Characterization of sequence determinants of enhancer function using natural genetic variation

Abstract
Data availability
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Abstract

Sequence variation in enhancers that control cell type-specific gene transcription contributes significantly to phenotypic variation within human populations. However, it remains difficult to predict precisely the effect of any given sequence variant on enhancer function due to the complexity of DNA sequence motifs that determine transcription factor (TF) binding to enhancers in their native genomic context. Using F₁-hybrid cells derived from crosses between distantly related inbred strains of mice, we identified thousands of enhancers with allele-specific TF binding and/or activity. We find that genetic variants located within the central region of enhancers are most likely to alter TF binding and enhancer activity. We observe that the AP-1 family of TFs (Fos/Jun) are frequently required for binding of TEAD TFs and for enhancer function. However, many sequence variants outside of core motifs for AP-1 and TEAD also impact enhancer function, including sequences flanking core TF motifs and AP-1 half sites. Taken together, these data represent one of the most comprehensive assessments of allele-specific TF binding and enhancer function to date and reveal how sequence changes at enhancers alter their function across evolutionary timescales.

Data availability

We submitted our data to GEO, and it is now accessible via GSE193728.

The following data sets were generated

(2022) Characterization of sequence determinants of enhancer function using natural genetic variation
NCBI Gene Expression Omnibus, GSE193728.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE193728

The following previously published data sets were used

(2017) AP-1 transcription factors and the BAF complex mediate signal-dependent enhancer selection
GEO: GSE83295.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE83295
1. Wouter Meuleman; John A. Stamatoyannopoulos
(2019) Index and biological spectrum of accessible DNA elements in the human genome
https://doi.org/10.1101/822510.

https://zenodo.org/record/3838751#.YcOHmGZKhBx

Article and author information

Author details

Marty G Yang

Department of Neurobiology, Harvard University, Boston, United States

Competing interests
The authors declare that no competing interests exist.
Emi Ling

Department of Neurobiology, Harvard University, Boston, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0001-5287-0284
Christopher J Cowley

Laboratory of Mammalian Cell Biology and Development, Rockefeller University, Howard Hughes Medical Institute, New York, United States

Competing interests
The authors declare that no competing interests exist.
Michael E Greenberg

Department of Neurobiology, Harvard University, Boston, United States

For correspondence
meg@hms.harvard.edu

Competing interests
The authors declare that no competing interests exist.
Thomas Vierbuchen

Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States

For correspondence
vierbuct@mskcc.org

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-5690-5680

Funding

NIH Office of the Director (T32EY00711030)

Marty G Yang

NIH Office of the Director (T32AG000222)

Marty G Yang

National Science Foundation (DGE0946799)

Emi Ling

National Science Foundation (DGE1144152)

Emi Ling

NIH Office of the Director (R01 NS115965)

Michael E Greenberg

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Ethics

Animal experimentation: All animal experiments were approved by the National Institutes of Health and the Harvard Medical School Institutional Animal Care and Use Committee and were conducted in compliance with the relevant ethical regulations (Protocol # IS00000074-3)

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.