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

Area of Science:

• Genetics
• Developmental Biology
• Molecular Biology

Background:

• Long non-coding RNAs (lncRNAs) are increasingly recognized for their roles in gene regulation.
• Their specific involvement in human Mendelian diseases remains largely uncharacterized.
• Congenital limb malformations represent a significant group of developmental disorders with diverse genetic etiologies.

Purpose of the Study:

• To investigate the role of lncRNA loci in human Mendelian diseases.
• To identify the genetic cause of a specific complex limb malformation.
• To elucidate the functional mechanism of a novel lncRNA in limb development.

Main Methods:

• Whole-genome sequencing to identify deletions in patients with limb malformations.
• Re-engineering of identified deletions in a mouse model.
• Genome-wide transcriptome analysis (RNA-seq) in developing mouse limbs.
• Functional studies of the lncRNA locus in vivo.

Main Results:

• Identified homozygous deletions upstream of the engrailed-1 (EN1) gene in patients with mesomelic shortening, syndactyly, and dorsal dimelia.
• Mouse models with re-engineered deletions exhibited loss of En1 expression and a double dorsal-limb phenotype mirroring human cases.
• Discovered and named the Maenli lncRNA, essential for limb-specific En1 activation in cis.
• Maenli transcriptional activity is crucial for regulating limb bud dorso-ventral polarity.

Conclusions:

• Genetic ablation of the Maenli lncRNA locus causes a severe human Mendelian limb malformation.
• Maenli fine-tunes gene-regulatory networks controlling limb development via cis-regulation of En1.
• This study highlights the critical role of lncRNAs in human developmental disorders and establishes Maenli as a key player in limb patterning.