TSA Promotes CRISPR/Cas9 Editing Efficiency and Expression of Cell Division-Related Genes from Plant Protoplasts

Microparticle-mediated CRISPR DNA delivery for genome editing in poplar

The use of CRISPR/Cas9 is currently the method of choice for precise genome engineering in plants, including in the biomass crop poplar. The most commonly used method for delivering CRISPR/Cas9 and its components in poplar is via Agrobacterium-mediated transformation, that besides the desired gene-editing event also results in stable T-DNA integration. Here we explore the delivery of the gene-editing reagents via DNA-coated microparticle bombardment into the model tree Populus tremula x P. alba to evaluate its potential for developing transgene-free, gene-edited trees, as well as its potential for integrating donor DNA at specific target sites. Using an optimized transformation method, which favors the regeneration of plants that transiently express the genes on the delivered donor DNA, we regenerated gene-edited plants that are free of the Cas9 and the antibiotic resistance-encoding transgenes. In addition, we report the frequent integration of donor DNA fragments at the Cas9-induced double-strand break, opening opportunities toward targeted gene insertions.

Strategies for delivery of CRISPR/Cas-mediated genome editing to obtain edited plants directly without transgene integration

Increased understanding of plant genetics and the development of powerful and easier-to-use gene editing tools over the past century have revolutionized humankind's ability to deliver precise genotypes in crops. Plant transformation techniques are well developed for making transgenic varieties in certain crops and model organisms, yet reagent delivery and plant regeneration remain key bottlenecks to applying the technology of gene editing to most crops. Typical plant transformation protocols to produce transgenic, genetically modified (GM) varieties rely on transgenes, chemical selection, and tissue culture. Typical protocols to make gene edited (GE) varieties also use transgenes, even though these may be undesirable in the final crop product. In some crops, the transgenes are routinely segregated away during meiosis by performing crosses, and thus only a minor concern. In other crops, particularly those propagated vegetatively, complex hybrids, or crops with long generation times, such crosses are impractical or impossible. This review highlights diverse strategies to deliver CRISPR/Cas gene editing reagents to regenerable plant cells and to recover edited plants without unwanted integration of transgenes. Some examples include delivering DNA-free gene editing reagents such as ribonucleoproteins or mRNA, relying on reagent expression from non-integrated DNA, using novel delivery mechanisms such as viruses or nanoparticles, using unconventional selection methods to avoid integration of transgenes, and/or avoiding tissue culture altogether. These methods are advancing rapidly and already enabling crop scientists to make use of the precision of CRISPR gene editing tools.

Evaluation of CRISPR/Cas9 Constructs in Wheat Cell Suspension Cultures

Despite intensive optimization efforts, developing an efficient sequence-specific CRISPR/Cas-mediated genome editing method remains a challenge, especially in polyploid cereal species such as wheat. Validating the efficacy of nuclease constructs prior to using them in planta is, thus, a major step of every editing experiment. Several construct evaluation strategies were proposed, with PEG-mediated plasmid transfection of seedling-derived protoplasts becoming the most popular. However, the usefulness of this approach is affected by associated construct copy number bias and chromatin relaxation, both influencing the outcome. Therefore, to achieve a reliable evaluation of CRISPR/Cas9 constructs, we proposed a system based on an Agrobacterium-mediated transformation of established wheat cell suspension cultures. This system was used for the evaluation of a CRISPR/Cas9 construct designed to target the ABA 8'-hydroxylase 1 gene. The efficiency of editing was verified by cost-effective means of Sanger sequencing and bioinformatic analysis. We discuss advantages and potential future developments of this method in contrast to other in vitro approaches.

Evaluation of genome and base editing tools in maize protoplasts

INTRODUCTION

Despite its rapid worldwide adoption as an efficient mutagenesis tool, plant genome editing remains a labor-intensive process requiring often several months of in vitro culture to obtain mutant plantlets. To avoid a waste in time and money and to test, in only a few days, the efficiency of molecular constructs or novel Cas9 variants (clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9) prior to stable transformation, rapid analysis tools are helpful.

METHODS

To this end, a streamlined maize protoplast system for transient expression of CRISPR/Cas9 tools coupled to NGS (next generation sequencing) analysis and a novel bioinformatics pipeline was established.

RESULTS AND DISCUSSION

Mutation types found with high frequency in maize leaf protoplasts had a trend to be the ones observed after stable transformation of immature maize embryos. The protoplast system also allowed to conclude that modifications of the sgRNA (single guide RNA) scaffold leave little room for improvement, that relaxed PAM (protospacer adjacent motif) sites increase the choice of target sites for genome editing, albeit with decreased frequency, and that efficient base editing in maize could be achieved for certain but not all target sites. Phenotypic analysis of base edited mutant maize plants demonstrated that the introduction of a stop codon but not the mutation of a serine predicted to be phosphorylated in the bHLH (basic helix loop helix) transcription factor ZmICEa (INDUCER OF CBF EXPRESSIONa) caused abnormal stomata, pale leaves and eventual plant death two months after sowing.

Methionine affects the expression of pluripotency genes and protein levels associated with methionine metabolism in adult, fetal, and cancer stem cells

Intracellular and extracellular regulatory factors promote the potency and self-renewal property of stem cells. Methionine is fundamental for protein synthesis and regulation of methylation reactions. Specifically, methionine metabolism in embryonic and fetal development processes regulates gene expression profile/epigenetic identity of stem cells to achieve pluripotency and cellular functions. We aimed to reveal the differences in methionine metabolism of bone marrow (BM)-mesenchymal stem cells (MSCs), umbilical cord blood (UCB)-MSCs, and cancer stem cells (CSCs), which reflect different metabolic profiles and developmental stages of stem cells. UCB-MSC, BM-MSCs, and breast CSCs were treated with different doses (0, 10, 25, 50, and 100 µM) of l-methionine. Cell surface marker and cell cycle assessment were performed by flow cytometry. Changes in gene expressions (OCT3/4, NANOG, DMNT1, DNMT3A, and DNMT3B, MAT2A, and MAT2B) with methionine supplementation were examined by quantitative real-time polymerase chain reaction and the changes in histone methylation (H3K4me3, H3K27me3) levels were demonstrated by western blot analysis. S-adenosylmethionine//S-adenosylhomocysteine (SAM/SAH) levels were evaluated by enzyme-linked immunosorbent assay. Cells that were exposed to different concentrations of l-methionine, were mostly arrested in the G0/G1 phase for each stem cell group. It was evaluated that BM-MSCs increased all gene expressions in the culture medium-containing 100 µM methionine, in addition to SAM/SAH levels. On the other hand, UCB-MSCs were found to increase OCT3/4, NANOG, and DNMT1 gene expressions and decrease MAT2A and MAT2B expressions in the culture medium containing 10 µM methionine. Moreover, an increase was observed in the He3K4me3 methylation profile. In addition, OCT3/4, NANOG, DNMT1, and MAT2B gene expressions in CSCs increased starting from the addition of 25 µM methionine. An increase was determined in H3K4me3 protein expression at 50 and 100 µM methionine-supplemented culture condition. This study demonstrates that methionine plays a critical role in metabolism and epigenetic regulation in different stem cell groups.