CRISPR/Cas9-induced DNA breaks trigger crossover, chromosomal loss, and chromothripsis-like rearrangements.

DNA double-stranded breaks (DSBs) generated by the Cas9 nuclease are commonly repaired via nonhomologous end-joining (NHEJ) or homologous recombination (HR). However, little is known about unrepaired DSBs and the type of damage they trigger in plants. We designed an assay that detects loss of heterozygosity (LOH) in somatic cells, enabling the study of a broad range of DSB-induced genomic events. The system relies on a mapped phenotypic marker which produces a light purple color (betalain pigment) in all plant tissues. Plants with sectors lacking the Betalain marker upon DSB induction between the marker and the centromere were tested for LOH events. Using this assay, we detected a tomato (Solanum lycopersicum) flower with a twin yellow and dark purple sector, corresponding to a germinally transmitted somatic crossover event. We also identified instances of small deletions of genomic regions spanning the T-DNA and whole chromosome loss. In addition, we show that major chromosomal rearrangements including loss of large fragments, inversions, and translocations were clearly associated with the CRISPR-induced DSB. Detailed characterization of complex rearrangements by whole-genome sequencing and molecular and cytological analyses supports a model in which a breakage-fusion-bridge cycle followed by chromothripsis-like rearrangements had been induced. Our LOH assay provides a tool for precise breeding via targeted crossover detection. It also uncovers CRISPR-mediated chromothripsis-like events in plants.

36-year study reveals stability of a wild wheat population across microhabitats.

Long-term genetic studies of wild populations are very scarce, but are essential for connecting ecological and population genetics models, and for understanding the dynamics of biodiversity. We present a study of a wild wheat population sampled over a 36-year period at high spatial resolution. We genotyped 832 individuals from regular sampling along transects during the course of the experiment. Genotypes were clustered into ecological microhabitats over scales of tens of metres, and this clustering was remarkably stable over the 36 generations of the study. Simulations show that it is difficult to determine whether this spatial and temporal stability reflects extremely limited dispersal or fine-scale local adaptation to ecological parameters. Using a common-garden experiment, we showed that the genotypes found in distinct microhabitats differ phenotypically. Our results provide a rare insight into the population genetics of a natural population over a long monitoring period.

Mutagenesis of the melon Prv gene by CRISPR/Cas9 breaks papaya ringspot virus resistance and generates an autoimmune allele with constitutive defense responses.

The majority of plant disease resistance (R) genes encode nucleotide binding-leucine-rich repeat (NLR) proteins. In melon, two closely linked NLR genes, Fom-1 and Prv, were mapped and identified as candidate genes that control resistance to Fusarium oxysporum f.sp. melonis races 0 and 2, and to papaya ringspot virus (PRSV), respectively. In this study, we validated the function of Prv and showed that it is essential for providing resistance against PRSV infection. We generated CRISPR/Cas9 [clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9] mutants using Agrobacterium-mediated transformation of a PRSV-resistant melon genotype, and the T1 progeny proved susceptible to PRSV, showing strong disease symptoms and viral spread upon infection. Three alleles having 144, 154, and ~3 kb deletions, respectively, were obtained, all of which caused loss of resistance. Interestingly, one of the Prv mutant alleles, prvΔ154, encoding a truncated product, caused an extreme dwarf phenotype, accompanied by leaf lesions, high salicylic acid levels, and defense gene expression. The autoimmune phenotype observed at 25 °C proved to be temperature dependent, being suppressed at 32 °C. This is a first report on the successful application of CRISPR/Cas9 to confirm R gene function in melon. Such validation opens up new opportunities for molecular breeding of disease resistance in this important vegetable crop.

Efficient in planta gene targeting in tomato using geminiviral replicons and the CRISPR/Cas9 system.

Current breeding relies mostly on random mutagenesis and recombination to generate novel genetic variation. However, targeted genome editing is becoming an increasingly important tool for precise plant breeding. Using the CRISPR-Cas system combined with the bean yellow dwarf virus rolling circle replicon, we optimized a method for targeted mutagenesis and gene replacement in tomato. The carotenoid isomerase (CRTISO) and phytoene synthase 1 (PSY1) genes from the carotenoid biosynthesis pathway were chosen as targets due to their easily detectable change of phenotype. We took advantage of the geminiviral replicon amplification as a means to provide a large amount of donor template for the repair of a CRISPR-Cas-induced DNA double-strand break (DSB) in the target gene, via homologous recombination (HR). Mutagenesis experiments, performed in the Micro-Tom variety, achieved precise modification of the CRTISO and PSY1 loci at an efficiency of up to 90%. In the gene targeting (GT) experiments, our target was a fast-neutron-induced crtiso allele that contained a 281-bp deletion. This deletion was repaired with the wild-type sequence through HR between the CRISPR-Cas-induced DSB in the crtiso target and the amplified donor in 25% of the plants transformed. This shows that efficient GT can be achieved in the absence of selection markers or reporters using a single and modular construct that is adaptable to other tomato targets and other crops.

Single Molecule Imaging of T-DNA Intermediates Following Agrobacterium tumefaciens Infection in Nicotiana benthamiana.

Plant transformation mediated by Agrobacterium tumefaciens is a well-studied phenomenon in which a bacterial DNA fragment (T-DNA), is transferred to the host plant cell, as a single strand, via type IV secretion system and has the potential to reach the nucleus and to be integrated into its genome. While Agrobacterium-mediated transformation has been widely used for laboratory-research and in breeding, the time-course of its journey from the bacterium to the nucleus, the conversion from single- to double-strand intermediates and several aspects of the integration in the genome remain obscure. In this study, we sought to follow T-DNA infection directly using single-molecule live imaging. To this end, we applied the LacO-LacI imaging system in Nicotiana benthamiana, which enabled us to identify double-stranded T-DNA (dsT-DNA) molecules as fluorescent foci. Using confocal microscopy, we detected progressive accumulation of dsT-DNA foci in the nucleus, starting 23 h after transfection and reaching an average of 5.4 and 8 foci per nucleus at 48 and 72 h post-infection, respectively. A time-course diffusion analysis of the T-DNA foci has demonstrated their spatial confinement.

Redistribution of Meiotic Crossovers Along Wheat Chromosomes by Virus-Induced Gene Silencing.

Meiotic recombination is the main driver of genetic diversity in wheat breeding. The rate and location of crossover (CO) events are regulated by genetic and epigenetic factors. In wheat, most COs occur in subtelomeric regions but are rare in centromeric and pericentric areas. The aim of this work was to increase COs in both "hot" and "cold" chromosomal locations. We used Virus-Induced gene Silencing (VIGS) to downregulate the expression of recombination-suppressing genes XRCC2 and FANCM and of epigenetic maintenance genes MET1 and DDM1 during meiosis. VIGS suppresses genes in a dominant, transient and non-transgenic manner, which is convenient in wheat, a hard-to-transform polyploid. F1 hybrids of a cross between two tetraploid lines whose genome was fully sequenced (wild emmer and durum wheat), were infected with a VIGS vector ∼ 2 weeks before meiosis. Recombination was measured in F2 seedlings derived from F1-infected plants and non-infected controls. We found significant up and down-regulation of CO rates along subtelomeric regions as a result of silencing either MET1, DDM1 or XRCC2 during meiosis. In addition, we found up to 93% increase in COs in XRCC2-VIGS treatment in the pericentric regions of some chromosomes. Silencing FANCM showed no effect on CO. Overall, we show that CO distribution was affected by VIGS treatments rather than the total number of COs which did not change. We conclude that transient silencing of specific genes during meiosis can be used as a simple, fast and non-transgenic strategy to improve breeding abilities in specific chromosomal regions.

CRISPR/Cas9 Induced Somatic Recombination at the CRTISO Locus in Tomato.

Homologous recombination (HR) in somatic cells is not as well understood as meiotic recombination and is thought to be rare. In a previous study, we showed that Inter-Homologous Somatic Recombination (IHSR) can be achieved by targeted induction of DNA double-strand breaks (DSBs). Here, we designed a novel IHSR assay to investigate this phenomenon in greater depth. We utilized F1 hybrids from divergent parental lines, each with a different mutation at the Carotenoid isomerase (CRTISO) locus. IHSR events, namely crossover or gene conversion (GC), between the two CRTISO mutant alleles (tangerine color) can restore gene activity and be visualized as gain-of-function, wildtype (red) phenotypes. Our results show that out of four intron DSB targets tested, three showed DSB formation, as seen from non-homologous end-joining (NHEJ) footprints, but only one target generated putative IHSR events as seen by red sectors on tangerine fruits. F2 seeds were grown to test for germinal transmission of HR events. Two out of five F1 plants showing red sectors had their IHSR events germinally transmitted to F2, mainly as gene conversion. Six independent recombinant alleles were characterized: three had truncated conversion tracts with an average length of ~1 kb. Two alleles were formed by a crossover as determined by genotyping and characterized by whole genome sequencing. We discuss how IHSR can be used for future research and for the development of novel gene editing and precise breeding tools.

Association of complement factor H Y402H polymorphism with phenotype of neovascular age related macular degeneration in Israel.

PURPOSE: The Tyr402His variant of complement factor H (CFH) is associated with age-related macular degeneration (AMD) in several populations. Our aim was to evaluate if this single nucleotide polymorphism (SNP) is associated with AMD in the Israeli population and see if it underlies heterogeneity in clinical manifestation and responses to photodynamic therapy (PDT), which characterize neovascular AMD (NVAMD). METHODS: Genotyping for the Tyr402His variant was performed in 240 NVAMD patients (78.1+/-7 age range) and 118 controls (70.8+/-8.2 age range). Genotyping was correlated with clinical characteristics and treatment parameters in sequential 131 NVAMD patients who underwent PDT. RESULTS: TheTyr402His coding allele was associated with NVAMD in the Israeli population: odds ratio (OR)=1.9; 95% confidence interval (CI)=1.3-2.6; p=0.0002. Homozygosity for this variant was associated with an OR of 3.4 (95% CI: 1.7-6.8) for having AMD. There was no association among this SNP and age of onset of NVAMD, gender, neovascular lesion size, initial or final visual acuity, and number of PDT sessions required. CONCLUSIONS: In accordance with findings from the majority of previous study populations, the Tyr402His variant of CFH is associated with NVAMD in Israel. However, heterogeneity in clinical manifestations of NVAMD and in its response to PDT is not underlined by this CFH variant and may be accounted for by other genetic and environmental factors.

Sequence variants in HTRA1 and LOC387715/ARMS2 and phenotype and response to photodynamic therapy in neovascular age-related macular degeneration in populations from Israel.

PURPOSE: Single nucleotide polymorphisms (SNPs) in the tightly linked LOC387715/ARMS2 and HTRA1 genes have been associated with age-related macular degeneration (AMD). We tested whether these SNPs are associated with AMD in Israeli populations, if they underlie variable phenotype and response to therapy in neovascular AMD (NVAMD), and if HTRA1 expression in vivo is associated with its promoter variant. METHODS: Genotyping for the rs10490924 SNP in LOC387715/ARMS2 and the rs11200638 SNP in HTRA1 was performed on 255 NVAMD patients and 119 unaffected controls from Ashkenazi and Sephardic Jewish, and from Arab origins which are the main ethnic groups composing the Israeli population. Genotyping was correlated with phenotype and response to therapy among 143 patients who underwent photodynamic therapy (PDT). HTRA1 mRNA levels in white blood cells (WBCs), measured by quantitative PCR, were correlated with genotype in 27 participants. RESULTS: Both SNPs were in almost complete linkage disequilibrium (D'=0.96-1). Homozygotes for the T allele of rs10490924 had an odds ratio (OR) of 8.6, with a 95% confidence interval (CI) of 3.5-20.8, and homozygotes for the A allele of rs11200638 had an OR of 10.7, with a 95% CI of 3.2-35.7, for having AMD (p<0.00001). There was no association among these SNPs and phenotype or response to PDT. HTRA1 mRNA levels in WBCs were not associated with rs11200638 genotypes. CONCLUSIONS: The rs10490924 SNP in LOC387715/ARMS2 and the rs11200638 SNP in HTRA1 are strongly associated with NVAMD in this Israeli population. These variants do not have a major contribution to the variable phenotype and response to PDT which characterize NVAMD.

The spatial distribution of monosomy 3 and network vasculogenic mimicry patterns in uveal melanoma.

PURPOSE: Monosomy of chromosome 3 and network vasculogenic mimicry patterns are associated with death in patients with uveal melanoma (UM). Networks are typically found in confined areas within the tumor, whereas the intratumor distribution of chromosome 3 aberrations is unknown. This study was conducted to assess the spatial correlation among chromosome 3 aberrations and networks in UM. METHODS: Vasculogenic mimicry patterns, proliferative activity, and cell type were characterized in 15 enucleated eyes with primary UM. Cells were isolated by laser capture microdissection (LCM) from two tumor regions and one normal retina area from each tissue block. In the eight tumors containing networks, the cells were microdissected from one area with networks and a different area without networks. In seven tumors without networks, cells were microdissected from two distinct tumor areas. The presence of chromosome 3 aberrations was assessed by microsatellite analysis (MSA) in each LCM sample. RESULTS: Useful MSA data was obtained from 43 of the 45 samples. Monosomy 3 was detected in 16 samples of eight tumors. There was no intratumor heterogeneity for monosomy 3, regardless of the existence of heterogeneity in networks, cell type, or proliferative activity across the two samples from the same tumor. Networks were associated with the presence of monosomy 3 throughout the entire tumor (P = 0.02). CONCLUSIONS: Of the histologic prognostic factors of metastasis in UM studied, only the presence of a network vasculogenic mimicry pattern but not its location is associated with monosomy 3. This suggests that monosomy 3 may contribute to but is not sufficient for the development of the network pattern.

Molecular characteristics of liver metastases from uveal melanoma.

PURPOSE: The liver is the most common site of systemic metastases from uveal melanoma (UM). Such metastases usually continue to develop despite the application of current treatment modalities. This study was conducted to obtain insight into the molecular pathways that underlie the development of UM metastasis and thus to identify potential novel therapeutic pathways for this disease. METHODS: Microarray analysis of seven primary UMs and seven liver metastases from UMs was performed by using oligonucleotide microarrays containing 35,035 features. Bioinformatics was applied to identify expression patterns associated with metastases. Results were validated with real-time quantitative RT-PCR (QPCR) and immunohistochemistry (IHC). RESULTS: Metastasis-associated expression was detected for 193 genes at the false discovery rate (FDR) level of 0%. QPCR confirmed microarray results for all 11 genes that were evaluated (r(2) = 0.9, P = 0.0001), and IHC validated microarray data for the two proteins (NFKB2 and CDK4) that were assessed. The gene expression pattern of UM liver metastases demonstrated a resemblance to normal liver tissue. Bioinformatics facilitate identification of transcription factors, among them NFKB, which potentially regulate expression of several metastasis-associated genes. CONCLUSIONS: Liver metastases from UMs have a distinct gene expression pattern compared with the primary tumor while sharing similarities with gene expression patterns of normal liver. Several candidate genes for involvement in UM metastasis have been identified -- among them several in the NFKB pathway.

Alteration in iron metabolism during retinal degeneration in rd10 mouse.

PURPOSE: Altered iron metabolism was implicated in retinal and macular degeneration. This study was designed to further elucidate iron homeostasis during the course of retinal degeneration in mice. METHODS: Retinal mRNA and protein expression of transferrin, transferrin receptor, and ceruloplasmin were evaluated during retinal degeneration in rd10 mice and chemokine receptor 2 (ccr2)-deficient mice. Retinal ferritin protein levels, ferritin-bound iron, and total iron were evaluated in rd10 mice. RESULTS: Transferrin and ceruloplasmin mRNA levels increased between 2- and 12-fold during the course of retinal degeneration in rd10 mice compared with same-age controls (P < 0.01), whereas transferrin receptor mRNA levels increased only at the late stages of degeneration in rd10 mice (2.7-fold; P = 0.005). Transferrin mRNA also increased in retinas of aged ccr2-deficient mice (1.5-fold; P = 0.05). Transferrin and ceruloplasmin protein levels corroborated with mRNA levels changes in rd10 mice albeit at a lower magnitude. Retinal ferritin protein levels increased between 1.5-fold and 2-fold (P < 0.03) in rd10 mice, and ferritin-bound iron levels increased 1.6-fold in 3-week-old rd10 mice (P = 0.03). Three-week-old rd10 mice also had a 1.4-fold increase in total retinal iron level (P = 0.05). CONCLUSIONS: Combined with previous reports, these data suggest that retinal degenerations are associated with altered iron homeostasis regardless of the primary insult. Given the potential of iron to generate oxidative injury, its role as a therapeutic target in retinal and macular degenerations should be evaluated.

Lack of association between the C2 allele of transferrin and age-related macular degeneration in the Israeli population.

BACKGROUND: Altered iron metabolism and transferrin expression were associated with neurodegenerations including age-related macular degeneration (AMD) and Alzheimer's disease (AD). Carriers of transferrin C2 allele alone or in combination with the hemochromatosis C282Y variant may have increased risk for developing AD. We aim to assess if these alleles also predispose to AMD. METHODS: DNA was collected from 290 AMD patients and 157 unaffected, age-matched, controls. Genotyping was performed for transferrin C1/C2 alleles and hemochromatosis C282Y allele, and association with AMD was evaluated. RESULTS: There was no association between the C1/C2 transferrin alleles and AMD. Hemochromatosis C282Y variant was identified in four individuals; one was an AMD patient and three were unaffected. CONCLUSION: Transferrin C2 and hemochromatosis C282Y alleles are not associated with increased risk for developing AMD in Israel.

Inhibitor of apoptosis proteins gene expression and its correlation with prognostic factors in primary and metastatic uveal melanoma.

PURPOSE: Members of the inhibitors of apoptosis proteins (IAPs) family are thought to promote tumor growth and interfere with response to therapy by suppressing apoptosis in several malignancies. We aimed to evaluate the expression of IAPs in uveal melanoma (UM) and its correlation with prognostic factors associated with death from metastatic UM. METHODS: Expression of eight IAP genes [Baculoviral IAP repeat-containing (BIRC) 1-8] was evaluated through reverse transcription (RT)-PCR. BIRC5 and BIRC7 expression was measured using quantitative PCR (QPCR). BIRC5 protein expression was assessed with immunohistochemistry. QPCR results were correlated with apoptosis rate and with prognostic factors in UM, including lesion dimensions, cell type, monosomy 3, and vascular mimicry patterns. RESULTS: IAP genes were expressed in the majority of primary and metastatic UM. BIRC5 and BIRC7 levels were 8.8-fold (p = 0.0003) and 7.0-fold (p = 0.003) higher in tumors (primary and metastatic tissue) vs. normal eye tissue, respectively. BIRC5 levels correlated with presence of monosomy 3 (p = 0.01) and higher levels of BIRC7 correlated with epithelioid cell type (p = 0.048). CONCLUSIONS: IAPs expression is up regulated in UM and is associated with some of its prognostic factors. Considering our findings together with previous reports on their role in a variety of malignancies and in UM cell lines, it is conceivable that IAPs contribute to the remarkable resistance of uveal melanoma to apoptosis-inducing chemotherapy.