@article {1021,
	title = {Deletion of CTCF sites in the SHH locus alters enhancer-promoter interactions and leads to acheiropodia.},
	journal = {Nat Commun},
	volume = {12},
	year = {2021},
	month = {2021 04 16},
	pages = {2282},
	abstract = {<p>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.</p>},
	keywords = {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, Congenital, Hedgehog Proteins, Humans, Introns, Male, Membrane Proteins, Mice, Mice, Knockout, Promoter Regions, Genetic, Sequence Deletion, Species Specificity, Whole Genome Sequencing},
	issn = {2041-1723},
	doi = {10.1038/s41467-021-22470-z},
	author = {Ushiki, Aki and Zhang, Yichi and Xiong, Chenling and Zhao, Jingjing and Georgakopoulos-Soares, Ilias and Kane, Lauren and Jamieson, Kirsty and Bamshad, Michael J and Nickerson, Deborah A and Shen, Yin and Lettice, Laura A and Silveira-Lucas, Elizabeth Lemos and Petit, Florence and Ahituv, Nadav}
}
@article {621,
	title = {Mutations in the fourth β-propeller domain of LRP4 are associated with isolated syndactyly with fusion of the third and fourth fingers.},
	journal = {Hum Mutat},
	volume = {39},
	year = {2018},
	month = {2018 06},
	pages = {811-815},
	abstract = {<p>Isolated hand syndactyly is a common limb malformation with limited known genetic etiology. We used exome sequencing to discover two novel variants, chr11 g.46896373C>G; p.D1403H and chr11 g.46893078G>T; p.Q1564K, in LRP4 in a child with isolated bilateral syndactyly of the third and fourth fingers. Each variant was inherited from a different parent and neither parent was affected. Variants in LRP4 have been previously associated with syndactyly in Cenani-Lenz syndactyly syndrome and Sclerosteosis 2, but have not been reported in individuals with isolated syndactyly. LRP4 inhibits LRP6/LRP5-mediated activation of canonical Wnt signaling and mediates sclerostin-dependent inhibition of bone formation. p.D1403H and p.Q1564K are located within the fourth β-propeller of the extracellular protein domain that has yet to be associated with human disease. Functional analyses of p.D1403H and p.Q1564K show that they significantly decrease LRP4{\textquoteright}s inhibition of Wnt signaling. These results suggest that variants in the fourth β-propeller of the extracellular protein domain may cause a phenotype distinct from previously characterized LRP4 variants.</p>},
	issn = {1098-1004},
	doi = {10.1002/humu.23417},
	author = {Sukenik Halevy, Rivka and Chien, Huan-Chieh and Heinz, Bo and Bamshad, Michael J and Nickerson, Deborah A and Kircher, Martin and Ahituv, Nadav}
}
