Dysregulation of hypothalamus-mediated metabolic homeostasis influences risk factors for T2D, such as BMI, pubertal timing and sleep. However, the gene regulatory landscape of the hypothalamus remains unclear. We characterized the physical relationships among gene promoters and their corresponding cis-regulatory elements in human embryonic stem cell (ESC)-derived hypothalamic cells by integrating RNA-seq, ATAC-seq and promoter-focused Capture C profiles. We conducted this effort in an in vitro model of hypothalamic neurons using human ESCs at 3 stages of differentiation: ESCs, hypothalamic progenitors (HPs) and hypothalamic-like neurons (HNs). We identified 87,170 open chromatin regions (OCRs) contacting promoters in at least 1 stage of HN differentiation. Interestingly, we observed that regardless of gene expression pattern during differentiation, overall accessibility of interacting OCRs first increased during the transition to HP, then decreased following differentiation to HN. In order to relate these findings to GWAS data, we tested for enrichment of SNPs within promoter-interacting OCRs. We found significant associations with BMI, sleep traits, age at menarche (AAM) and major depressive disorder (MDD). We mapped these trait-associated variants to their physically interacting genes. We identified 2 putative effector genes for AAM (RPS26 and SUOX at chr12q13.2) and 1 for BMI (DHRS11), which were also supported by colocalized hypothalamus eQTLs in GTEx. Additionally, HyPrColoc analyses revealed several putative effector genes associated with >1 trait, including ZRANB2 for AAM, BMI and MDD, and FEZF1 for AAM and BMI, the latter being known to harbor Mendelian mutations that impair puberty. Taken together, our analyses provide insight into cis-regulatory architecture during hypothalamic development and how it may contribute to phenotypes associated with T2D risk.


M.C. Pahl: None. S.H. Littleton: None. C. Doege: None. K.M. Hodge: None. M. Leonard: None. S. Lu: None. R. Hammond: None. K. Boehm: None. C. Lasconi: None. C. Su: None. A. Chesi: None. J.A. Pippin: None. M. Johnson: None. A.D. Wells: None. B.F. Voight: None. R. Leibel: None. S.F. Grant: None. D.L. Cousminer: None.


American Diabetes Association (1-17-PDF-077 to D.L.C.); National Institutes of Health (K99HD099330-01); National Center for Research Resources (UL1RR024134); National Center for Advancing Translational Sciences (UL1TR000003); Institute for Translational Medicine and Therapeutics; Children’s Hospital of Philadelphia

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