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A systematic p53 mutation library links differential functional impact to cancer mutation pattern and evolutionary conservation

ABSTRACT: A systematic p53 mutation library links differential functional impact to cancer mutation pattern and evolutionary conservation

PROVIDER: PRJNA473655 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7233510_1.fastq.gz	Fastqsanger.gz
	SRR7233510_2.fastq.gz	Fastqsanger.gz
	SRR7233520_1.fastq.gz	Fastqsanger.gz
	SRR7233520_2.fastq.gz	Fastqsanger.gz
	SRR7233530_1.fastq.gz	Fastqsanger.gz

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A systematic p53 mutation library links differential functional impact to cancer mutation pattern and evolutionary conservation

Project description:The TP53 gene is frequently mutated in human cancer. Research has focused predominantly on six major “hotspot” codons, accounting for only ~30% of cancer-associated p53 mutations. To comprehensively characterize the consequences of the p53 mutation spectrum, we created a synthetically designed library and measured the functional impact of ~10,000 DNA-binding domain (DBD) p53 variants in human cells in culture and in vivo. Our results highlight the differential outcome of distinct p53 mutations in human patients and elucidate the selective pressure driving p53 conservation throughout evolution. Furthermore, while loss of anti-proliferative functionality largely correlates with the occurrence of cancer-associated p53 mutations, we observe that selective gain-of-function may further favor particular mutants in vivo. Finally, when combined with additional acquired p53 mutations, seemingly neutral TP53 SNPs may modulate phenotypic outcome and presumably tumor progression.

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Project description:E.O. Wilson proposed in Sociobiology that similarities between human and animal societies reflect common mechanistic and evolutionary roots. When introduced in 1975 this controversial hypothesis was beyond science’s ability to test and remains unproven. We used genomic analyses to determine whether superficial behavioral similarities in humans and the highly social honey bee reflect common molecular mechanisms. Here we report that gene expression signatures for individual bees unresponsive to various salient social stimuli are significantly enriched for autism spectrum disorder-related genes. These signatures occur in the mushroom bodies, a high-level integration center of the insect brain. Further, our finding of enrichment was unique to autism spectrum disorders; brain gene expression signatures from other honey bee behaviors do not show this enrichment, nor do data sets from other human behavioral and health conditions. These results demonstrate deep conservation for genes associated with a human social pathology and individual differences in insect social behavior, thus providing an example of how comparative genomics can be used to test sociobiological theory.

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Project description:A number of genes of the developmental gene hierarchy in Drosophila encode transcription factors containing Cys2His2 zinc finger domains as DNA-binding motifs. To learn more about the evolution of these genes, it is necessary to clone the homologs, or more correctly the orthologs, from different species. Using PCR, we were able to obtain apparently orthologous fragments of hunchback (hb), Krüppel (Kr), and snail (sna) from a variety of arthropods and partly also from other animal phyla. Sequence alignments of these fragments show that the amino acid differences can normally not be correlated with the evolutionary distances of the respective species. This is due to an apparent saturation of potential replacements within the finger domains, which is also evident from the frequent occurrence of convergent replacements. Another recurrent feature of these alignments is that those amino acids that are directly involved in determining the DNA-binding specificity of the fingers are most conserved. Using in vitro bandshift experiments we can indeed show that the binding specificity of a hunchback finger fragment from different species is not changed. This implies that there is a high selective pressure to maintain the regulatory target elements of these genes during evolution.

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Project description:Identification of the coding elements in the genome is a fundamental step to understanding the building blocks of living systems. Short peptides (< 100 aa) have emerged as important regulators of development and physiology, but their identification has been limited by their size. We have leveraged the periodicity of ribosome movement on the mRNA to define actively translated ORFs by ribosome footprinting. This approach identifies several hundred translated small ORFs in zebrafish and human. Computational prediction of small ORFs from codon conservation patterns corroborates and extends these findings and identifies conserved sequences in zebrafish and human, suggesting functional peptide products (micropeptides). These results identify micropeptideM-bM-^@M-^Pencoding genes in vertebrates, providing an entry point to define their function in vivo. Ribosome profiling experiments at five timepoints across zebrafish development in WT embryos

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Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation

Project description:Identification of the coding elements in the genome is a fundamental step to understanding the building blocks of living systems. Short peptides (< 100 aa) have emerged as important regulators of development and physiology, but their identification has been limited by their size. We have leveraged the periodicity of ribosome movement on the mRNA to define actively translated ORFs by ribosome footprinting. This approach identifies several hundred translated small ORFs in zebrafish and human. Computational prediction of small ORFs from codon conservation patterns corroborates and extends these findings and identifies conserved sequences in zebrafish and human, suggesting functional peptide products (micropeptides). These results identify micropeptide‐encoding genes in vertebrates, providing an entry point to define their function in vivo.

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