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In Vivo Functional Study of Disease-associated Rare Human Variants Using Drosophila

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RefSeq Functional Elements as experimentally assayed nongenic reference standards and functional interactions in

Catherine M Farrell¹, Tamara Goldfarb¹, Sanjida H Rangwala¹

¹National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA.

Genome Research

|December 8, 2021

Summary

This summary is machine-generated.

The National Center for Biotechnology Information (NCBI) now offers RefSeq Functional Elements (RefSeqFEs), a curated database of experimentally validated non-genic elements. This resource aids in understanding genome function, disease, and epigenomic data interpretation.

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Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Eukaryotic genomes possess numerous non-genic elements crucial for gene regulation, chromosome organization, and DNA processes.
Mutations in these non-genic elements can disrupt genome function and lead to diseases.
Epigenomic studies often cover gene regulatory regions, but this data is not always integrated into standard genome annotations, posing accessibility challenges.

Purpose of the Study:

To introduce RefSeq Functional Elements (RefSeqFEs) as a curated resource for experimentally validated human and mouse non-genic elements.
To provide accessible and interpretable data on non-genic elements, supporting basic research and clinical applications.
To offer a complementary resource to existing epigenomic datasets, enhancing functional element discovery and interpretation.

Main Methods:

Data curation from scientific literature to identify experimentally validated non-genic elements.
Integration of curated data into richly annotated sequence records and the NCBI Gene database.
Development of a flexible data model incorporating reference genome feature annotation and interaction data.

Main Results:

RefSeqFEs provide succinct functional details with transparent experimental evidence.
The dataset includes sequence records, NCBI Gene database entries, and genome feature annotations.
Activity-based interactions between non-genic regions, target genes, and other elements are documented.

Conclusions:

RefSeqFEs offer a valuable, accessible, and adaptable resource for functional genomics research, bioinformatics, and genetic variant interpretation.
The dataset serves as a reference for evaluating epigenomic data and understanding functional interactions.
While smaller and subject to selection biases compared to some datasets, RefSeqFEs provide a unique, experimentally validated perspective on non-genic elements.