Similar Datasets
Project description:Somatic variation contributes to biological heterogeneity by modulating the cellular proclivity to differentiate, expand, adapt, or die. While large-scale sequencing efforts have revealed the foundational role of somatic variants to drive human tumor evolution, our understanding of the contribution of somatic variation to modulate cellular fitness in non-malignant contexts remains understudied. Here, we identify a somatic synonymous variant (m.7076A>G) in the mitochondrial DNA (mtDNA) encoded cytochrome c-oxidase subunit 1 gene (COX1), which was present at homoplasmy in 47% of immune cells from a healthy donor. Using single-cell multi-omics, we discover highly specific selection against the m.7076G mutant allele in the CD8+ effector memory T cell compartment in vivo, reminiscent of selection observed for pathogenic mtDNA alleles and indicative of lineage-specific metabolic vulnerabilities. Due to the limited transfer RNA (tRNA) pool in mitochondria, the m.7076G mutant allele requires wobble-dependent translation whereas the wildtype m.7076A allele can translate via Watson-Crick-Franklin (WCF) base-pairing. Mitochondrial ribosome profiling revealed that the synonymous m.7076G mutant allele altered codon-anticodon affinity by 33% at the wobble position, stalling translation at the glycine residue within COX1 encoded at m.7076. Leveraging population-based sequencing analyses, we identify evidence of synonymous somatic variants in tumor genomes and dozens of germline variants associated with complex diseases, suggesting broad functional effects of synonymous variation altering codon affinity across the mitochondrial genome. Together, these results provide a new ontogeny for mitochondrial genetic variation and elucidate a framework whereby somatic variation can impact cell state transitions in a lineage-specific manner.
2024-10-31 | GSE216912 | GEO
Project description:Somatic variation contributes to biological heterogeneity by modulating the cellular proclivity to differentiate, expand, adapt, or die. While large-scale sequencing efforts have revealed the foundational role of somatic variants to drive human tumor evolution, our understanding of the contribution of somatic variation to modulate cellular fitness in non-malignant contexts remains understudied. Here, we identify a somatic synonymous variant (m.7076A>G) in the mitochondrial DNA (mtDNA) encoded cytochrome c-oxidase subunit 1 gene (COX1), which was present at homoplasmy in 47% of immune cells from a healthy donor. Using single-cell multi-omics, we discover highly specific selection against the m.7076G mutant allele in the CD8+ effector memory T cell compartment in vivo, reminiscent of selection observed for pathogenic mtDNA alleles and indicative of lineage-specific metabolic vulnerabilities. Due to the limited transfer RNA (tRNA) pool in mitochondria, the m.7076G mutant allele requires wobble-dependent translation whereas the wildtype m.7076A allele can translate via Watson-Crick-Franklin (WCF) base-pairing. Mitochondrial ribosome profiling revealed that the synonymous m.7076G mutant allele altered codon-anticodon affinity by 33% at the wobble position, stalling translation at the glycine residue within COX1 encoded at m.7076. Leveraging population-based sequencing analyses, we identify evidence of synonymous somatic variants in tumor genomes and dozens of germline variants associated with complex diseases, suggesting broad functional effects of synonymous variation altering codon affinity across the mitochondrial genome. Together, these results provide a new ontogeny for mitochondrial genetic variation and elucidate a framework whereby somatic variation can impact cell state transitions in a lineage-specific manner.
2024-10-31 | GSE216904 | GEO
Project description:Somatic variation contributes to biological heterogeneity by modulating the cellular proclivity to differentiate, expand, adapt, or die. While large-scale sequencing efforts have revealed the foundational role of somatic variants to drive human tumor evolution, our understanding of the contribution of somatic variation to modulate cellular fitness in non-malignant contexts remains understudied. Here, we identify a somatic synonymous variant (m.7076A>G) in the mitochondrial DNA (mtDNA) encoded cytochrome c-oxidase subunit 1 gene (COX1), which was present at homoplasmy in 47% of immune cells from a healthy donor. Using single-cell multi-omics, we discover highly specific selection against the m.7076G mutant allele in the CD8+ effector memory T cell compartment in vivo, reminiscent of selection observed for pathogenic mtDNA alleles and indicative of lineage-specific metabolic vulnerabilities. Due to the limited transfer RNA (tRNA) pool in mitochondria, the m.7076G mutant allele requires wobble-dependent translation whereas the wildtype m.7076A allele can translate via Watson-Crick-Franklin (WCF) base-pairing. Mitochondrial ribosome profiling revealed that the synonymous m.7076G mutant allele altered codon-anticodon affinity by 33% at the wobble position, stalling translation at the glycine residue within COX1 encoded at m.7076. Leveraging population-based sequencing analyses, we identify evidence of synonymous somatic variants in tumor genomes and dozens of germline variants associated with complex diseases, suggesting broad functional effects of synonymous variation altering codon affinity across the mitochondrial genome. Together, these results provide a new ontogeny for mitochondrial genetic variation and elucidate a framework whereby somatic variation can impact cell state transitions in a lineage-specific manner.
2024-10-31 | GSE216903 | GEO
Project description:Somatic variation contributes to biological heterogeneity by modulating the cellular proclivity to differentiate, expand, adapt, or die. While large-scale sequencing efforts have revealed the foundational role of somatic variants to drive human tumor evolution, our understanding of the contribution of somatic variation to modulate cellular fitness in non-malignant contexts remains understudied. Here, we identify a somatic synonymous variant (m.7076A>G) in the mitochondrial DNA (mtDNA) encoded cytochrome c-oxidase subunit 1 gene (COX1), which was present at homoplasmy in 47% of immune cells from a healthy donor. Using single-cell multi-omics, we discover highly specific selection against the m.7076G mutant allele in the CD8+ effector memory T cell compartment in vivo, reminiscent of selection observed for pathogenic mtDNA alleles and indicative of lineage-specific metabolic vulnerabilities. Due to the limited transfer RNA (tRNA) pool in mitochondria, the m.7076G mutant allele requires wobble-dependent translation whereas the wildtype m.7076A allele can translate via Watson-Crick-Franklin (WCF) base-pairing. Mitochondrial ribosome profiling revealed that the synonymous m.7076G mutant allele altered codon-anticodon affinity by 33% at the wobble position, stalling translation at the glycine residue within COX1 encoded at m.7076. Leveraging population-based sequencing analyses, we identify evidence of synonymous somatic variants in tumor genomes and dozens of germline variants associated with complex diseases, suggesting broad functional effects of synonymous variation altering codon affinity across the mitochondrial genome. Together, these results provide a new ontogeny for mitochondrial genetic variation and elucidate a framework whereby somatic variation can impact cell state transitions in a lineage-specific manner.
2024-10-31 | GSE216911 | GEO
Project description:Synonymous mitochondrial DNA variation impairs CD8 T cell fate via codon affinity
| PRJNA896170 | ENA
Project description:Synonymous mitochondrial DNA variation impairs CD8 T cell fate via codon affinity [mitoRiboseq]
| PRJNA896177 | ENA
Project description:Synonymous mitochondrial DNA variation impairs CD8 T cell fate via codon affinity [TCR scRNA]
| PRJNA896162 | ENA
Project description:Synonymous mitochondrial DNA variation impairs CD8 T cell fate via codon affinity [PBMC scATAC]
| PRJNA896157 | ENA
Project description:Synonymous mitochondrial DNA variation impairs CD8 T cell fate via codon affinity [Tcell Culture scATAC]
| PRJNA896166 | ENA
Project description:Analysis of synonymous codon usage pattern in the genome of a thermophilic cyanobacterium, Thermosynechococcus elongatus BP-1 using multivariate statistical analysis revealed a single major explanatory axis accounting for codon usage variation in the organism. This axis is correlated with the GC content at third base of synonymous codons (GC3s) in correspondence analysis taking T. elongatus genes. A negative correlation was observed between effective number of codons i.e. Nc and GC3s. Results suggested a mutational bias as the major factor in shaping codon usage in this cyanobacterium. In comparison to the lowly expressed genes, highly expressed genes of this organism possess significantly higher proportion of pyrimidine-ending codons suggesting that besides, mutational bias, translational selection also influenced codon usage variation in T. elongatus. Correspondence analysis of relative synonymous codon usage (RSCU) with A, T, G, C at third positions (A3s, T3s, G3s, C3s, respectively) also supported this fact and expression levels of genes and gene length also influenced codon usage. A role of translational accuracy was identified in dictating the codon usage variation of this genome. Results indicated that although mutational bias is the major factor in shaping codon usage in T. elongatus, factors like translational selection, translational accuracy and gene expression level also influenced codon usage variation.
| S-EPMC3400985 | biostudies-literature