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

• Published in: Nature (London) Vol. 592; no. 7852; pp. 93 - 98
• Main Authors: Allou, Lila, Balzano, Sara, Magg, Andreas, Quinodoz, Mathieu, Royer-Bertrand, Beryl, Schöpflin, Robert, Chan, Wing-Lee, Speck-Martins, Carlos E., Carvalho, Daniel Rocha, Farage, Luciano, Lourenço, Charles Marques, Albuquerque, Regina, Rajagopal, Srilakshmi, Nampoothiri, Sheela, Campos-Xavier, Belinda, Chiesa, Carole, Niel-Bütschi, Florence, Wittler, Lars, Timmermann, Bernd, Spielmann, Malte, Robson, Michael I., Ringel, Alessa, Heinrich, Verena, Cova, Giulia, Andrey, Guillaume, Prada-Medina, Cesar A., Pescini-Gobert, Rosanna, Unger, Sheila, Bonafé, Luisa, Grote, Phillip, Rivolta, Carlo, Mundlos, Stefan, Superti-Furga, Andrea
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 01-04-2021; Nature Publishing Group
• Subjects: 13; 14/32; 38; 38/91; 45/41; 45/61; 49; 49/15; 631/136/1425; 631/208/199; 631/208/200; 631/337/384/2568; 64/110; 64/60; 692/420/2489/144; Ablation; Animals; Binding sites; Cell Line; Chromatin - genetics; Chromosome 2; Chromosomes; Disease Models, Animal; Extremities; Female; Gene expression; Gene regulation; Genomes; Genotype & phenotype; Homeodomain Proteins - genetics; Humanities and Social Sciences; Humans; Hypotheses; Limb buds; Limb Deformities, Congenital - genetics; Loci; Mice; Mice, Transgenic; multidisciplinary; Mutation; Non-coding RNA; Pathogenesis; Patients; Phenotypes; Polarity; RNA, Long Noncoding - genetics; Science; Science (multidisciplinary); Sequence Deletion - genetics; Stem cells; Syndactyly; Transcription; Transcription, Genetic; Transcriptional Activation - genetics; Transcriptomes
• ISSN: 0028-0836; 1476-4687
• DOI: 10.1038/s41586-021-03208-9

Long non-coding RNAs (lncRNAs) 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 ventral nails (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-wide transcriptome analysis in the developing mouse limb revealed a four-exon-long non-coding transcript within the deleted region, which we named Maenli. Functional dissection of the
Maenli
locus showed that its transcriptional activity is required for limb-specific
En1
activation in
cis
, thereby fine-tuning the 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.
The long non-coding RNA locus
Maenli
controls mouse limb development by regulating
En1
activity, and the absence of the homolgous
MAENLI
locus is associated with severe congenital limb defects in humans.