Functional enhancer annotation is a valuable first step for understanding tissue-specific transcriptional regulation and prioritizing disease-associated non-coding variants for investigation. However, unbiased enhancer discovery in physiologically relevant contexts remains a major challenge. To discover regulatory elements pertinent to diabetes, we conducted a CRISPR interference (CRISPRi) screen in the human pluripotent stem cell (hPSC) pancreatic differentiation system. Among the enhancers uncovered, we focused on a long-range enhancer ~664 kb from the ONECUT1 promoter, as coding mutations in ONECUT1 cause pancreatic hypoplasia and neonatal diabetes. Homozygous enhancer deletion in hPSCs was associated with a near-complete loss of ONECUT1 gene expression and compromised pancreatic differentiation. This enhancer contains a confidently fine-mapped type 2 diabetes (T2D) associated variant (rs528350911) which disrupts a GATA motif. Introduction of the risk variant into hPSCs revealed substantially reduced binding of key pancreatic transcription factors (GATA4, GATA6 and FOXA2) on the edited allele, accompanied by a slight reduction of ONECUT1 transcription, supporting a causal role for this risk variant in metabolic disease. This work expands our knowledge about transcriptional regulation in pancreatic development through the characterization of a long-range enhancer and highlights the utility of enhancer discovery in disease-relevant settings for understanding monogenic and complex disease.
Overall design: lab: Danwei Huangfu, MSKCC award: 1U01DK128852-01 accession: 4DNESOGBAIC7 condition: pancreatic precursor cells - H1 dataset_label: in situ Hi-C on PDX1-GFP idCAS9-KRAB H1 human embryonic stem cells differentiated to pancreatic progenitor cells (PP) experiment type: in situ Hi-C url: https://data.4dnucleome.org/experiment-set-replicates/4DNESOGBAIC7/ number_of_experiments: 2 experiment: in situ Hi-C on PDX1-eGFP dCAS9-KRAB H1 differentiated to endoderm of foregut with Arima - A1, A2 - 4DNEXMHLGGWC experiment: in situ Hi-C on PDX1-eGFP dCAS9-KRAB H1 differentiated to endoderm of foregut with Arima - A1, A2 - 4DNEXUDU96VW Series supplementary files: ****** workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/3e86c39e-47f3-4656-ac56-ab63aa493af7/ genome_assembly GRCh38 derived_from: 4DNFI823LSII.chrom.sizes, 4DNFITG6TM26.pairs.gz, 4DNFINK7ALPW.pairs.gz, 4DNFIU1RS39P.txt, description: This is an output file of the Hi-C processing pipeline file_type: contact list-combined file_format: pairs file_name: 4DNFIEAQ6DIR.pairs.gz ****** workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/3e86c39e-47f3-4656-ac56-ab63aa493af7/ genome_assembly GRCh38 derived_from: 4DNFI823LSII.chrom.sizes, 4DNFITG6TM26.pairs.gz, 4DNFINK7ALPW.pairs.gz, 4DNFIU1RS39P.txt, description: This is an output file of the Hi-C processing pipeline file_type: contact matrix file_format: mcool file_name: 4DNFIYC4AJW5.mcool ****** workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/4a5f3a30-c608-4367-953b-e5300001f22b/ genome_assembly GRCh38 derived_from: 4DNFIYC4AJW5.mcool, description: Boundaries calls on Hi-C contact matrices file_type: boundaries file_format: bed file_name: 4DNFINRZXAQF.bed.gz ****** workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/4a5f3a30-c608-4367-953b-e5300001f22b/ genome_assembly GRCh38 derived_from: 4DNFIYC4AJW5.mcool, description: Diamond insulation scores calls on Hi-C contact matrices file_type: insulation score-diamond file_format: bw file_name: 4DNFI4F6P2UE.bw ****** workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/d04948a9-1b41-47f2-80b0-8e3a74eb90af/ genome_assembly GRCh38 derived_from: 4DNFIYC4AJW5.mcool, 4DNFI7MCA4R6.bedGraph.gz, description: Compartments signals on Hi-C contact matrices file_type: compartments file_format: bw file_name: 4DNFI9C517H3.bw ******BED files: HiC-Pro (3.1.0) alignment, HiTC (1.34.0), HiCDC+(1.5.2), TopDom, 50 kb file_format: bed file_name: 4DNFIJI7XHPW.bed.gz
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