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

Allou, Lila and Balzano, Sara and Magg, Andreas and Quinodoz, Mathieu and Royer-Bertrand, Beryl and Schöpflin, Robert and Chan, Wing-Lee and Speck-Martins, Carlos E. and Carvalho, Daniel Rocha and Farage, Luciano and Lourenço, Charles Marques and Albuquerque, Regina and Rajagopal, Srilakshmi and Nampoothiri, Sheela and Campos-Xavier, Belinda and Chiesa, Carole and Niel-Bütschi, Florence and Wittler, Lars and Timmermann, Bernd and Spielmann, Malte and Robson, Michael I. and Ringel, Alessa and Heinrich, Verena and Cova, Giulia and Andrey, Guillaume and Prada-Medina, Cesar A. and Pescini-Gobert, Rosanna and Unger, Sheila and Bonafé, Luisa and Grote, Phillip and Rivolta, Carlo and Mundlos, Stefan and Superti-Furga, Andrea. (2021) Non-coding deletions identify Maenli lncRNA as a limb-specific En1 regulator. Nature, 592. pp. 93-98.

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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.
Faculties and Departments:03 Faculty of Medicine
09 Associated Institutions > Institute of Molecular and Clinical Ophthalmology Basel (IOB)
09 Associated Institutions > Institute of Molecular and Clinical Ophthalmology Basel (IOB) > Research Group Rivolta IOB
UniBasel Contributors:Rivolta, Carlo
Item Type:Article, refereed
Article Subtype:Research Article
Publisher:Nature Research
Note:Publication type according to Uni Basel Research Database: Journal article
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Last Modified:11 Sep 2023 07:18
Deposited On:31 Aug 2021 10:37

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