Noncoding deletions reveal a gene that is critical for intestinal function. Mus musculus

Large-scale genome sequencing is poised to provide a substantial increase in the rate of discovery of disease-associated mutations, but the functional interpretation of such mutations remains challenging. Here we show that deletions of a sequence on human chromosome 16 that we term the intestine-critical region (ICR) cause intractable congenital diarrhoea in infants. Reporter assays in transgenic mice show that the ICR contains a regulatory sequence that activates transcription during the development of the gastrointestinal system. Targeted deletion of the ICR in mice caused symptoms that recapitulated the human condition. Transcriptome analysis revealed that an unannotated open reading frame (Percc1) flanks the regulatory sequence, and the expression of this gene was lost in the developing gut of mice that lacked the ICR. Percc1 knockout mice displayed phenotypes similar to those observed on ICR deletion in mice and patients, whereas an ICR-driven Percc1 transgene was sufficient to rescue the phenotypes found in mice that lacked the ICR. Together, our results identify a gene that is critical for intestinal function and underscore the need for targeted in vivo studies to interpret the growing number of clinical genetic findings that do not affect known protein-coding genes. Overall design: Total RNA-seq from dissected regions of the digestive tract, from wild-type and percc1-/- mice.

大规模基因组测序有望显著提升疾病相关突变的发现速率，但此类突变的功能阐释仍极具挑战性。本研究证实，人类16号染色体上一段我们命名为肠道关键区域（intestine-critical region, ICR）的序列发生缺失，会导致婴儿罹患难治性先天性腹泻。转基因小鼠的报告基因实验显示，ICR包含一段可在胃肠道系统发育过程中激活转录的调控序列。对小鼠体内ICR进行靶向缺失，可引发与人类病症表型一致的症状。转录组分析揭示，一段未注释开放阅读框（Percc1）位于该调控序列侧翼，在缺失ICR的小鼠发育肠道中，该基因的表达完全丧失。Percc1基因敲除小鼠表现出的表型，与ICR缺失小鼠及患者的观测表型高度相似；而由ICR驱动的Percc1转基因元件，足以挽救ICR缺失小鼠的异常表型。综上，本研究鉴定出一种对肠道功能至关重要的基因，并强调：针对不影响已知蛋白编码基因的日益增多的临床遗传学发现，亟需开展靶向体内研究以完成其功能阐释。实验设计概要：取自野生型与percc1-/-小鼠胃肠道解剖区域的总RNA测序（Total RNA-seq）。