A Guided Protocol for Array Based T2C: A High-Quality Selective High-Resolution High-Throughput Chromosome Interaction Capture.

Three-dimensional (3D) stem cell differentiation cultures recently emerged as a novel model system for investigating human embryonic development and disease progression in vitro, complementing existing animal and two-dimensional (2D) cell culture models. Organoids, the 3D self-organizing structures derived from pluripotent or somatic stem cells, can recapitulate many aspects of structural organization and functionality of their in vivo organ counterparts, thus holding great promise for biomedical research and translational applications. Importantly, faithful recapitulation of disease and development processes relies on the ability to modify the genomic contents in organoid cells. The revolutionary genome engineering technologies, CRISPR/Cas9 in particular, enable investigators to generate various reporter cell lines for prompt validation of specific cell lineages as well as to introduce disease-associated mutations for disease modeling. In this review, we provide historical overviews, and discuss technical considerations, and potential future applications of genome engineering in 3D organoid models.

The development of novel genome editing tools has unlocked new opportunities that were not previously possible in basic and biomedical research. During the last two decades, several new genome editing methods have been developed that can be customized to modify specific regions of the genome. However, in the past couple of years, many newer and more exciting genome editing techniques have been developed that are more efficient, precise, and easier to use. These genome editing tools have helped to improve our understanding of genetic disorders by modeling them in cells and animal models, in addition to correcting the disease-causing mutations. Among the genome editing tools, the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) system has proven to be the most popular one due to its versatility and has been successfully used in a wide variety of laboratory animal models and plants. In this review, we summarize the customizable nucleases currently used for genome editing and their uses beyond the modification of genome. We also discuss the potential future applications of gene editing tools for both basic research and clinical purposes.

CRISPR/Cas9-based genome editing has yet to be reported in species of the Platyhelminthes. We tested this approach by targeting omega-1 (ω1) of Schistosoma mansoni as proof of principle. This secreted ribonuclease is crucial for Th2 polarization and granuloma formation. Schistosome eggs were exposed to Cas9 complexed with guide RNA complementary to ω1 by electroporation or by transduction with lentiviral particles. Some eggs were also transfected with a single stranded donor template. Sequences of amplicons from gene-edited parasites exhibited Cas9-catalyzed mutations including homology directed repaired alleles, and other analyses revealed depletion of ω1 transcripts and the ribonuclease. Gene-edited eggs failed to polarize Th2 cytokine responses in macrophage/T-cell co-cultures, while the volume of pulmonary granulomas surrounding ω1-mutated eggs following tail-vein injection into mice was vastly reduced. Knock-out of ω1 and the diminished levels of these cytokines following exposure showcase the novel application of programmed gene editing for functional genomics in schistosomes.

Genome editing facilitates alterations to DNA, large or subtle, in a precise fashion. In its most popular form it uses the programmable endonuclease system, CRISPR/Cas9. Edits can be made to any genome, including the human genome. This raises the possibility of genome editing in human embryos in both a research and reproductive context. All reports of genome editing in human embryos are included here, along with key papers examining the science and ethics of human genome editing. As a basic research tool, genome editing promises to accelerate our understanding of genome biology. It also shows great promise as a means of combatting disease through so-called somatic genome editing. Genome editing could be used to prevent human disease transmission in a reproductive context. Such germ line interventions are opposed by some, for a number of reasons. Some of these reasons are discussed and a comparison is made with preimplantation genetic diagnosis (PGD). It is important that scientists, clinicians, bioethicists and other stakeholders engage widely with all those with an interest in genome editing. In addition to offering new insights into human biology, basic (fundamental) research will deliver expertise allowing ever more precise and controllable genome editing methodologies and allied technologies. A range of clear and accessible ethical frameworks must be developed and scrutinized as part of a wider societal debate about possible applications of genome editing. In the UK, human reproductive genome editing can only take place if a change to primary legislation occurs. Inclusive discussions and assessments, involving difficult scientific and ethical concepts, must form part of any democratic decision.

Sugarcane, a leading source of sugar and bio-energy around the globe stands at the cross-road of genome complexity and agricultural innovation, offering the immense potential to fuel a sustainable future. Functional genomics with its precise identification and manipulation of genes could enable researchers unlock this potential and accelerate the breeding efforts. However, the polyploid genome of sugarcane with: high heterozygosity, high-repetitive DNA content, multiple copies of homo(eo)logous gene, epistatic interaction of alleles, etc., challenges the gene annotation, genome sequencing, genome editing, and phenotypic characterization. Similarly long breeding cycle, low transformation efficiency, time-consuming, and labor-intensive transformation methods further complicates the genome editing. Recent advances of functional genomics are transforming this scenario, such as current availability of reference genome “R570,” has provided a significant insight of genome architect and function. Genome wide association studies (GWAS)/genome selection (GS) are enhancing trait-mapping and prediction of breeding values to accelerate the breeding cycles. The current era of smart breeding with integrative bio-informatics, advance genome editing tools, i.e., CRISPR/Cas-systems (Cas-proteins, Cas-RNPs, d-Cas-RNPs, and CRISPRa/i), and high-throughput phenomics offers a significant approach to: overcome transformation bottlenecks, explore complex trait architect and address polyploidy challenges. Therefore, this review summarizes the key challenges and focuses on elaborating recent advances and suggests optimized strategies for future improvement in functional genomics of sugarcane breeding.

In recent years, research in life sciences has been remarkably revolutionized owing to the establishment, development and application of genome editing technologies. Genome editing has not only accelerated fundamental research but has also shown promising applications in agricultural breeding and therapy. In particular, the clustered, regularly interspaced, short palindromic repeat (CRISPR) technology has become an indispensable tool in molecular biology owing to its high efficacy and simplicity. Genome editing tools have also been established in silkworm (Bombyx mori), a model organism of Lepidoptera insects with high economic importance. This has remarkably improved the level and scope of silkworm research and could reveal new mechanisms or targets in basic entomology and pest management studies. In this review, we summarize the progress and potential of genome editing in silkworm and its applications in functional genomic studies for generating novel genetic materials.

Since the discovery of the DNA double helix, major advances in biology have been; the development of recombinant DNA technology in the 1970s, methods to amplify DNA and gene targeting technology in the late 1980s. In organisms such as yeast and mice, the ability to accurately add or delete genetic information transformed biology, allowing an unmatched level of precision in studies of gene function. But, the ability to easily and specifically edit the genetic material of other cells and organisms remained impossible until recently for molecular biologists. The recent advent of programmable nucleases has dramatically changed the efficiency and speed of genome manipulation in several model organisms including cultured cells, as well as whole animals and plants. These tools opened up a powerful technique for biology research now called “genome editing” or “genome engineering” (Carroll, 2011; Hsu et al., 2014; Kim and Kim, 2014). In the first half of my doctoral studies, I developed genome-editing strategies to discover drug targets for a rare genetic disease called Friedreich’s Ataxia. Friedreich’s Ataxia (FRDA) is a neurodegenerative disease caused by deficiency of the mitochondrial protein frataxin (FXN) (Campuzano et al., 1997). This deficiency results from an expansion of a trinucleotide GAA repeat in the first intron of the FXN gene (Campuzano et al., 1996; Durr et al., 1996). Therapeutics that reactivate FXN gene expression are expected to be beneficial to FRDA patients (Gottesfeld, 2007). However, high-throughput screening (HTS) for FXN activators has so far met with limited success because current cellular models do not accurately assess endogenous FXN gene regulation. Here I used genome-editing technologies to generate a cellular model in which a luciferase reporter is introduced into the endogenous FXN locus. Using this system in a high-throughput genomic screen, we discovered novel inhibitors of FXN-luciferase expression. I confirmed that reducing expression of one of these inhibitors, PRKD1, led to an increase in FXN expression in FRDA patient fibroblasts (Villasenor et al., 2015). We then used reprogramming technologies to create a disease-relevant situation and test small molecules that specifically modulate PRKD1. We found that WA-21-JO19, a chemical inhibitor of PRKD1, increases FXN expression levels in iPSC-derived FRDA patient neurons. This approach, developed at the interface between academic and pharmaceutical research, demonstrates how a combination of genome editing, cellular reprogramming, and high-throughput biology can generate an effective novel drug discovery platform. In the second part of my doctoral work, we developed an interface between genome editing and proteomics to isolate native protein complexes produced from their natural genomic contexts. In many biological processes, proteins act as members of protein complexes. Understanding the molecular composition of protein complexes is a key task towards explaining their function in the cell. Conventional affinity purification followed by mass spectrometry analysis is a broadly applicable method to decipher molecular interaction networks and infer protein function. However, traditional affinity purification methods are limited by a number of factors such as antibody specificity and are sensitive to perturbations induced by overexpressed target proteins. Here, we combined genome editing with tandem affinity purification to circumvent current limitations. I uncovered subunits and interactions among well-characterized complexes and report the isolation of novel Mettl3-binding partners. The multi-protein complex composed of two active methyltransferases Mettl3 and Mettl14 mediates methylation of adenosines at position N6 on RNA molecules (Bokar et al., 1994; Bokar et al., 1997; Liu et al., 2014). N6-methyladenosine is the most abundant internal modification in eukaryotic mRNA and is often found on introns, which implies that methylation occurs co-transcriptionally (Fu et al., 2014). My work identified a set of nuclear RNA binding proteins, which specifically interact with the Mettl3-Mettl14 complex. We are currently testing the ability of these factors to function as “recruiters” of the Mettl3-Mettl14 complex to nascent mRNAs in the cell nucleus. In summary, our approach solidly establishes how a combination of genome editing and proteomics can simplify explorations of protein complexes as well as the study of post-translational modifications. In addition, this approach opens up new opportunities to study native protein complexes in a wide variety of cells and model organisms and will likely enable the systematic investigation of mammalian proteome function.

The first complete plant genome sequence to be determined was that of the model plant Arabidopsis thaliana , which was published in 2000. This was followed by the first drafts of the rice genome sequence in 2002. Since the publication of these landmark genomes, the development of high throughput sequencing technologies has reduced the time and cost of obtaining genome sequences to a fraction of that required a decade ago. This has enabled the sequencing of many plant genomes and thus a vast amount of genome sequence information is available to the researcher. The goal of functional genomics is to determine how these genome sequences generate plant phenotypes. The focus of most functional genomics research is to determine the function of all the genes involved in a particular process. To achieve this, functional genomics uses techniques and analyses that can survey the entire complement of genes in a genome. This chapter discusses the most commonly used functional genomics methods. Key Concepts: Advances in sequencing technologies are making entire genome sequences relatively easy to obtain. The goal of plant functional genomics is to understand how the genome generates the phenotype of the plant. Comparison to other gene sequences can often identify a likely function for a gene. Array and sequencing based methods can be used to show where and when all the genes in an organism are expressed. Gene function can be determined by knocking out or reducing gene function and can be achieved by insertion, chemical mutagenesis or RNAi. High throughput methods using recombination‐based cloning enable many tests of gene function to be applied on a genome‐wide scale.

Current and Future Directions in Genomics of Amyotrophic Lateral Sclerosis

Genome editing using CRISPR/Cas9 has advanced very rapidly in its scope, versatility and ease of use. Zebrafish (Danio rerio) has been one of the vertebrate model species where CRISPR/Cas9 has been applied very extensively for many different purposes and with great success. In particular, disease modeling in zebrafish is useful for testing specific gene variants for pathogenicity in a preclinical setting. Here we describe multiple advances in diverse species and systems that can improve genome editing in zebrafish. To achieve temporal and spatial precision of genome editing, many new technologies can be applied in zebrafish such as artificial transcription factors, drug-inducible or optogenetically-driven expression of Cas9, or chemically-inducible activation of Cas9. Moreover, chemically- or optogenetically- inducible reconstitution of dead Cas9 (catalytically inactive, dCas9) can enable spatiotemporal control of gene regulation. In addition to controlling where and when genome editing occurs, using oligonucleotides allows for the introduction (knock-in) of precise modifications of the genome. We review recent trends to improve the precision and efficiency of oligo-based point mutation knock-ins and discuss how these improvements can apply to work in zebrafish. Similarly to how chemical mutagenesis enabled the first genetic screens in zebrafish, multiplexed sgRNA libraries and Cas9 can enable the next revolutionary transition in how genetic screens are performed in this species. We discuss the first examples and prospects of approaches using sgRNAs as specific and effective mutagens. Moreover, we have reviewed methods aimed at measuring the phenotypes of single cells after their mutagenic perturbation with vectors encoding individual sgRNAs. These methods can range from different cell-based reporters to single-cell RNA sequencing and can serve as great tools for high-throughput genetic screens.

Strategies to enhance rice productivity in response to global demand have been the paramount focus of breeders worldwide. Multiple factors, including agronomical traits such as plant architecture and grain formation and physiological traits such as photosynthetic efficiency and NUE (nitrogen use efficiency), as well as factors such as phytohormone perception and homeostasis and transcriptional regulation, indirectly influence rice grain yield. Advances in genetic analysis methodologies and functional genomics, numerous genes, QTLs (Quantitative Trait Loci), and SNPs (Single-Nucleotide Polymorphisms), linked to yield traits, have been identified and analyzed in rice. Genome editing allows for the targeted modification of identified genes to create novel mutations in rice, avoiding the unintended mutations often caused by random mutagenesis. Genome editing technologies, notably the CRISPR/Cas9 system, present a promising tool to generate precise and rapid modifications in the plant genome. Advancements in CRISPR have further enabled researchers to modify a larger number of genes with higher efficiency. This paper reviews recent research on genome editing of yield-related genes in rice, discusses available gene editing tools, and highlights their potential to expedite rice breeding programs.

Pacific abalone, Haliotis discus hannai, is an economically important marine mollusk species and an important model animal for studies on ecological, fertilization and developmental biology. While embryonic injection and genome editing have been wildly used in gene function study and trait improvement in many species, they have not been developed in abalones. In this study, we reported an effective method to inject exogenous materials in H. discus hannai unfertilized eggs. The injected eggs could be fertilized at a ratio of 52.6% ± 5.9% and hatch at a ratio of 14.6% ± 1.6%. On the base of this, we further developed an efficient genome editing approach in this species with the transcription activator-like effector nuclease (TALEN) technique. Two TALEN pairs targeting the coding sequence of the abalone nodal gene were assembled and tested. While one of the TALEN pairs showed no detectable mutation efficacy, the other one generated mutations in 50% of the targeted loci. The mutation includes small insertions and deletions and base pair replacements like that reported in other species when the TALEN method was applied. Overall, this is the first study to demonstrate site-specific genome editing in abalone. This work can serve as a reference for future studies focusing on the functional genomics in mollusks.

11 - Novel Technologies for Plant Functional Genomics

Recent advances in genomic technologies have enabled the identification of thousands of genetic variations that are associated with hundreds of complex human diseases or traits in genome-wide association studies (GWAS). The large number of genetic loci uncovered for each disease or trait along with the difficulty in pinpointing the underlying genes and mechanisms further testify to the complexity of human pathophysiology. To alleviate the challenges of GWAS, systems biology approaches have been utilized to map the molecular mechanisms underlying complex human diseases/traits via the integration of genetic variation, functional genomics (such as genetics of gene expression), pathways, and molecular networks. Similar approaches have been applied to a spectrum of drug metabolizing enzymes to discover novel functional genetic variations that affect the expression or activities of these enzymes as well as to define the regulatory pathways/networks of genes involved in drug metabolism and toxicology in key human tissues. We envision that the increased coverage of functional genetic polymorphisms, the availability of drug metabolism-centered gene networks, and the maturing methodologies previously developed for understanding complex human diseases can be applied to pharmacogenomic and toxicogenomic studies to further our understanding of inter-individual variability in drug efficacy and toxicity and eventually help direct personalized medicine.

Rhizobia are widespread gram-negative soil bacteria and indispensable symbiotic partners of leguminous plants that facilitate the most highly efficient biological nitrogen fixation in nature. Although genetic studies in Sinorhizobium meliloti have advanced our understanding of symbiotic nitrogen fixation (SNF), the current methods used for genetic manipulations in Sinorhizobium meliloti are time-consuming and labor-intensive. In this study, we report the development of a few precise gene modification tools that utilize the CRISPR/Cas9 system and various deaminases. By fusing the Cas9 nickase to an adenine deaminase, we developed an adenine base editor (ABE) system that facilitated adenine-to-guanine transitions at one-nucleotide resolution without forming double-strand breaks (DSB). We also engineered a cytidine base editor (CBE) and a guanine base editor (GBE) that catalyze cytidine-to-thymine substitutions and cytidine-to-guanine transversions, respectively, by replacing adenine deaminase with cytidine deaminase and other auxiliary enzymes. All of these base editors are amenable to the assembly of multiple synthetic guide RNA (sgRNA) cassettes using Golden Gate Assembly to simultaneously achieve multigene mutations or disruptions. These CRISPR-mediated base editing tools will accelerate the functional genomics study and genome manipulation of rhizobia.