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Massively parallel identification of cis-regulatory variants in yeast promoters - Annotation runs

ABSTRACT: Massively parallel identification of cis-regulatory variants in yeast promoters - Annotation runs

PROVIDER: PRJNA656370 | ENA |

REPOSITORIES: ENA

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Massively parallel identification of cis-regulatory variants in yeast promoters - Annotation runs

Project description:Sequence variation in regulatory DNA alters gene expression and shapes genetically complex traits. However, the identification of individual, causal regulatory variants is challenging. Here, we used a massively parallel reporter assay to measure the cis-regulatory consequences of 5,832 natural DNA variants in the promoters of 2,503 genes in the yeast Saccharomyces cerevisiae. We identified 451 causal variants, which underlie genetic loci known to affect gene expression. Several promoters harbored multiple causal variants. In five promoters, pairs of variants showed non-additive, epistatic interactions. Causal variants were enriched at conserved nucleotides, tended to have low derived allele frequency, and were depleted from promoters of essential genes, consistent with the action of negative selection. Causal variants were enriched for alterations in transcription factor binding sites. Models integrating these features provided modest, but statistically significant, ability to predict causal variants. This work revealed a complex molecular basis for cis-acting regulatory variation.

2020-08-31 | GSE155942 | GEO

Massively parallel identification of cis-regulatory variants in yeast promoters

Project description:Massively parallel identification of cis-regulatory variants in yeast promoters

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Massively parallel identification of cis-regulatory variants in yeast promoters - Experimental measurements

2020-08-31 | GSE155943 | GEO

Massively parallel identification of cis-regulatory variants in yeast promoters - Experimental measurements

Project description:Massively parallel identification of cis-regulatory variants in yeast promoters - Experimental measurements

| PRJNA656371 | ENA

Massively parallel identification of cis-regulatory variants in yeast promoters

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

2020-08-31 | GSE155944 | GEO

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Massively parallel functional testing of MSH2 missense variants conferring Lynch Syndrome risk

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Massively parallel profiling of human regulatory variants in endothelial cells

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Characterization of de novo promoter variants in autism spectrum disorder with massively parallel reporter assays

Project description:To functionaly test thousands of promoter based Autism associated de novo variants, we established neural progenitor cells from human embryonic stem cells and performed massively parallel reporter assays to collect transcription rates associated with reference and alternate allele sequences

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Massively parallel reporter assays (MPRAs) of 175bp human genomic fragments containing variants in high LD with lead variants from obesity GWAS associations.

Project description:We performed a massively parallel reporter assay on 2,396 genomic regions containing single nucleotide polymorphisms that are in high linkage disequilibrium with 97 lead variants from an obesity GWAS (PMID: 25673413). Regions were transfected into human SGBS preadipocytes, SGBS mature adipocytes, 3T3-L1 preadipocytes, HT22 hippocampal cells, and GT1-7 cells and assessed for enhancer activity. The processed file contains the MPRA barcodes.

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