Cited by 159Genomics and Chromatin DynamicsChromatin Remodeling and CancerEpigenetics and DNA Methylation

Functional assessment of human enhancer activities using whole-genome STARR-sequencing

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Liu, Yuwen, Yu, Shan, Dhiman, Vineet K., Brunetti, Tonya, Eckart, Heather, White, Kevin P.·2017·Genome Biology

Abstract

BACKGROUND: Genome-wide quantification of enhancer activity in the human genome has proven to be a challenging problem. Recent efforts have led to the development of powerful tools for enhancer quantification. However, because of genome size and complexity, these tools have yet to be applied to the whole human genome. RESULTS: In the current study, we use a human prostate cancer cell line, LNCaP as a model to perform whole human genome STARR-seq (WHG-STARR-seq) to reliably obtain an assessment of enhancer activity. This approach builds upon previously developed STARR-seq in the fly genome and CapSTARR-seq techniques in targeted human genomic regions. With an improved library preparation strategy, our approach greatly increases the library complexity per unit of starting material, which makes it feasible and cost-effective to explore the landscape of regulatory activity in the much larger human genome. In addition to our ability to identify active, accessible enhancers located in open chromatin regions, we can also detect sequences with the potential for enhancer activity that are located in inaccessible, closed chromatin regions. When treated with the histone deacetylase inhibitor, Trichostatin A, genes nearby this latter class of enhancers are up-regulated, demonstrating the potential for endogenous functionality of these regulatory elements. CONCLUSION: WHG-STARR-seq provides an improved approach to current pipelines for analysis of high complexity genomes to gain a better understanding of the intricacies of transcriptional regulation.

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  • Genome-wide 'shotgun MPRAs' avoid a priori assumptions about which sequences to test.

    “In contrast with MPRAs relying on re-synthesis of candidate sequences, genome-wide ‘shotgun MPRAs’108,174,183,188 nicely avoid a priori assumptions about which sequences to test.”
  • MPRAs have been applied to assess biochemically annotated candidate enhancers, candidate enhancers harbouring variants that potentially mediate eQTLs, and even scans of the entire human genome.

    “MPRAs have been applied to assess biochemically annotated candidate enhancers77,176-178, candidate enhancers harbouring variants that potentially mediate eQTLs179-182, and even scans of the entire human genome108,183.”

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  1. [39]Liu Y, Yu S, Dhiman V, Brunetti T, Scott H, White K. Genome-wide functional assessment of enhancer activities in the human genome. Gene Expression Omnibus. 2017. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE82204.

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Authors
Liu, Y., Yu, S., Dhiman, V. K., Brunetti, T., Eckart, H., & White, K. P.
Affiliations
  • Argonne National Laboratory (US)
  • University of Chicago (US)
Corresponding author
White, Kevin P.
Venue
Genome Biology
Published
2017-11-20
Volume
18
Issue
1
Pages
219-219
ISSN
  • 1465-6906 (ISSN-L)
  • 1474-760X
OpenAlex
W2769418303
Cited by
136
References
37
Citations by year
2026: 6 · 2025: 18 · 2024: 21 · 2023: 15 · 2022: 17 · 2021: 15 · 2020: 19 · 2019: 13 · 2018: 11 · 2017: 1
FWCI
5.67
Type
journal article
Language
en
Open access
Locations
  • Genome biology (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
National Institutes of Health (U54HG006996)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
Keywords
enhancer activity, STARR-seq, LNCaP cells, open chromatin, closed chromatin, histone deacetylase inhibition, trichostatin A, transcriptional regulation, library preparation, prostate cancer
MeSH terms
Whole Genome Sequencing, Cell Line, Chromatin, Enhancer Elements, Genetic, Humans, Genomic Library, Genome, Human, Genomics, Chromatin Immunoprecipitation, High-Throughput Nucleotide Sequencing

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