Enhancer Variants Synergistically Drive Dysfunction of a Gene Regulatory Network In Hirschsprung Disease

• Published in: Cell Vol. 167; no. 2; pp. 355 - 368.e10
• Main Authors: Chatterjee, Sumantra, Kapoor, Ashish, Akiyama, Jennifer A., Auer, Dallas R., Lee, Dongwon, Gabriel, Stacey, Berrios, Courtney, Pennacchio, Len A., Chakravarti, Aravinda
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 06.10.2016; Elsevier
• Subjects: Alleles; Animals; BASIC BIOLOGICAL SCIENCES; Binding Sites; digestive system; Disease Models, Animal; Enhancer Elements, Genetic; etiology; Gastrointestinal Tract - embryology; GATA transcription factors; GATA2 Transcription Factor - genetics; GATA2 Transcription Factor - metabolism; Gene Expression Regulation; Gene Regulatory Networks; genes; Hirschsprung Disease - genetics; Humans; Mice; Mice, Transgenic; Proto-Oncogene Proteins c-ret - genetics; Receptors, Retinoic Acid - genetics; Receptors, Retinoic Acid - metabolism; risk; RNA, Untranslated - genetics; SOXE Transcription Factors - genetics; SOXE Transcription Factors - metabolism; tissues
• ISSN: 0092-8674; 1097-4172
• DOI: 10.1016/j.cell.2016.09.005

Common sequence variants in cis-regulatory elements (CREs) are suspected etiological causes of complex disorders. We previously identified an intronic enhancer variant in the RET gene disrupting SOX10 binding and increasing Hirschsprung disease (HSCR) risk 4-fold. We now show that two other functionally independent CRE variants, one binding Gata2 and the other binding Rarb, also reduce Ret expression and increase risk 2- and 1.7-fold. By studying human and mouse fetal gut tissues and cell lines, we demonstrate that reduced RET expression propagates throughout its gene regulatory network, exerting effects on both its positive and negative feedback components. We also provide evidence that the presence of a combination of CRE variants synergistically reduces RET expression and its effects throughout the GRN. These studies show how the effects of functionally independent non-coding variants in a coordinated gene regulatory network amplify their individually small effects, providing a model for complex disorders. [Display omitted] •Variants at three RET enhancers act synergistically on Hirschsprung disease risk•These enhancers are bound by the transcription factors (TF) RARB, GATA2, and SOX10•Risk variants reduce TF binding to reduce enhancer activity and RET gene expression•Loss of RET gene expression affects its entire gene regulatory network in vivo How do multiple noncoding variants with individually small effects synergize to cause a complex disease?