Transposase-assisted target-site integration for efficient plant genome engineering.

The current technologies to place new DNA into specific locations in plant genomes are low frequency and error-prone, and this inefficiency hampers genome-editing approaches to develop improved crops1,2. Often considered to be genome 'parasites', transposable elements (TEs) evolved to insert their DNA seamlessly into genomes3-5. Eukaryotic TEs select their site of insertion based on preferences for chromatin contexts, which differ for each TE type6-9. Here we developed a genome engineering tool that controls the TE insertion site and cargo delivered, taking advantage of the natural ability of the TE to precisely excise and insert into the genome. Inspired by CRISPR-associated transposases that target transposition in a programmable manner in bacteria10-12, we fused the rice Pong transposase protein to the Cas9 or Cas12a programmable nucleases. We demonstrated sequence-specific targeted insertion (guided by the CRISPR gRNA) of enhancer elements, an open reading frame and a gene expression cassette into the genome of the model plant Arabidopsis. We then translated this system into soybean-a major global crop in need of targeted insertion technology. We have engineered a TE 'parasite' into a usable and accessible toolkit that enables the sequence-specific targeting of custom DNA into plant genomes.

The catalytic core of DEMETER guides active DNA demethylation in Arabidopsis.

The Arabidopsis DEMETER (DME) DNA glycosylase demethylates the maternal genome in the central cell prior to fertilization and is essential for seed viability. DME preferentially targets small transposons that flank coding genes, influencing their expression and initiating plant gene imprinting. DME also targets intergenic and heterochromatic regions, but how it is recruited to these differing chromatin landscapes is unknown. The C-terminal half of DME consists of 3 conserved regions required for catalysis in vitro. We show that this catalytic core guides active demethylation at endogenous targets, rescuing dme developmental and genomic hypermethylation phenotypes. However, without the N terminus, heterochromatin demethylation is significantly impeded, and abundant CG-methylated genic sequences are ectopically demethylated. Comparative analysis revealed that the conserved DME N-terminal domains are present only in flowering plants, whereas the domain architecture of DME-like proteins in nonvascular plants mainly resembles the catalytic core, suggesting that it might represent the ancestral form of the 5mC DNA glycosylase found in plant lineages. We propose a bipartite model for DME protein action and suggest that the DME N terminus was acquired late during land plant evolution to improve specificity and facilitate demethylation at heterochromatin targets.

Rice OsPEX1, an extensin-like protein, affects lignin biosynthesis and plant growth.

KEY MESSAGE: Rice leucine-rich repeat extensin-like protein OsPEX1 mediates the intersection of lignin deposition and plant growth. Lignin, a major structural component of secondary cell wall, is essential for normal plant growth and development. However, the molecular and genetic regulation of lignin biosynthesis is not fully understood in rice. Here we report the identification and characterization of a rice semi-dominant dwarf mutant (pex1) with stiff culm. Molecular and genetic analyses revealed that the pex1 phenotype was caused by ectopic expression of a leucine-rich repeat extension-like gene, OsPEX1. Interestingly, the pex1 mutant showed significantly higher lignin content and increased expression levels of lignin-related genes compared with wild type plants. Conversely, OsPEX1-suppresssed transgenics displayed low lignin content and reduced transcriptional abundance of genes associated with lignin biosynthesis, indicating that the OsPEX1 mediates lignin biosynthesis and/or deposition in rice. When OsPEX1 was ectopically expressed in rice cultivars with tall stature that lacks the allele of semi-dwarf 1, well-known green revolution gene, the resulting transgenic plants displayed reduced height and enhanced lodging resistance. Our study uncovers a causative effect between the expression of OsPEX1 and lignin deposition. Lastly, we demonstrated that modulating OsPEX1 expression could provide a tool for improving rice lodging resistance.

A naturally occurring conditional albino mutant in rice caused by defects in the plastid-localized OsABCI8 transporter.

A wide range of molecules are transported across membranes by the ATP binding cassette (ABC) transporters. Plants possess a collection of ABC proteins bearing similarities to the components of prokaryotic multi subunit ABC transporters, designed as ABC group I. However the functions of most of them are not well understood. Here, we characterized a naturally occurring rice mutant that exhibited albino phenotype under continuous rainy days in the field, but gradually recovered to normal green after the rainy season. Molecular and genetic analyses revealed that the phenotypes were caused by a mutation in the OsABCI8 that encoded a member of the ABCI family. Subcellular localization demonstrated that OsABCI8 is a chloroplast ABC transporter. Expression of OsABCI8 is significantly enhanced in rainy days compared to sunny days. Besides defects in chloroplast development and chlorophyll biosynthesis, the mutant phenotype is accompanied by a higher accumulation of iron, suggesting that OsABCI8 is involved in iron transportation and/or homeostasis in rice. Our results demonstrate that OsABCI8 represents a conserved ABCI protein involved in transition metals transportation and/or homeostasis and suggest an important role of the plastid-localized OsABCI8 for chloroplast development.

A plant tethering system for the functional study of protein-RNA interactions in vivo.

The sorting of RNA transcripts dictates their ultimate post-transcriptional fates, such as translation, decay or degradation by RNA interference (RNAi). This sorting of RNAs into distinct fates is mediated by their interaction with RNA-binding proteins. While hundreds of RNA binding proteins have been identified, which act to sort RNAs into different pathways is largely unknown. Particularly in plants, this is due to the lack of reliable protein-RNA artificial tethering tools necessary to determine the mechanism of protein action on an RNA in vivo. Here we generated a protein-RNA tethering system which functions on an endogenous Arabidopsis RNA that is tracked by the quantitative flowering time phenotype. Unlike other protein-RNA tethering systems that have been attempted in plants, our system circumvents the inadvertent triggering of RNAi. We successfully in vivo tethered a protein epitope, deadenylase protein and translation factor to the target RNA, which function to tag, decay and boost protein production, respectively. We demonstrated that our tethering system (1) is sufficient to engineer the downstream fate of an RNA, (2) enables the determination of any protein's function upon recruitment to an RNA, and (3) can be used to discover new interactions with RNA-binding proteins.

Loss of linker histone H1 in the maternal genome influences DEMETER-mediated demethylation and affects the endosperm DNA methylation landscape.

The Arabidopsis DEMETER (DME) DNA glycosylase demethylates the central cell genome prior to fertilization. This epigenetic reconfiguration of the female gamete companion cell establishes gene imprinting in the endosperm and is essential for seed viability. DME demethylates small and genic-flanking transposons as well as intergenic and heterochromatin sequences, but how DME is recruited to these loci remains unknown. H1.2 was identified as a DME-interacting protein in a yeast two-hybrid screen, and maternal genome H1 loss affects DNA methylation and expression of selected imprinted genes in the endosperm. Yet, the extent to which H1 influences DME demethylation and gene imprinting in the Arabidopsis endosperm has not been investigated. Here, we showed that without the maternal linker histones, DME-mediated demethylation is facilitated, particularly in the heterochromatin regions, indicating that H1-bound heterochromatins are barriers for DME demethylation. Loss of H1 in the maternal genome has a very limited effect on gene transcription or gene imprinting regulation in the endosperm; however, it variably influences euchromatin TE methylation and causes a slight hypermethylation and a reduced expression in selected imprinted genes. We conclude that loss of maternal H1 indirectly influences DME-mediated demethylation and endosperm DNA methylation landscape but does not appear to affect endosperm gene transcription and overall imprinting regulation.

The initiation of RNA interference (RNAi) in plants.

When an mRNA enters into the RNA degradation pathway called RNA interference (RNAi), it is cleaved into small interfering RNAs (siRNAs) that then target complementary mRNAs for destruction. The consequence of entry into RNAi is mRNA degradation, post-transcriptional silencing and in some cases transcriptional silencing. RNAi functions as a defense against transposable element and virus activity, and in plants, RNAi additionally plays a role in development by regulating some genes. However, it is unknown how specific transcripts are selected for RNAi, and how most genic mRNAs steer clear. This Current Opinion article explores the key question of how RNAs are selected for entry into RNAi, and proposes models that enable the cell to distinguish between transcripts to translate versus destroy.

Inhibitor IkappaBalpha promoter functional polymorphisms in patients with rheumatoid arthritis.

INTRODUCTION: Rheumatoid arthritis (RA) is a chronic inflammation disease that may involve extra-articular organs in addition to joints. Many proinflammatory cytokines are involved in the inflammatory process of RA. IkappaBalpha conjugates with NF-kappaB and is a key player in regulation of the inflammatory process. We carried out experiments to define the effect of different promoter polymorphisms on the transcriptional activities of IkappaBalpha promoter and the development of RA. METHODS: Different IkappaBalpha promoter reporters were constructed and were examined in human mononuclear cells, THP-1 cells. One hundred forty patients and 115 healthy controls were recruited from the Kaohsiung Medical University Hospital. RESULTS: The activities of IkappaBalpha promoter constructs with -826C, -550A, -519T, and -826T, -550A, -519T genotypes were expressed at one half the activity level of other constructs. Promoter constructs containing the sites -550A/T and -519T had a reduced risk of rheumatoid arthritis. The odds ratio of -826C/T genotype was significantly associated with an increase of risk in causing rheumatoid arthritis, whereas -826T/T genotype was associated only with a slightly increased risk of RA, but without statistical significance (odds ratio = 1.2; 95% confidence interval, 0.4-3.8). CONCLUSION: The increase of T allele was associated with a significant increased risk and the tendency to the pathogenesis of RA. The association between IkappaBalpha promoter polymorphisms and disease severity of rheumatoid arthritis is partly due to different transcriptional activities of IkappaBalpha promoter and the activation of NF-kappaB.

Targeted methylation of CMV and E1A viral promoters.

DNA methylation is a gene-silencing and host defense system that can down-regulate viral gene expression in mammalian cells. An established targeted DNA methylation method was used to demonstrate that genome-integrated CMV and adenovirus type 5 E1A promoters were hypermethylated after MCF7 and HEK293 cells were transfected with in vitro methylated viral promoter fragments. In both cases, the targeted methylation-induced gene silencing could be reversed by addition of 5-aza-2'-deoxycytidine, confirming that the CMV and E1A promoters are regulated by DNA methylation. The kinetics of the targeted DNA methylation was determined using a reporter system in live cells. In conclusion, targeted DNA methylation is able to efficiently silence susceptible viral promoters and provides an alternative strategy to study the impact of loci-specific DNA methylation in viral gene expression.

IkBα promoter polymorphisms in patients with ankylosing spondylitis.

The purpose of this study is to investigate the association of IκBα with the development of ankylosing spondylitis (AS) in Taiwan. One hundred and fifty-four patients with AS and 112 unrelated healthy controls were enrolled in this study. The IκBα-881A/G, -826C/T, -550A/T, -519C/T, and -297C/T polymorphisms were determined by the polymerase chain reaction/restriction fragment length polymorphism method. This study demonstrated that the genotype frequencies of IκBα-826C/T and -826T/T, and allele frequencies of IκBα-826T were significantly higher in the patients with AS than in the controls. We also found that the estimated haplotype frequencies of IκBα-881A -826T -550A -519C -297C and IκBα-881A -826C -550A -519T -297C were significantly increased in the patient with AS in comparison with that of the controls. In contrast, the estimated haplotype frequency of IκBα-881A -826C -550A -519C -297C was significantly decreased in the patients with AS. This study demonstrates that IκBα-826T is associated with the development of AS. Furthermore, the IκBα-881A -826T -550A -519C -297C and IκBα-881A -826C -550A -519T -297C haplotypes are related to susceptibility to AS in Taiwan.

Role of Salivary Immune Parameters in Patients With Primary Sjögren's Syndrome.

BACKGROUND: Several factors, including clinical manifestations and laboratory data, have been used to evaluate the disease activity of Sjögren's syndrome (SS). We investigated saliva indicators of disease activity in primary SS patients. METHODS: We enrolled 138 Taiwanese patients with primary SS and 100 Taiwanese normal controls. Interleukin (IL)-6, IL-17A, tumor necrosis factor-alpha (TNF-α), and rheumatoid factor (RF)-IgA levels in saliva samples were measured using ELISA or fluorescent enzyme-linked immunoassay. Serum IgG, IgA, and IgM levels were measured by nephelometry. Erythrocyte sedimentation rate (ESR) was measured with an automatic ESR analyzer. The t-test and Pearson correlation test were used. RESULTS: IL-6 level was higher in primary SS patients than in normal controls (14.23±14.77 vs 9.87±7.32, P=0.012), but there were no significant differences in IL-17A, TNF-α, and RF-IgA levels. In primary SS patients, IL-6 level correlated weakly with ESR and IgG levels (r=0.252, P=0.015, and r=0.248, P=0.017, respectively), and TNF-α level correlated weakly with IgG level (r=0.231, P=0.024). CONCLUSIONS: IL-6 may play a role in SS pathogenesis. Saliva IL-6 might be an indicator of disease activity in primary SS patients.

IkappaBalpha promoter polymorphisms in patients with Behçet's disease.

To investigate the role of IkappaBalpha promoter polymorphisms in the development of Behçet's disease, eighty-six patients with Behçet's disease and 120 healthy controls were enrolled in this study. The IkappaBalpha -881A/G, -826C/T, -550A/T, -519C/T, and -297C/T polymorphisms were measured by the method of polymerase chain reaction/ restriction fragment length polymorphism. This study demonstrated that the genotype frequencies of IkappaBalpha -826C/T and -826T/T were significantly higher in the patients with Behçet's disease than in the controls. Both in the dominant and in the recessive models, the patients with Behçet's disease have higher frequencies of the IkappaBalpha -826T containing genotype than the controls. The allele frequency of IkappaBalpha -826T was significantly increased in the patients with Behçet's disease. The frequencies of the IkappaBalpha -881A -826T -550A -519C -297C and IkappaBalpha -881A -826T -550A -519T -297C haplotypes were significantly higher in the patients with Behçet's disease than in the controls. In contrast, the haplotype frequency of IkappaBalpha -881A -826C -550A -519C -297C in the patients with Behçet's disease was significantly decreased. This study also revealed that the Behçet's disease patients with IkappaBalpha -826T/T have higher prevalence of skin lesions than those without IkappaBalpha -826T/T. In summary, the IkappaBalpha -826T allele, IkappaBalpha -881A -826T -550A -519C -297C and IkappaBalpha -881A -826T -550A -519T -297C haplotypes might be associated with susceptibility to Behçet's disease. The IkappaBalpha -826T/T genotype was related to the development of skin lesions in the patients with Behçet's disease.