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KAT6A mutations in Arboleda-Tham syndrome affect regulation and expression of HOXC genes.

ABSTRACT: KAT6A mutations in Arboleda-Tham syndrome affect regulation and expression of HOXC genes.

PROVIDER: PRJNA993369 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR25224500.fastq.gz	Fastqsanger.gz
	SRR25224501.fastq.gz	Fastqsanger.gz
	SRR25224502.fastq.gz	Fastqsanger.gz
	SRR25224503_1.fastq.gz	Fastqsanger.gz
	SRR25224503_2.fastq.gz	Fastqsanger.gz

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KAT6A mutations in Arboleda-Tham syndrome affect regulation and expression of HOXC genes [RNA-seq]

Project description:Arboleda-Tham Syndrome (ARTHS) is a rare genetic disorder caused by heterozygous, de novo truncating mutations in the gene KAT6A (Lysine(K) acetyltransferase 6A). ARTHS is clinically heterogeneous but characterized by several common features including intellectual disability, developmental and speech delay, hypotonia, congenital heart defects and gastrointestinal problems. KAT6A mRNA is highly expressed throughout early development and the levels of expression are lower levels in differentiated tissues, suggesting a key role maintenance of the stem cell characteristics. Across these cell types, the gene-regulatory mechanisms controlled by KAT6A and the histone-acetylation complex in which it works remain unknown. In this study, we created ARTHS patient-derived (n=7) and control (n=13) dermal fibroblasts from skin punch biopsies. KAT6A is expressed at moderate levels in human fibroblast cells and we performed a comprehensive profiling of the epigenomic and transcriptomic changes in ARTHS.

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KAT6A mutations in Arboleda-Tham syndrome affect regulation and expression of HOXC genes [ChIP-seq]

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KAT6A mutations in Arboleda-Tham syndrome affect regulation and expression of HOXC genes [RNA-seq]

Project description:KAT6A mutations in Arboleda-Tham syndrome affect regulation and expression of HOXC genes [RNA-seq]

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KAT6A mutations in Arboleda-Tham syndrome affect regulation and expression of HOXC genes [ATAC-seq]

Project description:KAT6A mutations in Arboleda-Tham syndrome affect regulation and expression of HOXC genes [ATAC-seq]

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KAT6A mutations in Arboleda-Tham syndrome affect regulation and expression of HOXC genes [ChIP-seq]

Project description:KAT6A mutations in Arboleda-Tham syndrome affect regulation and expression of HOXC genes [ChIP-seq]

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DNA methylation profiling of Arboleda-Tham syndrome in primary human fibroblasts

Project description:Arboleda-Tham Syndrome is a rare disease caused by de novo mutations in the KAT6A gene. Epigenetic changes to the genome resulting from pathogenic mutations were investigated by DNAme profiling.

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KAT6A mutations in Arboleda-Tham syndrome drive epigenetic regulation of posterior HOXC cluster.

Project description:Arboleda-Tham Syndrome (ARTHS) is a rare genetic disorder caused by heterozygous, de novo mutations in Lysine(K) acetyltransferase 6A (KAT6A). ARTHS is clinically heterogeneous and characterized by several common features, including intellectual disability, developmental and speech delay, and hypotonia, and affects multiple organ systems. KAT6A is the enzymatic core of a histone-acetylation protein complex; however, the direct histone targets and gene regulatory effects remain unknown. In this study, we use ARTHS patient (n = 8) and control (n = 14) dermal fibroblasts and perform comprehensive profiling of the epigenome and transcriptome caused by KAT6A mutations. We identified differential chromatin accessibility within the promoter or gene body of 23% (14/60) of genes that were differentially expressed between ARTHS and controls. Within fibroblasts, we show a distinct set of genes from the posterior HOXC gene cluster (HOXC10, HOXC11, HOXC-AS3, HOXC-AS2, and HOTAIR) that are overexpressed in ARTHS and are transcription factors critical for early development body segment patterning. The genomic loci harboring HOXC genes are epigenetically regulated with increased chromatin accessibility, high levels of H3K23ac, and increased gene-body DNA methylation compared to controls, all of which are consistent with transcriptomic overexpression. Finally, we used unbiased proteomic mass spectrometry and identified two new histone post-translational modifications (PTMs) that are disrupted in ARTHS: H2A and H3K56 acetylation. Our multi-omics assays have identified novel histone and gene regulatory roles of KAT6A in a large group of ARTHS patients harboring diverse pathogenic mutations. This work provides insight into the role of KAT6A on the epigenomic regulation in somatic cell types.

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<i>KAT6A</i> mutations in Arboleda-Tham syndrome drive epigenetic regulation of posterior <i>HOXC</i> cluster.

Project description:Arboleda-Tham Syndrome (ARTHS) is a rare genetic disorder caused by heterozygous, de novo truncating mutations in Lysine(K) acetyltransferase 6A (KAT6A). ARTHS is clinically heterogeneous and characterized by several common features including intellectual disability, developmental and speech delay, hypotonia and affects multiple organ systems. KAT6A is highly expressed in early development and plays a key role in cell-type specific differentiation. KAT6A is the enzymatic core of a histone-acetylation protein complex, however the direct histone targets and gene regulatory effects remain unknown. In this study, we use ARTHS patient (n=8) and control (n=14) dermal fibroblasts and perform comprehensive profiling of the epigenome and transcriptome caused by KAT6A mutations. We identified differential chromatin accessibility within the promoter or gene body of 23%(14/60) of genes that were differentially expressed between ARTHS and controls. Within fibroblasts, we show a distinct set of genes from the posterior HOXC gene cluster (HOXC10, HOXC11, HOXC-AS3, HOXC-AS2, HOTAIR) that are overexpressed in ARTHS and are transcription factors critical for early development body segment patterning. The genomic loci harboring HOXC genes are epigenetically regulated with increased chromatin accessibility, high levels of H3K23ac, and increased gene-body DNA methylation compared to controls, all of which are consistent with transcriptomic overexpression. Finally, we used unbiased proteomic mass spectrometry and identified two new histone post-translational modifications (PTMs) that are disrupted in ARTHS: H2A and H3K56 acetylation. Our multi-omics assays have identified novel histone and gene regulatory roles of KAT6A in a large group of ARTHS patients harboring diverse pathogenic mutations. This work provides insight into the role of KAT6A on the epigenomic regulation in somatic cell types.

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KAT6A mutations in Arboleda-Tham syndrome affect regulation and expression of HOXC genes.

Project description:This SuperSeries is composed of the SubSeries listed below.

2023-08-15 | GSE237023 | GEO