Deletion of CTCF sites in the SHH locus alters enhancer-promoter interactions and leads to acheiropodia.

TitleDeletion of CTCF sites in the SHH locus alters enhancer-promoter interactions and leads to acheiropodia.
Publication TypeJournal Article
Year of Publication2021
AuthorsUshiki, A, Zhang, Y, Xiong, C, Zhao, J, Georgakopoulos-Soares, I, Kane, L, Jamieson, K, Bamshad, MJ, Nickerson, DA, Shen, Y, Lettice, LA, Silveira-Lucas, ELemos, Petit, F, Ahituv, N
Corporate AuthorsUniversity of Washington Center for Mendelian Genomics
JournalNat Commun
Date Published2021 04 16
KeywordsAnimals, 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, Congenital, Hedgehog Proteins, Humans, Introns, Male, Membrane Proteins, Mice, Mice, Knockout, Promoter Regions, Genetic, Sequence Deletion, Species Specificity, Whole Genome Sequencing

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.

Alternate JournalNat Commun
PubMed ID33863876
PubMed Central IDPMC8052326
Grant ListP01 HD084387 / HD / NICHD NIH HHS / United States
U24 HG008956 / HG / NHGRI NIH HHS / United States
R01 HD059862 / HD / NICHD NIH HHS / United States
S10 OD021553 / OD / NIH HHS / United States
UM1 HG006493 / HG / NHGRI NIH HHS / United States
MM_UU_00007/8 / MR / Medical Research Council / United Kingdom