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Systematic Functional Dissection of Common Genetic Variation Affecting Red Blood Cell Traits [MPRA]

ABSTRACT: Systematic Functional Dissection of Common Genetic Variation Affecting Red Blood Cell Traits [MPRA]

PROVIDER: PRJNA345666 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR4370070.fastq.gz	Fastqsanger.gz
	SRR4370071.fastq.gz	Fastqsanger.gz
	SRR4370072.fastq.gz	Fastqsanger.gz
	SRR4370073.fastq.gz	Fastqsanger.gz
	SRR4370074.fastq.gz	Fastqsanger.gz

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Systematic Functional Dissection of Common Genetic Variation Affecting Red Blood Cell Traits [MPRA]

Project description:Genome-wide association studies (GWAS) have successfully identified thousands of associations between common genetic variants and human disease phenotypes, but the majority of these variants are non-coding, often requiring genetic fine-mapping, epigenomic profiling, and individual reporter assays to delineate potential causal variants. We employ a massively parallel reporter assay (MPRA) to simultaneously screen 2,756 variants in strong linkage disequilibrium with 75 sentinel variants associated with red blood cell traits. We show that this assay identifies elements with endogenous erythroid regulatory activity. Across 23 sentinel variants, we conservatively identified 32 MPRA functional variants (MFVs). We used targeted genome editing to demonstrate endogenous enhancer activity across 3 MFVs that predominantly affect the transcription of SMIM1, RBM38, and CD164. Functional follow-up of RBM38 delineates a key role for this gene in the alternative splicing program occurring during terminal erythropoiesis. Finally, we provide evidence for how common GWAS-nominated variants can disrupt cell-type-specific transcriptional regulatory pathways.

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Systematic Functional Dissection of Common Genetic Variation Affecting Red Blood Cell Traits

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Systematic Functional Dissection of Common Genetic Variation Affecting Red Blood Cell Traits [Microarray]

Project description:Genome-wide association studies (GWAS) have successfully identified thousands of associations between common genetic variants and human disease phenotypes, but the majority of these variants are non-coding, often requiring genetic fine-mapping, extensive epigenomic profiling, and individual reporter assays to delineate potential causal variants. We employ a massively parallel reporter assay to simultaneous screen 2756 variants in strong linkage-disequilibrium with 75 sentinel variants associated with red blood cell traits. We show that this assay identifies elements with erythroid-specific endogenous regulatory activity. Across 23 variants, we conservatively identified 32 putative causal variants (PCVs). We demonstrate endogenous enhancer activity for three PCVs that predominantly affect the transcription of SMIM1, RBM38, and CD164 using targeted genome editing. Functional follow up of RBM38 delineates a key role for this gene in the dramatic alternative splicing program occurring during terminal erythropoiesis. Finally, we provide evidence for how common GWAS-nominated variants can disrupt cell-type specific transcriptional regulatory pathways.

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