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Polygenic trait SNPs in noncoding genomic regions: using chromatin maps to elucidate potential regulatory mechanisms in blood pressure [RNA-seq]

ABSTRACT: Polygenic trait SNPs in noncoding genomic regions: using chromatin maps to elucidate potential regulatory mechanisms in blood pressure [RNA-seq]

PROVIDER: PRJNA1136018 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR29836536_1.fastq.gz	Fastqsanger.gz
	SRR29836536_2.fastq.gz	Fastqsanger.gz
	SRR29836537_1.fastq.gz	Fastqsanger.gz
	SRR29836537_2.fastq.gz	Fastqsanger.gz
	SRR29836538_1.fastq.gz	Fastqsanger.gz

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Polygenic trait SNPs in noncoding genomic regions: using chromatin maps to elucidate potential regulatory mechanisms in blood pressure [RNA-seq]

Project description:Many polygenic traits are associated with hundreds of single nucleotide polymorphisms (SNPs), which predominantly (>95%) reside within noncoding genomic regions, making it difficult to understand how they regulate complex traits, such as blood pressure (BP). Given the central role of the kidney in regulating BP, we hypothesized that chromatin-accessible regions in renal tissue would be enriched for BP-associated SNPs (bpSNPs). We developed chromatin state and transcriptomic maps of the proximal tubules (PT) and medullary thick ascending limbs (mTAL) isolated from humans and rats. These maps revealed shared cis-regulatory elements (CREs) across humans and rats, including upstream transcriptional regulators. Notably, bpSNPs were significantly enriched within open chromatin regions, suggesting they potentially alter the activity of CREs and near genes critical to renal development and function. Collectively, this work lays a foundation for interrogating how intergenic SNPs may regulate polygenic traits such as BP.

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Polygenic trait SNPs in noncoding genomic regions: using chromatin maps to elucidate potential regulatory mechanisms in blood pressure [ATAC-seq]

Project description:Polygenic trait SNPs in noncoding genomic regions: using chromatin maps to elucidate potential regulatory mechanisms in blood pressure [ATAC-seq]

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Evaluation of expression quantitative trait loci within two interacting blood pressure quantitative trait loci

Project description:Genetic dissection of the S rat genome has provided strong evidence for the presence of two interacting blood pressure (BP) quantitative trait loci (QTLs), termed QTL1 and QTL2, on rat chromosome 5. However, the identities of the underlying interacting genetic factors remain unknown. Further experiments targeted to identify the interacting genetic factors by the substitution mapping approach alone are difficult because of the interdependency of natural recombinations to occur at the two QTLs. We hypothesized that the interacting genetic factors underlying these two QTLs may interact at the level of gene transcription and thereby represent expression QTLs (eQTLs). To detect these interacting eQTLs, a custom QTL chip containing the annotated genes within QTL1 and QTL2 was developed and used to conduct a transcriptional profiling study of S and two congenic strains that retain either one or both the QTLs. The results uncovered an interaction between two transcription factors, DMRTA2 and NFIA. Further, the ‘biological signature’ elicited by these two transcription factors was differential between the congenic strain that retained LEW alleles at both QTL1 and 2 compared to the congenic strain that retained LEW alleles at QTL1 alone. A network of transcription factors potentially affecting BP could be traced, lending support to our hypothesis. Keywords: rat, hypertension, genetics, polygenic trait, microarray, gene expression

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