Genome-wide profiling of p63 DNA-binding sites identifies an element that regulates gene expression during limb development in the 7q21 SHFM1 locus.
Heterozygous mutations in p63 are associated with split hand/foot malformations (SHFM), orofacial clefting, and ectodermal abnormalities. Elucidation of the p63 gene network that includes target genes and regulatory elements may reveal new genes for other malformation disorders. We performed genome-wide DNA-binding profiling by chromatin immunoprecipitation (ChIP), followed by deep sequencing (ChIP-seq) in primary human keratinocytes, and identified potential target genes and regulatory elements controlled by p63. We show that p63 binds to an enhancer element in the SHFM1 locus on chromosome 7q and that this element controls expression of DLX6 and possibly DLX5, both of which are important for limb development. A unique micro-deletion including this enhancer element, but not the DLX5/DLX6 genes, was identified in a patient with SHFM. Our study strongly indicates disruption of a non-coding cis-regulatory element located more than 250 kb from the DLX5/DLX6 genes as a novel disease mechanism in SHFM1. These data provide a proof-of-concept that the catalogue of p63 binding sites identified in this study may be of relevance to the studies of SHFM and other congenital malformations that resemble the p63-associated phenotypes.
Kouwenhoven
Evelyn N
EN
Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands.
van Heeringen
Simon J
SJ
Tena
Juan J
JJ
Oti
Martin
M
Dutilh
Bas E
BE
Alonso
M Eva
ME
de la Calle-Mustienes
Elisa
E
Smeenk
Leonie
L
Rinne
Tuula
T
Parsaulian
Lilian
L
Bolat
Emine
E
Jurgelenaite
Rasa
R
Huynen
Martijn A
MA
Hoischen
Alexander
A
Veltman
Joris A
JA
Brunner
Han G
HG
Roscioli
Tony
T
Oates
Emily
E
Wilson
Meredith
M
Manzanares
Miguel
M
Gómez-Skarmeta
José Luis
JL
Stunnenberg
Hendrik G
HG
Lohrum
Marion
M
van Bokhoven
Hans
H
Zhou
Huiqing
H
D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D002478:Cells, Cultured; D002675:Child, Preschool; D047369:Chromatin Immunoprecipitation; D002897:Chromosomes, Human, Pair 7 / Q000235:genetics* / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D004742:Enhancer Elements, Genetic; D005260:Female; D018507:Gene Expression Regulation, Developmental; D055106:Genome-Wide Association Study; D018398:Homeodomain Proteins / Q000235:genetics* / Q000378:metabolism; D006801:Humans; D015603:Keratinocytes / Q000378:metabolism; D017880:Limb Deformities, Congenital / Q000235:genetics* / Q000378:metabolism; D008297:Male; D008565:Membrane Proteins / Q000235:genetics / Q000378:metabolism*; D051379:Mice; D008969:Molecular Sequence Data; D046988:Proteasome Endopeptidase Complex / Q000235:genetics* / Q000378:metabolism; D011485:Protein Binding; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism; D015027:Zebrafish
C081876:CKAP4 protein, human; C100596:DLX5 protein, human; C491014:DLX6 protein, human; D004268:DNA-Binding Proteins; D018398:Homeodomain Proteins; D008565:Membrane Proteins; C484606:SEM1 protein, human; D014157:Transcription Factors; D046988:Proteasome Endopeptidase Complex
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