Towards a comprehensive catalogue of validated and target-linked human enhancers

The human gene catalogue is essentially complete, but we lack an equivalently vetted inventory of bona fide human enhancers. Hundreds of thousands of candidate enhancers have been nominated via biochemical annotations; however, only a handful of these have been validated and confidently linked to th...

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Bibliographic Details
Published in:Nature reviews. Genetics 2020-05, Vol.21 (5), p.292-310
Main Authors: Gasperini, Molly, Tome, Jacob M., Shendure, Jay
Format: Article
Language:English
Subjects:
631/1647/2163
631/208/200
631/208/212/2019
631/208/4041/3196
631/208/514/1949
631/208/726/2102
631/61/191/2018
Agriculture
Animal Genetics and Genomics
Biochemical assays
Biomedical and Life Sciences
Biomedicine
Cancer Research
Clustered Regularly Interspaced Short Palindromic Repeats
CRISPR
DNA sequencing
Enhancer Elements, Genetic
Enhancers
Gene Function
Genome, Human
Genomic libraries
Human Genetics
Humans
Identification and classification
Methods
Nucleotide sequencing
Review Article
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Summary:The human gene catalogue is essentially complete, but we lack an equivalently vetted inventory of bona fide human enhancers. Hundreds of thousands of candidate enhancers have been nominated via biochemical annotations; however, only a handful of these have been validated and confidently linked to their target genes. Here we review emerging technologies for discovering, characterizing and validating human enhancers at scale. We furthermore propose a new framework for operationally defining enhancers that accommodates the heterogeneous and complementary results that are emerging from reporter assays, biochemical measurements and CRISPR screens. In this Review, Gasperini, Tome and Shendure discuss the evolving definitions of transcriptional enhancers, as well as diverse modern experimental tools to identify them. The authors describe how these diverse mindsets and methods provide differing but complementary insights into enhancers, each with notable strengths and caveats. They discuss how such views and approaches might be combined in a comprehensive catalogue of functional enhancers.
ISSN:1471-0056
1471-0064
1471-0064
DOI:10.1038/s41576-019-0209-0