Deletion of CTCF sites in the SHH locus alters enhancer-promoter interactions and leads to acheiropodia.
Résumé
Acheiropodia, congenital limb truncation, is associated with homozygous deletions in the LMBR1 gene around ZRS, an enhancer regulating SHH during limb development. How these deletions lead to this phenotype is unknown. Using whole-genome sequencing, we fine-mapped the acheiropodia-associated region to 12 kb and show that it does not function as an enhancer. CTCF and RAD21 ChIP-seq together with 4C-seq and DNA FISH identify three CTCF sites within the acheiropodia-deleted region that mediate the interaction between the ZRS and the SHH promoter. This interaction is substituted with other CTCF sites centromeric to the ZRS in the disease state. Mouse knockouts of the orthologous 12 kb sequence have no apparent abnormalities, showcasing the challenges in modelling CTCF alterations in animal models due to inherent motif differences between species. Our results show that alterations in CTCF motifs can lead to a Mendelian condition due to altered enhancer-promoter interactions.
Mots clés
Animals
Binding Sites
CCCTC-Binding Factor
Chromatin Immunoprecipitation Sequencing
Disease Models
Animal
Embryo
Mammalian
Enhancer Elements
Genetic
Exons
Extremities
Female
Foot Deformities
Congenital
Gene Expression Regulation
Developmental
Genetic Loci
Genetic Testing
Hand Deformities
Hedgehog Proteins
Humans
Introns
Male
Membrane Proteins
Mice
Knockout
Promoter Regions
Sequence Deletion
Species Specificity
Whole Genome Sequencing
Domaines
Sciences du Vivant [q-bio]
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