PRDM1 DNA-binding zinc finger domain is required for normal limb development and is disrupted in Split Hand/Foot Malformation

Abstract

ABSTRACTSplit Hand/Foot Malformation (SHFM) is a rare limb abnormality with clefting of the fingers and/or toes. For many patients, the genetic etiology is unknown. Through whole exome and targeted sequencing, we detected three novel variants in a transcription factor,PRDM1that arosede novoin families with SHFM or segregated with the phenotype. PRDM1 is required for limb development; however, its role is not well understood, and it is unclear how thePRDM1variants affect protein function. Using transient and stable overexpression rescue experiments in zebrafish, we show that the variants, which disrupt the proline/serine-rich and DNA-binding zinc finger domains have reduced function compared to wildtypePRDM1. Through gene expression assays, RNA-seq, and CUT&RUN in isolated pectoral fin cells, we demonstrate that Prdm1a directly binds to and regulates genes required for limb induction, outgrowth, and anterior/posterior patterning, such asfgfr1a, dlx5a, dlx6a, andsmo. Together, these results improve our understanding of the role of PRDM1 in the limb gene regulatory network and demonstrate the pathogenicity ofPRDM1variants in humans.SUMMARY STATEMENTPRDM1 proline/serine and zinc finger domains are required to regulate limb induction, outgrowth, and anterior/posterior patterning. Variants in PRDM1 are shown to cause Split Hand/Foot Malformation in humans.