Unreported off-target integration of beta-lactamase from plasmid in gene-edited hornless cows

2019 ◽  
Author(s):  
Sandeep Chakraborty

Concerns about the unintended effects of gene-editing is not new. Kim, et al, 2014 warned about ”unwanted integration of DNA segments derived from plasmids encoding Cas9 and guide RNA at both on- target and off-target sites”. Thus, there was nothing unexpected when in 2019 a FDA-authored pre-print reported template plasmid integration in the 2016 TALEN-edited hornless cows (Accid:PRJNA316122). Soon, yet another paper confirmed this on-target integration (Accid:PRJNA494431), and also reported that 4 out of 6 calves sired by one of the cow have inherited this plasmid in the targeted site on chromosome 1. However, this paper failed to report another definite off-target integration (in chromosome 14) of the beta-lactamase from the plasmid. Sequencing fragments, and then, samples the genome in any single pass, with the hope with enough passes the full genome would have been covered. For a roughly 3GB genome (as the bovine genome), 10-15 passes is not enough. In fact a read that is completely plasmid (and there are many) could be an integration anywhere. Thus, there might remain other integrations of the plasmid that are unobserved.

Author(s):  
Shalu Kumari Pathak ◽  
Arvind Sonwane ◽  
Subodh Kumar

Background: Programmable nucleases are very promising tools of genome editing (GE), but they suffer from limitations including potential risk of genotoxicity which led to the exploration of safer approach of GE based on RNA-guided recombinase (RGR) platform. RNA-guided recombinase (RGR) platform operates on a typical recognition or target site comprised of the minimal pseudo-core recombinase site, a 5 to 6-base pair spacer flanking it and whole this central region is flanked by two guide RNA-specified DNA sequences or Cas9 binding sites followed by protospacer adjacent motifs (PAMs). Methods: The current study focuses on analysis of entire cattle genome to prepare a detailed map of target sites for RNA-guided hyperactivated recombinase Gin with spacer length six. For this, chromosome wise whole genomic sequence data was retrieved from Ensembl. After that search pattern for recombinase Gin with spacer length six was designed. By using this search pattern, RGR target sites were located by using dreg program of Emboss package. Result: Total number of RGR target sites identified in bovine genome for recombinase Gin was 677 with spacer length six. It was also investigated that whether these RGR target sites are present with in any gene or not and it was found that RGR target sites lies in both genic and intergenic region. Besides this, description of genes in context with these target sites was identified.


2021 ◽  
Author(s):  
Rammyani Bagchi ◽  
Rachel Tinker-Kulberg ◽  
Tinku Supakar ◽  
Sydney Chamberlain ◽  
Ayalew Ligaba-Osena ◽  
...  

ABSTRACTCRISPR biotechnologies, where CRISPR effectors recognize and degrade specific nucleic acid targets that are complementary to their guide RNA (gRNA) cofactors, have been primarily used as a tool for precision gene editing1 but possess an emerging potential for novel antiviral diagnostics, prophylactics, and therapeutics.2–5 In gene editing applications, significant efforts are made to limit the natural tolerance of CRISPR effectors for nucleic acids with imperfect complementarity to their gRNAs in order to prevent degradation and mutation at unintended or “off-target” sites; here we exploit those tolerances to engineer gRNAs that are optimized to promote activity at multiple viral target sites, simultaneously, given that multiplexed targeting is a critical tactic for improving viral detection sensitivity,3 expanding recognition of clinical strain variants,6 and suppressing viral mutagenic escape from CRISPR antivirals.7 We demonstrate in vitro and in higher plants that single “polyvalent” gRNAs (pgRNAs) in complex with CRISPR effectors Cas9 or Cas13 can effectively degrade pairs of viral targets with significant sequence divergence (up to 40% nucleotide differences) that are prevalent in viral genomes. We find that CRISPR antivirals using pgRNAs can robustly suppress the propagation of plant RNA viruses, in vivo, better than those with a “monovalent” gRNA counterpart. These results represent a powerful new approach to gRNA design for antiviral applications that can be readily incorporated into current viral detection and therapeutic strategies, and highlight the need for specific approaches and tools that can address the differential requirements of precision gene editing vs. CRISPR antiviral applications in order to mature these promising biotechnologies.


2021 ◽  
Author(s):  
Ofir Yaish ◽  
Maor Asif ◽  
Yaron Orenstein

AbstractCRISPR/Cas9 system is widely used in a broad range of gene-editing applications. While this gene-editing technique is quite accurate in the target region, there may be many unplanned off-target edited sites. Consequently, a plethora of computational methods have been developed to predict off-target cleavage sites given a guide RNA and a reference genome. However, these methods are based on small-scale datasets (only tens to hundreds of off-target sites) produced by experimental techniques to detect off-target sites with a low signal-to-noise ratio. Recently, CHANGE-seq, a new in vitro experimental technique to detect off-target sites, was used to produce a dataset of unprecedented scale and quality (more than 200,000 off-target sites over 110 guide RNAs). In addition, the same study included GUIDE-seq experiments for 58 of the guide RNAs to produce in vivo measurements of off-target sites. Here, we fill the gap in previous computational methods by utilizing these data to perform a systematic evaluation of data processing and formulation of the CRISPR off-target site prediction problem. Our evaluations show that data transformation as a pre-processing phase is critical prior to model training. Moreover, we demonstrate the improvement gained by adding potential inactive off-target sites to the training datasets. Furthermore, our results point to the importance of adding the number of mismatches between the guide RNA and the off-target site as a feature. Finally, we present predictive off-target in vivo models based on transfer learning from in vitro. Our conclusions will be instrumental to any future development of an off-target predictor based on high-throughput datasets.


Plant Methods ◽  
2021 ◽  
Vol 17 (1) ◽  
Author(s):  
Yan Zhang ◽  
Ping Zhou ◽  
Tohir A. Bozorov ◽  
Daoyuan Zhang

Abstract Background Xinjiang wild apple is an important tree of the Tianshan Mountains, and in recent years, it has undergone destruction by many biotic and abiotic stress and human activities. It is necessary to use new technologies to research its genomic function and molecular improvement. The clustered regulatory interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) system has been successfully applied to genetic improvement in many crops, but its editing capability varies depending on the different combinations of the synthetic guide RNA (sgRNA) and Cas9 protein expression devices. Results In this study, we used 2 systems of vectors with paired sgRNAs targeting to MsPDS. As expected, we successfully induced the albino phenotype of calli and buds in both systems. Conclusions We conclude that CRISPR/Cas9 is a powerful system for editing the wild apple genome and expands the range of plants available for gene editing.


Gene Therapy ◽  
2021 ◽  
Author(s):  
Jonathan O’Keeffe Ahern ◽  
Irene Lara-Sáez ◽  
Dezhong Zhou ◽  
Rodolfo Murillas ◽  
Jose Bonafont ◽  
...  

AbstractRecent advances in molecular biology have led to the CRISPR revolution, but the lack of an efficient and safe delivery system into cells and tissues continues to hinder clinical translation of CRISPR approaches. Polymeric vectors offer an attractive alternative to viruses as delivery vectors due to their large packaging capacity and safety profile. In this paper, we have demonstrated the potential use of a highly branched poly(β-amino ester) polymer, HPAE-EB, to enable genomic editing via CRISPRCas9-targeted genomic excision of exon 80 in the COL7A1 gene, through a dual-guide RNA sequence system. The biophysical properties of HPAE-EB were screened in a human embryonic 293 cell line (HEK293), to elucidate optimal conditions for efficient and cytocompatible delivery of a DNA construct encoding Cas9 along with two RNA guides, obtaining 15–20% target genomic excision. When translated to human recessive dystrophic epidermolysis bullosa (RDEB) keratinocytes, transfection efficiency and targeted genomic excision dropped. However, upon delivery of CRISPR–Cas9 as a ribonucleoprotein complex, targeted genomic deletion of exon 80 was increased to over 40%. Our study provides renewed perspective for the further development of polymer delivery systems for application in the gene editing field in general, and specifically for the treatment of RDEB.


2016 ◽  
Vol 28 (10) ◽  
pp. 1618 ◽  
Author(s):  
María E. Fernández ◽  
Alberto Prando ◽  
Andrés Rogberg-Muñoz ◽  
Pilar Peral-García ◽  
Andrés Baldo ◽  
...  

Age at puberty is an important component of reproductive performance in cattle, so it is important to identify genes that contribute to the regulation of the onset of puberty and polymorphisms that explain differences between bulls. In a previous study, we found putative associations between age at puberty in Angus bulls and single-nucleotide polymorphisms (SNPs) in Chromosomes 1 and X. In the present work we aimed to confirm these findings in a larger sample of Angus bulls (n = 276). Four SNPs located in these regions were genotyped using SEQUENOM technology and the genotypes obtained were tested for association with age at puberty. The results showed that SNPs rs135953349 and rs110604205 on BTA1 were still significantly associated with age of puberty estimated at progressive sperm motility of 10% (P < 0.05). The association previously found on Chromosome X could not be confirmed. Analysis of the bovine genome revealed that the associated region (99.17–99.99 Mb) contained four predicted loci: myelodysplasia syndrome 1 (MDS1) and ecotropic virus integration site 1 (EVI1) complex locus (MECOM), eGF-like and EMI domain-containing 1 pseudogene-like (LOC100337483), microRNA mir-551b (MIR551B) and mCG140927-like (LOC100139843). The results obtained could contribute to the understanding of puberty regulation and could be useful for further identification and annotation of gene function in the context of reproduction.


2019 ◽  
Author(s):  
Patrick C. Fiaux ◽  
Hsiuyi V. Chen ◽  
Aaron R. Chen ◽  
Poshen B. Chen ◽  
Graham McVicker

AbstractCRISPR screens are a powerful new technology for the identification of genome sequences that affect cellular phenotypes such as gene expression, survival, and proliferation. By tiling single-guide RNA (sgRNA) target sites across large genomic regions, CRISPR screens have the potential to systematically discovery novel functional sequences, however, a lack of purpose-built analysis tools limits the effectiveness of this approach. Here we describe RELICS, a Bayesian hierarchical model for the discovery of functional sequences from tiling CRISPR screens. RELICS considers the overlapping effects of multiple nearby functional sequences, accounts for the ‘area of effect’ surrounding sgRNA target sites, models overdispersion in sgRNA counts, combines information across multiple pools, and estimates the number of functional sequences supported by the data. In simulations, RELICS outperforms existing methods and provides higher resolution predictions. We apply RELICS to published CRISPR interference and CRISPR activation screens and predict novel regulatory sequences, several of which we experimentally validate. In summary, RELICS is a powerful new analysis method for tiling CRISPR screens that enables the discovery of functional sequences with unprecedented resolution and accuracy.


mBio ◽  
2021 ◽  
Vol 12 (2) ◽  
Author(s):  
Zhiwei Hu ◽  
Yannan Wang ◽  
Qian Liu ◽  
Yan Qiu ◽  
Zhiyu Zhong ◽  
...  

ABSTRACT Base editing is a powerful genome editing approach that enables single-nucleotide changes without double-stranded DNA breaks (DSBs). However, off-target effects as well as other undesired editings at on-target sites remain obstacles for its application. Here, we report that bubble hairpin single guide RNAs (BH-sgRNAs), which contain a hairpin structure with a bubble region on the 5′ end of the guide sequence, can be efficiently applied to both cytosine base editor (CBE) and adenine base editor (ABE) and significantly decrease off-target editing without sacrificing on-target editing efficiency. Meanwhile, such a design also improves the purity of C-to-T conversions induced by base editor 3 (BE3) at on-target sites. Our results present a distinctive and effective strategy to improve the specificity of base editing. IMPORTANCE Base editors are DSB-free genome editing tools and have been widely used in diverse living systems. However, it is reported that these tools can cause substantial off-target editings. To meet this challenge, we developed a new approach to improve the specificity of base editors by using hairpin sgRNAs with a bubble. Furthermore, our sgRNA design also dramatically reduced indels and unwanted base substitutions at on-target sites. We believe that the BH-sgRNA design is a significant improvement over existing sgRNAs of base editors, and our design promises to be adaptable to various base editors. We expect that it will make contributions to improving the safety of gene therapy.


2018 ◽  
Vol 19 (10) ◽  
pp. 3000 ◽  
Author(s):  
Shouhong Zhu ◽  
Xiuli Yu ◽  
Yanjun Li ◽  
Yuqiang Sun ◽  
Qianhao Zhu ◽  
...  

The clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) gene editing system has been shown to be able to induce highly efficient mutagenesis in the targeted DNA of many plants, including cotton, and has become an important tool for investigation of gene function and crop improvement. Here, we developed a simple and easy to operate CRISPR/Cas9 system and demonstrated its high editing efficiency in cotton by targeting-ALARP, a gene encoding alanine-rich protein that is preferentially expressed in cotton fibers. Based on sequence analysis of the target site in the 10 transgenic cottons containing CRISPR/Cas9, we found that the mutation frequencies of GhALARP-A and GhALARP-D target sites were 71.4–100% and 92.9–100%, respectively. The most common editing event was deletion, but deletion together with large insertion was also observed. Mosaic mutation editing events were detected in most transgenic plants. No off-target mutation event was detected in any the 15 predicted sites analyzed. This study provided mutants for further study of the function of GhALARP in cotton fiber development. Our results further demonstrated the feasibility of use of CRISPR/Cas9 as a targeted mutagenesis tool in cotton, and provided an efficient tool for targeted mutagenesis and functional genomics in cotton.


2020 ◽  
Vol 32 (2) ◽  
pp. 193
Author(s):  
D. Miskel ◽  
L. Beunink ◽  
M. Poirier ◽  
V. Havlicek ◽  
F. Rings ◽  
...  

In recent years, CRISPR/Cas9 has been used to efficiently edit the genomes of embryos in many animal models. Due to smaller anatomy, lower costs, and multiple ovulations, it is relatively simple to derive large numbers of invivo fertilized zygotes for gene editing experiments in small mammal models. In cattle, however, harvesting invivo fertilized zygotes generally requires a highly invasive surgical procedure. Here, we use the combination of a minimally invasive endoscopic method for harvesting invivo fertilized zygotes by oviductal flushing of superovulated heifers and the subsequent electroporation of zygotes with CRISPR/Cas9 ribonucleoproteins (RNP). After superstimulation of 21 heifers, on average 12 zygotes were flushed per animal with fetal bovine serum, then stored in synthetic oviductal fluid (SOFaa) before electroporation. Targeting exon 1 of the tyrosinase (Tyr) gene, zygotes were electroporated in 1-mm gap cuvettes (Biorad) in groups of ~20 in 20μL of OptiMEM media containing 3μM Cas9 RNP (IDT Cas9 protein pre-incubated with anti-Tyr guide RNA). Electroporation was performed in 3 replicates of 3 electrical potentials, namely 20, 25, and 30V using a Biojet CF 50. The other electroporation parameters were fixed at 5 repetitions of 2-ms square wave pulses at 100-ms intervals. The zygotes were than cultured under standard embryo culture conditions (SOFaa + 0.3% bovine serum albumin, 5% CO2, 5% O2, 39°C, humidified air). Embryo survival, cleavage, and developmental rates to the blastocyst stage were tracked. Statistical significance between groups was determined by pairwise one-way ANOVA using Sidak correction for multiple comparisons. Electroporation of invivo-derived zygotes using 20V yielded significantly higher survival (83.6% vs. 42.8% vs. 20.7% for 20, 25, and 30V, respectively), cleavage (65.6% vs. 37.9% vs. 40.0%), and developmental rates (47.5% vs. 21.4% vs. 16.5%) than 25 or 30V. There was no statistical difference between 25 and 30V. Subsequently, editing rates were determined using the T7 mismatch assay and verified with Sanger sequencing followed by sequence alignment and analysis using Tracking of Indels by Decomposition (TIDE) software (https://tide.nki.nl/). Although there was high variance between electroporation groups, blastocyst editing rates of up to 80.0% were achieved using 30V. To our knowledge, these are the first confirmed gene-edited bovine embryos produced from invivo fertilized zygotes. This method offers the ability to utilise the embryos of high-value cows or cows with known genotypes for genetic engineering experiments. In addition, given that electroporated bovine zygotes can be transferred back to the oviduct endoscopically, our future attempts will focus on genome editing in bovine embryos developed nearly completely within the physiological invivo environment.


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