Cited by 283Genomics and Chromatin DynamicsGenetic Associations and EpidemiologyCRISPR and Genetic Engineering

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Decoding enhancers using massively parallel reporter assays

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Inoue, Fumitaka, Ahituv, Nadav·2015·Genomics

DOI 10.1016/j.ygeno.2015.06.005PMC PMC4540663

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Abstract

Enhancers control the timing, location and expression levels of their target genes. Nucleotide variation in enhancers has been shown to lead to numerous phenotypes, including human disease. While putative enhancer sequences and nucleotide variation within them can now be detected in a rapid manner using various genomic technologies, the understanding of the functional consequences of these variants still remains largely unknown. Massively parallel reporter assays (MPRAs) can overcome this hurdle by providing the ability to test thousands of sequences and nucleotide variants within them for enhancer activity en masse. Here, we describe this technology and specifically focus on how it is being used to obtain an increased understanding of enhancer regulatory code and grammar.

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Authors: Inoue, F., & Ahituv, N.
Affiliations: University of California, San Francisco (US)
Corresponding author: Ahituv, Nadav
ORCID: Inoue, Fumitaka
Ahituv, Nadav
Venue: Genomics
Publisher: Elsevier BV
Published: 2015-09
Volume: 106
Issue: 3
Pages: 159-164
ISSN: 0888-7543 (ISSN-L)
DOI: 10.1016/j.ygeno.2015.06.005
PMC: PMC4540663
OpenAlex: W655820313
Cited by: 272
References: 50
Citations by year: 2026: 26 · 2025: 36 · 2024: 25 · 2023: 28 · 2022: 29 · 2021: 36 · 2020: 30 · 2019: 25 · 2018: 11 · 2017: 20 · 2016: 5
FWCI: 1.16
Type: journal article
Language: en
Open access: bronze
doi.org
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
www.elsevier.com/open-access/userlicense/1.0/ (vor, 909 d)
Locations: Genomics (publishedVersion)
PubMed (publishedVersion)
PubMed Central (acceptedVersion)
eScholarship (California Digital Library) (submittedVersion)
Funders: National Human Genome Research Institute (1R01HG006768)
National Cancer Institute (1R01CA197139)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
Keywords: enhancers, massively parallel reporter assay, enhancer activity, nucleotide variants, regulatory codes, enhancer function, gene expression regulation, variant effect prediction
MeSH terms: Binding Sites, Enhancer Elements, Genetic, Gene Expression Regulation, Humans, Promoter Regions, Genetic, Transcription Factors, Sequence Analysis, DNA, Genomics, High-Throughput Nucleotide Sequencing

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Decoding enhancers using massively parallel reporter assays

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