Similar Datasets
Project description:The transcription factor p63 shares a high sequence identity with the tumour suppressor p53 which manifests itself in high structural similarity and preference for DNA sequences. Mutations in the DNA binding domain (DBD) of p53 have been studied in great detail, enabling a general mechanism-based classification. In this study we provide a detailed investigation of all currently known mutations in the p63 DBD, which are associated with developmental syndromes, by measuring their impact on transcriptional activity, DNA binding affinity, zinc binding capacity and thermodynamic stability. Some of the mutations we have further characterized with respect to their ability to convert human dermal fibroblasts into induced keratinocytes. Here we propose a classification of the p63 DBD mutations based on the four different mechanisms of DNA binding impairment which we identified: direct DNA contact, zinc finger region, H2 region, and dimer interface mutations. The data also demonstrate that, in contrast to p53 cancer mutations, no p63 mutation induces global unfolding and subsequent aggregation of the domain. The dimer interface mutations that affect the DNA binding affinity by disturbing the interaction between the individual DBDs retain partial DNA binding capacity which correlates with a milder patient phenotype.
| S-EPMC10113246 | biostudies-literature
Project description:The transcription factor p63 shares a high sequence identity with the tumour suppressor p53 which manifests itself in high structural similarity and preference for DNA sequences. While mutations in the DNA binding domain of p53 cause cancer, mutations in the p63 DNA binding domain result in developmental syndromes affecting lip/palate, skin and limbs. For p53 the effect of mutations has been studied in great detail, enabling the identification of several mechanisms by which mutations inhibit high affinity binding of p53 to DNA. In this study we provide a similar detailed investigation of all currently known mutations in the p63 DNA binding domain by measuring the transcriptional activity, DNA binding affinity, zinc binding capacity and thermodynamic stability. Some of the mutations we have further characterized with respect to their ability to convert human dermal fibroblasts into induced keratinocytes, to elicit changes in the transcriptional program similar to those observed by wild type p63, and to bind regulatory regions in the genome. The data demonstrate that no mutation globally destabilizes and unfolds the domain. Several mutations affect the DNA binding affinity by disturbing the interaction between the DNA binding domains, thereby disrupting p63 ability to bind DNA as a tetramer cooperatively. These mutations retain partial DNA binding capacity which correlates with a milder patient phenotype.
2025-11-28 | GSE221529 | GEO
Project description:The transcription factor p63 shares a high sequence identity with the tumour suppressor p53 which manifests itself in high structural similarity and preference for DNA sequences. While mutations in the DNA binding domain of p53 cause cancer, mutations in the p63 DNA binding domain result in developmental syndromes affecting lip/palate, skin and limbs. For p53 the effect of mutations has been studied in great detail, enabling the identification of several mechanisms by which mutations inhibit high affinity binding of p53 to DNA. In this study we provide a similar detailed investigation of all currently known mutations in the p63 DNA binding domain by measuring the transcriptional activity, DNA binding affinity, zinc binding capacity and thermodynamic stability. Some of the mutations we have further characterized with respect to their ability to convert human dermal fibroblasts into induced keratinocytes, to elicit changes in the transcriptional program similar to those observed by wild type p63, and to bind regulatory regions in the genome. The data demonstrate that no mutation globally destabilizes and unfolds the domain. Several mutations affect the DNA binding affinity by disturbing the interaction between the DNA binding domains, thereby disrupting p63 ability to bind DNA as a tetramer cooperatively. These mutations retain partial DNA binding capacity which correlates with a milder patient phenotype.
2025-11-28 | GSE221525 | GEO
Project description:The transcription factor p63 shares a high sequence identity with the tumour suppressor p53 which manifests itself in high structural similarity and preference for DNA sequences. While mutations in the DNA binding domain of p53 cause cancer, mutations in the p63 DNA binding domain result in developmental syndromes affecting lip/palate, skin and limbs. For p53 the effect of mutations has been studied in great detail, enabling the identification of several mechanisms by which mutations inhibit high affinity binding of p53 to DNA. In this study we provide a similar detailed investigation of all currently known mutations in the p63 DNA binding domain by measuring the transcriptional activity, DNA binding affinity, zinc binding capacity and thermodynamic stability. Some of the mutations we have further characterized with respect to their ability to convert human dermal fibroblasts into induced keratinocytes, to elicit changes in the transcriptional program similar to those observed by wild type p63, and to bind regulatory regions in the genome. The data demonstrate that no mutation globally destabilizes and unfolds the domain. Several mutations affect the DNA binding affinity by disturbing the interaction between the DNA binding domains, thereby disrupting p63 ability to bind DNA as a tetramer cooperatively. These mutations retain partial DNA binding capacity which correlates with a milder patient phenotype.
2025-11-28 | GSE221520 | GEO
Project description:Disease-related p63 DBD mutations impair DNA binding by distinct mechanisms and varying degree
| PRJNA914737 | ENA
Project description:Disease-related p63 DBD mutations impair DNA binding by distinct mechanisms and varying degree [ChIP-seq]
| PRJNA914733 | ENA
Project description:Disease-related p63 DBD mutations impair DNA binding by distinct mechanisms and varying degree [RNA-seq]
| PRJNA914739 | ENA
Project description:Disease-related p63 DBD mutations impair DNA binding by distinct mechanisms and varying degree [ATAC-seq]
| PRJNA914871 | ENA
Project description:Wilms tumour is the most common childhood kidney cancer. Here we report the whole-exome sequencing of 44 Wilms tumours, identifying missense mutations in the microRNA (miRNA)-processing enzymes DROSHA and DICER1, and novel mutations in MYCN, SMARCA4 and ARID1A. Examination of tumour miRNA expression, in vitro processing assays and genomic editing in human cells demonstrates that DICER1 and DROSHA mutations influence miRNA processing through distinct mechanisms. DICER1 RNase IIIB mutations preferentially impair processing of miRNAs deriving from the 5'-arm of pre-miRNA hairpins, while DROSHA RNase IIIB mutations globally inhibit miRNA biogenesis through a dominant-negative mechanism. Both DROSHA and DICER1 mutations impair expression of tumour-suppressing miRNAs, including the let-7 family, important regulators of MYCN, LIN28 and other Wilms tumour oncogenes. These results provide new insights into the mechanisms through which mutations in miRNA biogenesis components reprogramme miRNA expression in human cancer and suggest that these defects define a distinct subclass of Wilms tumours.
| S-EPMC4159681 | biostudies-literature
Project description:The type 1 ryanodine receptor (RyR1) is an intracellular calcium (Ca2+) release channel on the sarcoplasmic/endoplasmic reticulum that is required for skeletal muscle contraction. RyR1 channel activity is modulated by ligands, including the activators Ca2+ and ATP. Patients with inherited mutations in RyR1 may exhibit muscle weakness as part of a heterogeneous, complex disorder known as RYR1-related myopathy (RYR1-RM) or more recently termed RYR1-related disorders (RYR1-RD). Guided by high-resolution structures of skeletal muscle RyR1, obtained using cryogenic electron microscopy, we introduced mutations into putative Ca2+ and ATP binding sites and studied the function of the resulting mutant channels. These mutations confirmed the functional significance of the Ca2+ and ATP binding sites identified by structural studies based on the effects on channel regulation. Under normal conditions, Ca2+ activates RyR1 at low concentrations (µM) and inhibits it at high concentrations (mM). Mutations in the Ca2+-binding site impaired both activating and inhibitory regulation of the channel, suggesting a single site for both high and low affinity Ca2+-dependent regulation of RyR1 function. Mutation of residues that interact with the adenine ring of ATP abrogated ATP binding to the channel, whereas mutating residues that interact with the triphosphate tail only affected the degree of activation. In addition, patients with mutations at the Ca2+ or ATP binding sites suffer from muscle weakness, therefore impaired RyR1 channel regulation by either Ca2+ or ATP may contribute to the pathophysiology of RYR1-RM in some patients.
| S-EPMC8609856 | biostudies-literature