Analysis of zebrafish periderm enhancers facilitates identification of a regulatory variant near human KRT8/18

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Abstract

Genome wide association studies for non-syndromic orofacial cleft (OFC) have identified single nucleotide polymorphisms (SNPs) at loci where the presumed risk-relevant gene is expressed in oral periderm. The functional subsets of such SNPs are difficult to predict because the sequence underpinnings of periderm enhancers are unknown. We applied ATAC-seq to models of human palate periderm, including zebrafish periderm, mouse embryonic palate epithelia, and a human oral epithelium cell line, and to complementary mesenchymal cell types. We identified sets of enhancers specific to the epithelial cells and trained gapped-kmer support-vector-machine classifiers on these sets. We used the classifiers to predict the effect of 14 OFC-associated SNPs at 12q13 near KRT18. All the classifiers picked the same SNP as having the strongest effect, but the significance was highest with the classifier trained on zebrafish periderm. Reporter and deletion analyses support this SNP as lying within a periderm enhancer regulating KRT18/KRT8 expression.

Data availability

1 Raw and processed sequencing data were deposited in GEO repository (GSE140241, GSE139945 and GSE139809).2 Custom scripts and piplines we deployed for sequencing data analysis and visualization are available at https://github.com/Badgerliu/periderm_ATACSeq.3 All data generated or analysed during this study are included in the manuscript and supporting files. Source data files have been provided for Figures.

The following data sets were generated

1. Liu H
2. Cornell RA
(2019) Zebrafish periderm at 4-somite stage
NCBI Gene Expression Omnibus, GSE140241.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE140241
1. Liu H
2. Cornell RA
(2019) ATAC-seq profile of mouse palatal epithelium at E14.5
NCBI Gene Expression Omnibus, GSE139945.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE139945
1. Liu H
2. Cornell RA
(2019) Human oral epithelial cell line HIOEC
NCBI Gene Expression Omnibus, GSE139809.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE139809

The following previously published data sets were used

(2012) Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis
NCBI Gene Expression Omnibus, GSE32483.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE32483
1. ENCODE Pilot Project Research Consortium
(2016) ChIP-seq from embryonic facial prominence (ENCSR481SGM)
NCBI Gene Expression Omnibus, GSE82727.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE82727
1. NIH Roadmap Epigenomics Mapping Consortium
(2015) 127-reference epigenome/25-state Imputation Based Chromatin State Model
127-reference epigenome/25-state Imputation Based Chromatin State Model.

http://egg2.wustl.edu/roadmap/data/byFileType/chromhmmSegmentations/ChmmModels/imputed12marks/jointModel/final/

Article and author information

Author details

Huan Liu

State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory for Oral Biomedicine of Ministry of Education (KLOBM), School and Hospital of Stomatology, Wuhan University, Wuhan, China

For correspondence
liu.huan@whu.edu.cn

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-9947-6687
Kaylia Duncan

College of Medicine, University of Iowa, Iowa City, United States

Competing interests
The authors declare that no competing interests exist.
Annika Helverson

College of Medicine, University of Iowa, Iowa City, United States

Competing interests
The authors declare that no competing interests exist.
Priyanka Kumari

College of Medicine, University of Iowa, Iowa City, United States

Competing interests
The authors declare that no competing interests exist.
Camille Mumm

College of Medicine, University of Iowa, Iowa City, United States

Competing interests
The authors declare that no competing interests exist.
Yao Xiao

State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory for Oral Biomedicine of Ministry of Education (KLOBM), School and Hospital of Stomatology, Wuhan University, Wuhan, China

Competing interests
The authors declare that no competing interests exist.
Jenna Colavincenzo Carlson

Department of Biostatistics, University of Pittsburgh, Pittsburgh, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0001-5483-0833
Fabrice Darbellay

Environmental Genomics and Systems Biology Division, Lawrence Berkeley Laboratories, Berkeley, United States

Competing interests
The authors declare that no competing interests exist.
Axel Visel

DOE Joint Genome Institute, Berkeley, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-4130-7784
Elizabeth Leslie

Department of Human Genetics, Emory University School of Medicine, Atlanta, United States

Competing interests
The authors declare that no competing interests exist.
Patrick Breheny

Department of Biostatistics, University of Iowa, Iowa City, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-0650-1119
Albert J Erives

Department of Biology, University of Iowa, Iowa City, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0001-7107-5518
Robert A Cornell

College of Medicine, University of Iowa, Iowa City, United States

For correspondence
robert-cornell@uiowa.edu

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0003-4207-9100

Funding

National Institutes of Health (DE023575)

Robert A Cornell

National Institute for Health Research (DE027362)

Robert A Cornell

National Institute of Dental and Craniofacial Research (DE025060)

Elizabeth Leslie

National Institute of Dental and Craniofacial Research (DE024427)

Axel Visel

National Institute of Dental and Craniofacial Research (DE028599)

Axel Visel

National Natural Science Foundation of China (81771057)

Huan Liu

National Natural Science Foundation of China (81400477)

Huan Liu

Natural Science Foundation of Hubei Province (2017CFB515)

Huan Liu

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

Ethics

Animal experimentation: D. rerio were maintained in the University of Iowa Animal Care Facility according to a standard protocol (protocol no. 6011616). All mouse experiments were performed in accordance with approval of the Institutional Animal Care and Use Committees at the School and Hospital of Stomatology of Wuhan University (protocol no. 00271454).Mouse experiments for LacZ reporter transgenic animal work performed at the Lawrence Berkeley National Laboratory (LBNL) were reviewed and approved by the LBNL Animal Welfare and Research Committee.

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.