Noncoding deletions reveal a gene that is critical for intestinal function

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. 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表明，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。在小鼠体内定向敲除ICR后，其出现的症状可复现人类患者的病症。转录组分析显示，该调控序列侧翼存在一个未注释开放阅读框（Percc1）；在缺失ICR的小鼠发育中的肠道内，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敲除小鼠及人类患者所观察到的表型高度相似；而由ICR驱动的Percc1转基因元件，足以挽救缺失ICR的小鼠所出现的表型。综上，本研究鉴定出一个对肠道功能至关重要的基因，并强调：针对未影响已知蛋白编码基因的日益增多的临床遗传学发现，亟需开展定向体内研究以完成其功能解读。本数据集包含野生型与percc1基因敲除（percc1-/-）小鼠消化道解剖区域的总RNA测序（Total RNA-seq）数据。