scholarly journals Prediction of activity of CRISPR-Cpf1 guide RNA via in vivo high-throughput screening

2021 ◽  
Author(s):  
gancheng wang ◽  
dan zhu ◽  
juan li ◽  
junyi wang ◽  
jianzhong xi
Keyword(s):  
Dna Cleavage ◽  
High Throughput Screening ◽  
Large Scale ◽  
Genome Engineering ◽  
Limited Information ◽  
Editing Efficiency ◽  
Guide Rna ◽  
Guide Rnas ◽  
Promising Tool

Background: CRISPR-cpf1 is a single RNA-guided endonuclease system, becoming a promising tool in both prokaryotic and eukaryotic genome engineering. The editing efficiency of Cpf1 based engineering still requires improvements. However, limited information regarding the relationship between guide RNA sequence and on-target activity is available. To address these challenges, we developed a screening platform based on the association of Acidaminococcus sp. Cpf1(AsCpf1) DNA cleavage with cellular lethality. Major results: In total, we measured the activities of 12,544 guide RNAs, and observed a substantial variation of the editing efficiency depending on the design of the sequence. Based on this large-scale dataset, we designed and implemented a comprehensive computational model to predict activities of guide RNAs. Through comparison using simulated and experimental data, our approach outperformed existing algorithms, enabling selection of efficient guide RNAs. Conclusions: We refine on-target design rules and isolate the important sequence features that contribute to DNA cleavage, that is, AH dimers at position1-8 of protospacer promoting Cas12a activity while TK, GB dimer playing an inhibitory role. We validate guide RNA affinities designed by our optimized rules in both E.coli and 293T cells.

scholarly journals Improved sgRNA design in bacteria via genome-wide activity profiling

2018 ◽  
Author(s):  
Jiahui Guo ◽  
Tianmin Wang ◽  
Changge Guan ◽  
Bing Liu ◽  
Cheng Luo ◽  
...  
Keyword(s):  
Dna Cleavage ◽  
Large Scale ◽  
Genome Engineering ◽  
Prediction Models ◽  
Prokaryotic Genome ◽  
Model Organism ◽  
Bacterial Cells ◽  
Highly Active ◽  
Promising Tool ◽  
A Genome

AbstractCRISPR/Cas9 is a promising tool in prokaryotic genome engineering, but its success is limited by the widely varying on-target activity of single guide RNAs (sgRNAs). Based on the association of CRISPR/Cas9-induced DNA cleavage with cellular lethality, we systematically profiled sgRNA activity by co-expressing a genome-scale library (~70,000 sgRNAs) with Cas9 or its specificity-improved mutant in E. coli. Based on this large-scale dataset, we constructed a comprehensive and high-density sgRNA activity map, which enables selecting highly active sgRNAs for any locus across the genome in this model organism. We also identified ‘resistant’ genomic loci with respect to CRISPR/Cas9 activity, notwithstanding the highly accessible DNA in bacterial cells. Moreover, we found that previous sgRNA activity prediction models that were trained on mammalian cell datasets were inadequate when coping with our results, highlighting the key limitations and biases of previous models. We hence developed an integrated algorithm to accurately predict highly effective sgRNAs, aiming to facilitate the design of CRISPR/Cas9-based genome engineering or screenings in bacteria. We also isolated the important sgRNA features that contribute to DNA cleavage and characterized their key differences among wild type Cas9 and its mutant, shedding light on the biophysical mechanisms of the CRISPR/Cas9 system.

scholarly journals Extinction of all infectious HIV in cell culture by the CRISPR-Cas12a system with only a single crRNA

2020 ◽  
Vol 48 (10) ◽  
pp. 5527-5539 ◽  
Author(s):  
Zongliang Gao ◽  
Minghui Fan ◽  
Atze T Das ◽  
Elena Herrera-Carrillo ◽  
Ben Berkhout
Keyword(s):  
Cell Culture ◽  
Dna Cleavage ◽  
Genome Engineering ◽  
Viral Escape ◽  
Sequence Profile ◽  
Guide Rna ◽  
Complete Inactivation ◽  
Promising Tool ◽  
Immunodeficiency Virus ◽  
Increased Activity

Abstract The CRISPR-Cas9 system has been used for genome editing of various organisms. We reported inhibition of the human immunodeficiency virus (HIV) in cell culture infections with a single guide RNA (gRNA) and subsequent viral escape, but complete inactivation of infectious HIV with certain combinations of two gRNAs. The new RNA-guided endonuclease system CRISPR-Cas12a (formerly Cpf1) may provide a more promising tool for genome engineering with increased activity and specificity. We compared Cas12a to the original Cas9 system for inactivation of the integrated HIV DNA genome. Superior antiviral activity is reported for Cas12a, which can achieve full HIV inactivation with only a single gRNA (called crRNA). We propose that the different architecture of Cas9 versus Cas12a endonuclease explains this effect. We also disclose that DNA cleavage by the Cas12a endonuclease and subsequent DNA repair causes mutations with a sequence profile that is distinct from that of Cas9. Both CRISPR systems can induce the typical small deletions around the site of DNA cleavage and subsequent repair, but Cas12a does not induce the pure DNA insertions that are routinely observed for Cas9. Although these typical signatures are apparent in many literature studies, this is the first report that documents these striking differences.

scholarly journals Programming PAM antennae for efficient CRISPR-Cas9 DNA editing

2020 ◽  
Vol 6 (19) ◽  
pp. eaay9948
Author(s):  
Fei Wang ◽  
Yaya Hao ◽  
Qian Li ◽  
Jiang Li ◽  
Honglu Zhang ◽  
...  
Keyword(s):  
Genome Editing ◽  
Single Molecule ◽  
Dna Cleavage ◽  
Super Resolution ◽  
Single Molecule Level ◽  
Guide Rna ◽  
Guide Rnas ◽  
Protospacer Adjacent Motif ◽  
Target Dna

Bacterial CRISPR-Cas9 nucleases have been repurposed as powerful genome editing tools. Whereas engineering guide RNAs or Cas nucleases have proven to improve the efficiency of CRISPR editing, modulation of protospacer-adjacent motif (PAM), indispensable for CRISPR, has been less explored. Here, we develop a DNA origami–based platform to program a PAM antenna microenvironment and address its performance at the single-molecule level with submolecular resolution. To mimic spatially controlled in vivo PAM distribution as may occur in chromatin, we investigate the effect of PAM antennae surrounding target DNA. We find that PAM antennae effectively sensitize the DNA cleavage by recruiting Cas9 molecules. Super-resolution tracking of single single-guide RNA/Cas9s reveals localized translocation of Cas9 among spatially proximal PAMs. We find that the introduction of the PAM antennae effectively modulates the microenvironment for enhanced target cleavage (up to ~50%). These results provide insight into factors that promote more efficient genome editing.

scholarly journals Simple and large-scale chromosomal engineering of mouse zygotes via in vitro and in vivo electroporation

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Satoru Iwata ◽  
Hitomi Nakadai ◽  
Daisuke Fukushi ◽  
Mami Jose ◽  
Miki Nagahara ◽  
...  
Keyword(s):  
Large Scale ◽  
Genome Engineering ◽  
Genetically Engineered ◽  
Guide Rna ◽  
Chromosomal Inversions ◽  
Genetically Engineered Mice ◽  
Cas9 Protein ◽  
Mouse Zygotes

Abstract The clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system has facilitated dramatic progress in the field of genome engineering. Whilst microinjection of the Cas9 protein and a single guide RNA (sgRNA) into mouse zygotes is a widespread method for producing genetically engineered mice, in vitro and in vivo electroporation (which are much more convenient strategies) have recently been developed. However, it remains unknown whether these electroporation methods are able to manipulate genomes at the chromosome level. In the present study, we used these techniques to introduce chromosomal inversions of several megabases (Mb) in length in mouse zygotes. Using in vitro electroporation, we successfully introduced a 7.67 Mb inversion, which is longer than any previously reported inversion produced using microinjection-based methods. Additionally, using in vivo electroporation, we also introduced a long chromosomal inversion by targeting an allele in F1 hybrid mice. To our knowledge, the present study is the first report of target-specific chromosomal inversions in mammalian zygotes using electroporation.

scholarly journals Evaluation and rational design of guide RNAs for efficient CRISPR/Cas9-mediated mutagenesis in Ciona

2016 ◽  
Author(s):  
Shashank Gandhi ◽  
Maximilian Haeussler ◽  
Florian Razy-Krajka ◽  
Lionel Christiaen ◽  
Alberto Stolfi
Keyword(s):  
High Throughput ◽  
Rational Design ◽  
Genome Engineering ◽  
High Throughput Sequencing ◽  
Loss Of Function ◽  
Tissue Specific ◽  
Guide Rna ◽  
Guide Rnas ◽  
Highly Active

AbstractThe CRISPR/Cas9 system has emerged as an important tool for various genome engineering applications. A current obstacle to high throughput applications of CRISPR/Cas9 is the imprecise prediction of highly active single guide. RNAs (sgRNAs). We previously implemented the CRISPR/Cas9 system to induce tissue-specific mutations in the tunicate Ciona. In the present study, we designed and tested 83 single guide RNA (sgRNA) vectors targeting 23 genes expressed in the cardiopharyngeal progenitors and surrounding tissues of Ciona embryo. Using high-throughput sequencing of mutagenized alleles, we identified guide sequences that correlate with sgRNA mutagenesis activity and used this information for the rational design of all possible sgRNAs targeting the Ciona transcriptome. We also describe a one-step cloning-free protocol for the assembly of sgRNA expression cassettes. These cassettes can be directly electroporated as unpurified PCR products into Ciona embryos for sgRNA expression in vivo, resulting in high frequency of CRISPR/Cas9-mediated mutagenesis in somatic cells of electroporated embryos.We found a strong correlation between the frequency of an Ebf loss-of-function phenotype and the mutagenesis efficacies of individual Ebf-targeting sgRNAs tested using this method. We anticipate that our approach can be scaled up to systematically design and deliver highly efficient sgRNAs for the tissue-specific investigation of gene functions in Ciona.

scholarly journals A multiplex guide RNA expression system and its efficacy for plant genome engineering

2020 ◽  
Author(s):  
Youngbin Oh ◽  
Hyeonjin Kim ◽  
Bora Lee ◽  
Sang-Gyu Kim
Keyword(s):  
Genome Engineering ◽  
Binary Vector ◽  
Expression System ◽  
Plant Genome ◽  
Nicotiana Attenuata ◽  
Specific Sequence ◽  
Editing Efficiency ◽  
Guide Rna ◽  
Assembly Method ◽  
A Genome

Abstract BackgroundThe Streptococcus pyogenes CRISPR system is composed of a Cas9 endonuclease (SpCas9) and a single-stranded guide RNA (gRNA) harboring a target-specific sequence. Theoretically, SpCas9 proteins could cleave as many targeted loci as gRNAs bind in a genome.ResultsWe introduce a PCR-free multiple gRNA cloning system for editing plant genomes. This method consists of two steps: (1) cloning annealed products of two oligonucleotides harboring target-binding sequence between tRNA and gRNA scaffold sequences in a pGRNA vector; and (2) assembling tRNA-gRNA units from several pGRNA vectors with a plant binary vector containing a SpCas9 expression cassette using the Golden Gate assembly method. We validated the editing efficiency and patterns of the multiplex gRNA expression system in wild tobacco (Nicotiana attenuata) protoplasts and in transformed plants by performing targeted deep sequencing. Two proximal cleavages by SpCas9-gRNA largely increased the editing efficiency and induced large deletions between two cleavage sites.ConclusionsThis multiplex gRNA expression system enables high-throughput production of a single binary vector and increases the efficiency of plant genome editing.

scholarly journals Humanized large-scale expanded endothelial colony–forming cells function in vitro and in vivo

Blood ◽  
2009 ◽  
Vol 113 (26) ◽  
pp. 6716-6725 ◽  
Author(s):  
Andreas Reinisch ◽  
Nicole A. Hofmann ◽  
Anna C. Obenauf ◽  
Karl Kashofer ◽  
Eva Rohde ◽  
...  
Keyword(s):  
Progenitor Cells ◽  
Endothelial Progenitor Cells ◽  
Large Scale ◽  
Proliferative Potential ◽  
Vascular Networks ◽  
Endothelial Progenitor ◽  
Endothelial Colony Forming Cells ◽  
Promising Tool

Abstract Endothelial progenitor cells are critically involved in essential biologic processes, such as vascular homeostasis, regeneration, and tumor angiogenesis. Endothelial colony–forming cells (ECFCs) are endothelial progenitor cells with robust proliferative potential. Their profound vessel-forming capacity makes them a promising tool for innovative experimental, diagnostic, and therapeutic strategies. Efficient and safe methods for their isolation and expansion are presently lacking. Based on the previously established efficacy of animal serum–free large-scale clinical-grade propagation of mesenchymal stromal cells, we hypothesized that endothelial lineage cells may also be propagated efficiently following a comparable strategy. Here we demonstrate that human ECFCs can be recovered directly from unmanipulated whole blood. A novel large-scale animal protein-free humanized expansion strategy preserves the progenitor hierarchy with sustained proliferation potential of more than 30 population doublings. By applying large-scale propagated ECFCs in various test systems, we observed vascular networks in vitro and perfused vessels in vivo. After large-scale expansion and cryopreservation phenotype, function, proliferation, and genomic stability were maintained. For the first time, proliferative, functional, and storable ECFCs propagated under humanized conditions can be explored in terms of their therapeutic applicability and risk profile.

scholarly journals A conformational checkpoint between DNA binding and cleavage by CRISPR-Cas9

2017 ◽  
Author(s):  
Yavuz S. Dagdas ◽  
Janice S. Chen ◽  
Samuel H. Sternberg ◽  
Jennifer A. Doudna ◽  
Ahmet Yildiz
Keyword(s):  
Dna Binding ◽  
Single Molecule ◽  
Dna Cleavage ◽  
Genome Engineering ◽  
Divalent Cations ◽  
Guide Rna ◽  
Single Molecule Fret ◽  
Target Sites ◽  
Multiple Conformations ◽  
Dna Binding And Cleavage

AbstractThe Cas9 endonuclease is widely utilized for genome engineering applications by programming its single-guide RNA and ongoing work is aimed at improving the accuracy and efficiency of DNA targeting. DNA cleavage of Cas9 is controlled by the conformational state of the HNH nuclease domain, but the mechanism that governs HNH activation at on-target DNA while reducing cleavage activity at off-target sites remains poorly understood. Using single-molecule FRET, we identified an intermediate state of S. pyogenes Cas9, representing a conformational checkpoint between DNA binding and cleavage. Upon DNA binding, the HNH domain transitions between multiple conformations before docking into its active state. HNH docking requires divalent cations, but not strand scission, and this docked conformation persists following DNA cleavage. Sequence mismatches between the DNA target and guide RNA prevent transitions from the checkpoint intermediate to the active conformation, providing selective avoidance of DNA cleavage at stably bound off-target sites.

scholarly journals Caenorhabditis elegans, a Host to Investigate the Probiotic Properties of Beneficial Microorganisms

2020 ◽  
Vol 7 ◽  
Author(s):  
Cyril Poupet ◽  
Christophe Chassard ◽  
Adrien Nivoliez ◽  
Stéphanie Bornes
Keyword(s):  
Caenorhabditis Elegans ◽  
High Throughput Screening ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
Probiotic Properties ◽  
C Elegans ◽  
Probiotic Potential ◽  
Challenges And Opportunities ◽  
Future Challenges

Caenorhabditis elegans, a non-parasitic nematode emerges as a relevant and powerful candidate as an in vivo model for microorganisms-microorganisms and microorganisms-host interactions studies. Experiments have demonstrated the probiotic potential of bacteria since they can provide to the worm a longer lifespan, an increased resistance to pathogens and to oxidative or heat stresses. Probiotics are used to prevent or treat microbiota dysbiosis and associated pathologies but the molecular mechanisms underlying their capacities are still unknown. Beyond safety and healthy aspects of probiotics, C. elegans represents a powerful way to design large-scale studies to explore transkingdom interactions and to solve questioning about the molecular aspect of these interactions. Future challenges and opportunities would be to validate C. elegans as an in vivo tool for high-throughput screening of microorganisms for their potential probiotic use on human health and to enlarge the panels of microorganisms studied as well as the human diseases investigated.

scholarly journals Simultaneous Multiplex Genome Engineering via Accelerated Natural Transformation in Bacillus subtilis

2021 ◽  
Vol 12 ◽  
Author(s):  
Aihua Deng ◽  
Zhaopeng Sun ◽  
Tiantian Wang ◽  
Di Cui ◽  
Lai Li ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Synthetic Biology ◽  
High Throughput Screening ◽  
Large Scale ◽  
Genome Engineering ◽  
Natural Transformation ◽  
Efficient Design ◽  
Accelerated Evolution ◽  
One Step ◽  
Tyrosine Biosynthesis

Multiplex engineering at the scale of whole genomes has become increasingly important for synthetic biology and biotechnology applications. Although several methods have been reported for engineering microbe genomes, their use is limited by their complex procedures using multi-cycle transformations. Natural transformation, involving in species evolution by horizontal gene transfer in many organisms, indicates its potential as a genetic tool. Here, we aimed to develop simultaneous multiplex genome engineering (SMGE) for the simple, rapid, and efficient design of bacterial genomes via one-step of natural transformation in Bacillus subtilis. The transformed DNA, competency factors, and recombinases were adapted to improved co-editing frequencies above 27-fold. Single to octuplet variants with genetic diversity were simultaneously generated using all-in-one vectors harboring multi-gene cassettes. To demonstrate its potential application, the tyrosine biosynthesis pathway was further optimized for producing commercially important resveratrol by high-throughput screening of variant pool in B. subtilis. SMGE represents an accelerated evolution platform that generates diverse multiplex mutations for large-scale genetic engineering and synthetic biology in B. subtilis.

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