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

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

PROVIDER: PRJNA892131 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR21974173_1.fastq.gz	Fastqsanger.gz
	SRR21974173_2.fastq.gz	Fastqsanger.gz
	SRR21974174_1.fastq.gz	Fastqsanger.gz
	SRR21974174_2.fastq.gz	Fastqsanger.gz
	SRR21974175_1.fastq.gz	Fastqsanger.gz

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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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Best Practices for Massively Parallel Reporter Assays – Analyses, Diagnostics, and Interpretation

Project description:This GEO submission accompanies the study “Best Practices for Massively Parallel Reporter Assays – Analyses, Diagnostics, and Interpretation” and includes five MPRA datasets used as illustrative examples in the manuscript figures. The datasets represent common MPRA experimental designs and are provided to demonstrate recommended analytical workflows, quality-control diagnostics, and interpretation strategies. These data serve as reference resources for analysis benchmarking, rather than for deriving new biological conclusions.

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Best Practices for Massively Parallel Reporter Assays – Analyses, Diagnostics, and Interpretation

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Single cell gene expression profile from wild-type and mutant canine retinas following massively parallel reporter assays using pooled AAV5-promoter-GFP vectors.

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Project description:Transcriptional-Regulatory Convergence Across Functional MDD Risk Variants Identified by Massively Parallel Reporter Assays

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Characterization of De Novo Promoter Variants in Autism Spectrum Disorder with Massively Parallel Reporter Assays.

Project description:Autism spectrum disorder (ASD) is a common, complex, and highly heritable condition with contributions from both common and rare genetic variations. While disruptive, rare variants in protein-coding regions clearly contribute to symptoms, the role of rare non-coding remains unclear. Variants in these regions, including promoters, can alter downstream RNA and protein quantity; however, the functional impacts of specific variants observed in ASD cohorts remain largely uncharacterized. Here, we analyzed 3600 de novo mutations in promoter regions previously identified by whole-genome sequencing of autistic probands and neurotypical siblings to test the hypothesis that mutations in cases have a greater functional impact than those in controls. We leveraged massively parallel reporter assays (MPRAs) to detect transcriptional consequences of these variants in neural progenitor cells and identified 165 functionally high confidence de novo variants (HcDNVs). While these HcDNVs are enriched for markers of active transcription, disruption to transcription factor binding sites, and open chromatin, we did not identify differences in functional impact based on ASD diagnostic status.

| S-EPMC9959321 | biostudies-literature

Transcriptional-Regulatory Convergence Across Functional MDD Risk Variants Identified by Massively Parallel Reporter Assays [Expt1]

Project description:Transcriptional-Regulatory Convergence Across Functional MDD Risk Variants Identified by Massively Parallel Reporter Assays [Expt1]

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Transcriptional-Regulatory Convergence Across Functional MDD Risk Variants Identified by Massively Parallel Reporter Assays [Expt2]

Project description:Transcriptional-Regulatory Convergence Across Functional MDD Risk Variants Identified by Massively Parallel Reporter Assays [Expt2]

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A systematic evaluation of the design, orientation, and sequence context dependencies of massively parallel reporter assays

Project description:Enhancers play important roles in evolution and disease. However, traditional assays to test enhancers are low throughput and not scalable to the >100,000 enhancers in the human genome. To better prioritize variants associated with disease and to study the role of enhancers, our group and others developed massively parallel reporter assays (MPRAs), which functionally screen thousands of sequences for regulatory activity in parallel. Although MPRAs have been applied to address diverse questions in gene regulation, there has been no systematic comparison of how differences in experimental design influence findings, making it difficult to interpret results and compare between groups. Here, we screen a library of 2,440 sequences, representing candidate liver enhancers and controls, in HepG2 cells for regulatory activity using nine different approaches (including conventional episomal, STARR-seq, and lentiviral MPRA designs). We identify subtle but significant differences in the resulting measurements that correlate with epigenetic and sequence-level features. We also test this library in both orientations with respect to the promoter, validating en masse that enhancer activity is robustly independent of orientation. Finally, we develop and apply a novel method to assemble and functionally test libraries of the same putative enhancers as 192-mers, 354-mers, and 678-mers, and observe surprisingly large differences in functional activity. This work provides a framework for the experimental design of high-throughput reporter assays, suggesting that the extended sequence context of tested elements, and to a lesser degree the precise assay, influence MPRA results.

2019-12-30 | GSE142696 | GEO

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