Project description:The non-coding genome is substantially larger than the protein-coding genome, but has been largely unexplored by genetic association studies. Here, we performed region-based rare-variant association analysis of >25,000 variants in untranslated regions of 6,139 amyotrophic lateral sclerosis (ALS) whole-genomes and those of 70,403 non-ALS controls. We identified Interleukin-18 Receptor Accessory Protein (IL18RAP) 3′UTR variants as significantly enriched in non-ALS genomes and associated with five-fold reduced risk of developing ALS, and this was replicated in an independent cohort. These variants in the IL18RAP 3′UTR reduce mRNA stability and the binding of double-stranded RNA-binding proteins. Finally, the variants of IL18RAP 3′UTR confer a survival advantage for motor neurons because they dampen neurotoxicity of human iPSC-derived microglia bearing an ALS-associated expansion in C9orf72, and this depends on NF-κB signaling. This study reveals genetic variants that protect against ALS by reducing neuroinflammation, and emphasizes the importance of non-coding genetic association studies.
Project description:<p><strong>BACKGROUND:</strong> Amaranth (<em>Amaranthus spp.</em>) has high nutritional quality, with edible grain and leaves, and many agronomic advantages, making it a promising part of the solution for global food insecurity. However, we lack comprehensive metabolomic and genome sequence data for many cultivars. To support the improvement of this versatile, sustainable crop, a detailed metabolome profiling of the edible grains and leaves and genome sequencing resources is required for the widely cultivated grain amaranth cultivars such as Coral Fountain (CF), Emerald Tassels (ET), Golden Giant (GG), Hopi Red Dye (HR), and New Mexico (NM).</p><p><strong>RESULTS:</strong> Through a non-targeted high-throughput metabolic profiling using ultra-performance liquid chromatography-tandem mass spectrometry, we precisely determined the whole-grain and leaf metabolites of these five cultivars. This analysis identified 426 and 420 metabolites with known chemical structures in the grain and leaf, respectively. The five amaranth cultivars differed significantly in the levels of several nutritionally valuable compounds in grains and leaves, including sulfur amino acids, vitamins, and chlorogenic acids, as well as potentially anti-nutritive compounds, such as oxalate and raffinose family oligosaccharides. On average, the cultivars CF and ET had more favorable levels of most identified health-promoting compounds compared to GG, HR, and NM. In addition, we provide high-quality reference genome sequences for the five cultivars using the PacBio Sequel II sequencing platform with an estimated genome size of 465-483 Mb comprising 46.9-48.7% repetitive elements. We generated an iso-seq library from different amaranth plant parts and utilized it to predict the amaranth genes and annotate their function into their respective gene ontology terms.</p><p><strong>CONCLUSIONS:</strong> These resources will assist in breeding improved amaranth varieties and identifying targeted genes for trait modification and advancement through genome editing and engineering technologies.</p><p><br></p><p><strong>Seed assays</strong> are reported in the current study <a href='https://www.ebi.ac.uk/metabolights/MTBLS815' rel='noopener noreferrer' target='_blank'><strong>MTBLS815</strong></a><strong>.</strong></p><p><strong>Leaf assays</strong> are reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS3498' rel='noopener noreferrer' target='_blank'><strong>MTBLS3498</strong></a><strong>.</strong></p>
Project description:<p><strong>BACKGROUND:</strong> Amaranth (<em>Amaranthus spp.</em>) has high nutritional quality, with edible grain and leaves, and many agronomic advantages, making it a promising part of the solution for global food insecurity. However, we lack comprehensive metabolomic and genome sequence data for many cultivars. To support the improvement of this versatile, sustainable crop, a detailed metabolome profiling of the edible grains and leaves and genome sequencing resources is required for the widely cultivated grain amaranth cultivars such as Coral Fountain (CF), Emerald Tassels (ET), Golden Giant (GG), Hopi Red Dye (HR), and New Mexico (NM).</p><p><strong>RESULTS:</strong> Through a non-targeted high-throughput metabolic profiling using ultra-performance liquid chromatography-tandem mass spectrometry, we precisely determined the whole-grain and leaf metabolites of these five cultivars. This analysis identified 426 and 420 metabolites with known chemical structures in the grain and leaf, respectively. The five amaranth cultivars differed significantly in the levels of several nutritionally valuable compounds in grains and leaves, including sulfur amino acids, vitamins, and chlorogenic acids, as well as potentially anti-nutritive compounds, such as oxalate and raffinose family oligosaccharides. On average, the cultivars CF and ET had more favorable levels of most identified health-promoting compounds compared to GG, HR, and NM. In addition, we provide high-quality reference genome sequences for the five cultivars using the PacBio Sequel II sequencing platform with an estimated genome size of 465-483 Mb comprising 46.9-48.7% repetitive elements. We generated an iso-seq library from different amaranth plant parts and utilized it to predict the amaranth genes and annotate their function into their respective gene ontology terms.</p><p><strong>CONCLUSIONS:</strong> These resources will assist in breeding improved amaranth varieties and identifying targeted genes for trait modification and advancement through genome editing and engineering technologies.</p><p><br></p><p><strong>Leaf assays</strong> are reported in the current study <a href='https://www.ebi.ac.uk/metabolights/MTBLS3498' rel='noopener noreferrer' target='_blank'><strong>MTBLS3498</strong></a>.</p><p><strong>Seed assays</strong> are reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS815' rel='noopener noreferrer' target='_blank'><strong>MTBLS815</strong></a>.</p>
Project description:The identification of the genetic risk factors in patients with isolated cleft palate by whole genome sequencing analysis. Pathogenic or likely pathogenic variants were discovered in genes associated with CP (TBX22, COL2A1, FBN1, PCGF2, and KMT2D) in five patients; hence, rare disease variants were identified in 17% of patients with non-syndromic isolated CP. Our results are relevant to routine genetic counselling practice and genetic testing recommendations.
Project description:tRNAs are encoded by a large gene family, usually with several isogenic tRNAs interacting with the same codon. Mutations in the anticodon region of other tRNAs can overcome specific tRNA deficiencies. Phylogenetic analysis suggests that such mutations have occurred in evolution, but the driving force is unclear. We show that in yeast suppressor mutations in other tRNAs are able to overcome deficiency of the essential TRT2-encoded tRNAThrCGU at high temperature (40°C). Surprisingly, these tRNA suppressor mutations were obtained after whole-genome transformation with DNA from thermotolerant Kluyveromyces marxianus or Ogataea polymorpha strains, but from which the mutations did apparently not originate. We suggest that transient presence of donor DNA in the host facilitates proliferation at high temperature and thus increases the chances for occurrence of spontaneous mutations suppressing defective growth at high temperature. Whole-genome sequence analysis of three transformants revealed only four to five non-synonymous mutations of which one causing TRT2 anticodon stem stabilization and two anticodon mutations in non-threonyl-tRNAs, tRNALysCUU and tRNAeMetCAU, were causative. Both anticodon mutations suppressed lethality of TRT2 deletion and apparently caused the respective tRNAs to become novel substrates for threonyl-tRNA synthetase. LC-MS/MS data could not detect any significant mistranslation and RT-qPCR results contradicted induction of the unfolded protein response. We suggest that stress conditions have been a driving force in evolution for the selection of anticodon-switching mutations in tRNAs as revealed by phylogenetic analysis. Importance of the work In this work we have identified for the first time the causative elements in a eukaryotic organism introduced by applying whole-genome transformation and responsible for the selectable trait of interest, i.e. high temperature tolerance. Surprisingly, the whole-genome transformants contained just a few SNPs, which were unrelated to the sequence of the donor DNA. In each of three independent transformants, we have identified a SNP in a tRNA, either stabilizing the essential tRNAThrCGU at high temperature or switching the anticodon of tRNALysCUU or tRNAeMetCAU into CGU, which is apparently enough for in vivo recognition by threonyl-tRNA synthetase. LC-MS/MS analysis indeed indicated absence of significant mistranslation. Phylogenetic analysis showed that similar mutations have occurred throughout evolution and we suggest that stress conditions may have been a driving force for their selection. The low number of SNPs introduced by whole-genome transformation may favor its application for improvement of industrial yeast strains.
Project description:This study investigates multidrug-resistant Klebsiella pneumoniae KP21-10C using whole genome sequencing and targeted energy metabolomics. Genomic sequencing data were generated to characterize the bacterial genome, and targeted LC-MS/MS metabolomics was performed to quantify energy metabolism-related metabolites under doxycycline monotherapy and cepharanthine hydrochloride plus doxycycline combination treatment.