Non-coding deletions identify Maenli lncRNA as a limb-specific En1 regulator

Long non-coding RNAs (IncRNAs) can be important components in gene-regulatory networks(1), but the exact nature and extent of their involvement in human Mendelian disease is largely unknown. Here we show that genetic ablation of a lncRNA locus on human chromosome 2 causes a severe congenital limb malformation. We identified homozygous 27-63-kilobase deletions located 300 kilobases upstream of the engrailed-1 gene (EN1) in patients with a complex limb malformation featuring mesomelic shortening, syndactyly and ventralnails (dorsal dimelia). Re-engineering of the human deletions in mice resulted in a complete loss of En1 expression in the limb and a double dorsal-limb phenotype that recapitulates the human disease phenotype. Genome-widetranscriptome analysis in the developing mouse limb revealed a four-exon-longnon-codingtranscript with in the deleted region, which we named Maenli. Functional dissection of the Maenli locus showed that its transcriptional activity is required for limb-specificEn1 activation in cis, thereby fine-tuningthe gene-regulatory networks controlling dorso-ventral polarity in the developing limb bud. Its loss results in the En1-related dorsal ventral limb phenotype, a subset of the full En1-associated phenotype. Our findings demonstrate that mutations involving lncRNA loci can result in human Mendelian disease.

Automated summary

This study demonstrates that genetic ablation of a lncRNA locus on human chromosome 2 can result in a severe congenital limb malformation. The findings highlight the importance of the lncRNA locus in regulating En1 gene expression and controlling dorso-ventral polarity in the developing limb bud, leading to a specific subset of the En1-associated phenotype in human Mendelian disease.