Long non-coding RNAs (lncRNAs) can be important components in gene-regulatory networks¹, 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.

长链非编码 RNA (lncRNA) 可能是基因调控网络¹中的重要组成部分，但它们在人类孟德尔病中的确切性质和程度在很大程度上是未知的。在这里，我们表明人类 2 号染色体上的 lncRNA 基因座的基因消融会导致严重的先天性肢体畸形。我们确定了位于 engrailed-1 基因 ( EN1 ) 上游 300 kb 处的纯合 27-63 kb 缺失，这些缺失位于具有中体缩短、并指和腹甲（背侧二肢）的复杂肢体畸形的患者中。重新设计小鼠中的人类缺失导致En1完全丧失在肢体中的表达和复述人类疾病表型的双背肢表型。在发育中的小鼠肢体中的全基因组转录组分析揭示了缺失区域内的四个外显子长的非编码转录本，我们将其命名为 Maenli。Maenli基因座的功能解剖表明，其转录活性是顺式中肢体特异性En1激活所必需的，从而微调控制发育中肢芽中背腹极性的基因调节网络。它的丢失导致与En1相关的背腹侧肢体表型，完整En1的一个子集-相关的表型。我们的研究结果表明，涉及 lncRNA 基因座的突变可导致人类孟德尔病。