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. 2021 Feb 5;10:e59067. doi: 10.7554/eLife.59067

Figure 5. A T2D risk-associated CRB2 pancreatic progenitor-specific stretch enhancer regulates CRB2 expression specifically in pancreatic progenitors.

(A) (Top) Locus plots showing T2D association p-values for variants in a 35 kb window (hg19 chr9:126,112,000–126,147,000) at the CRB2 locus and CRB2 PSSE (red box). Fine mapped variants within the 99% credible set for the novel CRB2 locus are colored black. All other variants are colored light gray. (Bottom) Chromatin states and ATAC-seq signal in ES, DE, GT, PP1, and PP2. TssA, active promoter; TssFlnk, flanking transcription start site; TssBiv, bivalent promoter; Repr, repressed; EnhA, active enhancer; EnhP, poised enhancer. (B) FOXA1, FOXA2, GATA4, GATA6, HNF6, SOX9, and PDX1 ChIP-seq profiles at the CRB2 PSSE in PP2. The variant rs2491353 (black) overlaps with transcription factor binding sites. (C) CRB2 mRNA expression at each developmental stage determined by RNA-seq, measured in fragments per kilobase per million fragments mapped (FPKM). Data shown as mean ± S.E.M. (n = 3 replicates from independent differentiations). Light blue and purple indicate classification of the CRB2 PSSE as typical enhancer (TE) and stretch enhancer (SE), respectively. Plotted points represent average of technical replicates for each differentiation. (D) CRB2 mRNA expression at each developmental stage determined by qPCR in control and ∆CRB2Enh cells. Data are shown as mean ± S.E.M. (n = 3 replicates from independent differentiations for control cells. ∆CRB2Enh cells represent combined data from two clonal lines with three replicates for each line from independent differentiations. n = 3 technical replicates for each sample; p=7.03 × 10−4,<1 × 10−6,<1 × 10−6, 1.46 × 10−2, and <1 × 10−6 for comparisons in ES, DE, GT, PP1, and PP2, respectively; student’s t-test, two sided; ***p<0.001 **p<0.01). Light blue and purple indicate classification of the CRB2 PSSE as TE and SE, respectively. Each plotted point represents the average of technical replicates for each differentiation. (E) mRNA expression determined by RNA-seq at PP2 of genes expressed in either control or ∆CRB2Enh cells (FPKM ≥ 1 at PP2) and located within the same topologically associated domain as CRB2. Data are shown as mean FPKM ± S.E.M. (n = 2 replicates from independent differentiations for control cells. ∆CRB2Enh cells represent combined data from two clonal lines with two replicates for each line from independent differentiations. p adj. = 0.158, 1.00, and 3.51 × 10−3, for MIR600HG, STRBP, and CRB2, respectively; DESeq2; **p<0.01, n.s., not significant). See also Figure 5—figure supplements 1–3.

Figure 5—source data 1. Genes downregulated in ∆CRB2Enh PP2 stage cells compared to control cells (p adj. <0.05).

Figure 5.

Figure 5—figure supplement 1. Activity of CRB2- and PGM1-associated pancreatic progenitor-specific stretch enhancers across human tissues.

Figure 5—figure supplement 1.

(A) (Top) Locus plots showing T2D association p-values for variants in a 43 kb window (hg19 chr1:64,084,000–64,127,000) at the PGM1 locus and PGM1 PSSE (red box). Fine mapped variants within the 99% credible set for the novel PGM1 locus are colored black. All other variants are colored light gray. (Bottom) Chromatin states and ATAC-seq signal in ES, DE, GT, PP1, and PP2. TssA, active promoter; TssFlnk, flanking transcription start site; TssBiv, bivalent promoter; Repr, repressed; EnhA, active enhancer; EnhP, poised enhancer. (B) FOXA1, FOXA2, GATA4, GATA6, HNF6, SOX9, and PDX1 ChIP-seq profiles at the PGM1 PSSE in PP2 cells. The variants rs2269247, rs2301055, rs2301054, and rs2269246 (black) overlap with transcription factor binding sites. (C) H3K27ac signal at CRB2-associated PSSE in tissues and cell lines from the ENCODE and Epigenome Roadmap projects as well as in developmental intermediates and islets (ISL). (D) H3K27ac signal at PGM1-associated PSSE in tissues and cell lines from the ENCODE and Epigenome Roadmap projects as well as in developmental intermediates and islets.
Figure 5—figure supplement 2. Deletion of the CRB2-associated pancreatic progenitor-specific enhancer does not affect pancreatic lineage specification.

Figure 5—figure supplement 2.

(A) Schematic illustrating CRISPR-Cas9-mediated deletion strategy of CRB2-associated PSSE to generate independent ∆CRB2Enh hESC clones with different DNA cleavage products. (B) Flow cytometry analysis for NKX6.1 and PDX1 comparing control and ∆CRB2Enh PP2 cells. Isotype control (ISO) for each antibody is shown in red and target protein staining in green. Percentage of cells expressing each protein is indicated (representative experiment, n = 3 independent differentiations). (C) Immunofluorescent staining for NKX6.1 and PDX1 in control and ∆CRB2Enh PP2 cells (representative images, n = 2 independent slides). Scale bar, 50 μm. (D) mRNA expression of pancreatic transcription factors determined by RNA-seq in control and ∆CRB2Enh PP2 cells. Data are shown as mean of fragments per kilobase per million fragments mapped (FPKM) ± S.E.M. (n = 2 replicates from independent differentiations for control cells ∆CRB2Enh cells represent combined data from two clonal lines with two replicates for each line from independent differentiations. p adj. = 1.00, 1.00, 1.00, 1.00, and 1.00, for comparisons of PDX1, NKX6.1, PROX1, PTF1A, and SOX9, respectively; DESeq2; n.s., not significant). (E) Similarity matrix showing Pearson correlations for normalized transcriptomes (log transformed expression for genes with FPKM ≥1 in ≥1 replicates) in control and ∆CRB2Enh PP2 cells (n = 2 independent differentiations for control cells and for each ∆CRB2Enh clone). See also Figure 5—source data 1.
Figure 5—figure supplement 3. Deletion of CRB2 does not affect pancreatic lineage specification.

Figure 5—figure supplement 3.

(A) Schematic illustrating CRISPR-Cas9-mediated deletion strategy of CRB2 to generate ∆CRB2 hESC clonal line. (B) Immunofluorescent staining for CRB2 in control and ∆CRB2 PP2 cells (representative images, n = 2 independent slides). Scale bar, 50 μm. (C) Flow cytometry analysis for NKX6.1 and PDX1 comparing control and ∆CRB2 PP2 cells. Isotype control (ISO) for each antibody is shown in red and target protein staining in green. Percentage of cells expressing each protein is indicated. (D) Immunofluorescent staining for NKX6.1 and PDX1 in control and ∆CRB2 PP2 cells (representative images, n = 2 independent slides). Scale bar, 50 μm. (E) mRNA expression of pancreatic transcription factors determined by qPCR in control and ∆CRB2 PP2 cells. Data are shown as mean ± S.E.M. (n = 3 replicates from independent differentiations. n = 3 technical replicates for each sample; p=0.241, 0.971, 0.397, 0.374, and 0.311 for comparisons of PDX1, NKX6.1, PROX1, PTF1A, and SOX9 expression in control compared to ∆CRB2 PP2 cells, respectively; student’s t-test, two sided; n.s., not significant). Each plotted point represents the average of technical replicates for each differentiation.