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

View ORCID ProfileHuan Liu, Kaylia Duncan, Annika Helverson, Priyanka Kumari, Camille Mumm, Yao Xiao, Jenna Carlson, Fabrice Darbellay, Axel Visel, Elizabeth Leslie, Patrick Breheny, View ORCID ProfileAlbert Erives, Robert A. Cornell
doi: https://doi.org/10.1101/2020.01.27.921320
Huan Liu
1State 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 430079, China
2Department of Anatomy and Cell Biology, University of Iowa, Iowa City, Iowa
3Department of Periodontology, School of Stomatology, Wuhan University, Wuhan, China
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  • For correspondence: robert-cornell@uiowa.edu liu.huan@whu.edu.cn
Kaylia Duncan
4Interdisciplinary Program in Molecular Medicine, University of Iowa, Iowa City, Iowa
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Annika Helverson
2Department of Anatomy and Cell Biology, University of Iowa, Iowa City, Iowa
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Priyanka Kumari
2Department of Anatomy and Cell Biology, University of Iowa, Iowa City, Iowa
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Camille Mumm
2Department of Anatomy and Cell Biology, University of Iowa, Iowa City, Iowa
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Yao Xiao
1State 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 430079, China
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Jenna Carlson
5Department of Biostatistics, University of Pittsburgh
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Fabrice Darbellay
6Environmental Genomics and Systems Biology Division, Lawrence Berkeley Laboratories, Berkeley, California
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Axel Visel
6Environmental Genomics and Systems Biology Division, Lawrence Berkeley Laboratories, Berkeley, California
10U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley Laboratories, Berkeley, California
11University of California at Merced, Merced, California
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Elizabeth Leslie
7Department of Human Genetics, Emory University School of Medicine
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Patrick Breheny
8Department of Biostatistics, University of Iowa, Iowa City, Iowa
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Albert Erives
9Department of Biology, University of Iowa, Iowa City, Iowa
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Robert A. Cornell
2Department of Anatomy and Cell Biology, University of Iowa, Iowa City, Iowa
4Interdisciplinary Program in Molecular Medicine, University of Iowa, Iowa City, Iowa
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  • For correspondence: robert-cornell@uiowa.edu liu.huan@whu.edu.cn
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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.

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Posted January 28, 2020.
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Analysis of zebrafish periderm enhancers facilitates identification of a regulatory variant near human KRT8/18
Huan Liu, Kaylia Duncan, Annika Helverson, Priyanka Kumari, Camille Mumm, Yao Xiao, Jenna Carlson, Fabrice Darbellay, Axel Visel, Elizabeth Leslie, Patrick Breheny, Albert Erives, Robert A. Cornell
bioRxiv 2020.01.27.921320; doi: https://doi.org/10.1101/2020.01.27.921320
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Analysis of zebrafish periderm enhancers facilitates identification of a regulatory variant near human KRT8/18
Huan Liu, Kaylia Duncan, Annika Helverson, Priyanka Kumari, Camille Mumm, Yao Xiao, Jenna Carlson, Fabrice Darbellay, Axel Visel, Elizabeth Leslie, Patrick Breheny, Albert Erives, Robert A. Cornell
bioRxiv 2020.01.27.921320; doi: https://doi.org/10.1101/2020.01.27.921320

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