimble ◽

R. Jude Samulski ◽

Andrew M. Davidoff ◽

...

Keyword(s):

Fluorescent Protein ◽

Transduction Efficiency ◽

Sensory Cells ◽

Adeno Associated Virus ◽

Large Numbers ◽

Green Fluorescent ◽

Interest In Research ◽

Tyrphostin 23

Sensorineural hearing loss is one of the most common disabilities worldwide. Such prevalence necessitates effective tools for studying the molecular workings of cochlear cells. One prominent and effective vector for expressing genes of interest in research models is adeno-associated virus (AAV). However, AAV efficacy in transducing cochlear cells can vary for a number of reasons including serotype, species, and methodology, and oftentimes requires high multiplicity of infection which can damage the sensory cells. Reports in other systems suggest multiple approaches can be used to enhance AAV transduction including self-complementary vector design and pharmacological inhibition of degradation. Here we produced AAV to drive green fluorescent protein (GFP) expression in explanted neonatal mouse cochleae. Treatment with eeyarestatin I, tyrphostin 23, or lipofectamine 2000 did not result in increased transduction, however, self-complementary vector design resulted in significantly more GFP positive cells when compared to single-stranded controls. Similarly, self-complementary AAV2 vectors demonstrated enhanced transduction efficiency compared to single stranded AAV2 when injected via the posterior semicircular canal, in vivo. Self-complementary vectors for AAV1, 8, and 9 serotypes also demonstrated robust GFP transduction in cochlear cells in vivo, though these were not directly compared to single stranded vectors. These findings suggest that second-strand synthesis may be a rate limiting step in AAV transduction of cochlear tissues and that self-complementary AAV can be used to effectively target large numbers of cochlear cells in vitro and in vivo.

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