Extended Data Fig. 10: HNF1A binding to HASTER promoter reduces HNF1A promoter – enhancer interactions.
From: The HASTER lncRNA promoter is a cis-acting transcriptional stabilizer of HNF1A
a, Top, UMI-4C profile trends using a viewpoint region upstream of Hnf1a (V1), near a CTCF-bound C site, in adult liver from n = 3 wild type (blue) or mutant (red) mice. Bottom, chromatin features and transcription factor binding in adult mouse liver. The Hnf1a upstream region contacts several enhancers, promoters and CTCF/cohesin sites in control and HasterLKO liver. The interaction between Hnf1a upstream region and E (asterisk) is increased in HasterLKO liver (see also Fig. 7). The region deleted in HasterLKO mice is highlighted in blue. b, UMI-4C profile trends of doxycycline-induced HNF1A overexpression in HASTER+ / + and HASTERΔP/ΔP EndoC-βH3 cells with HNF1A promoter as viewpoint. Strongest contacts occurred within < 20 kb 3’ of HNF1A promoter, while weaker contacts were predominantly observed in a ~400 kb region 5’ of HNF1A promoter. Top tracks, genes and regulatory elements in human pancreatic islets (Miguel-Escalada, et al., 2019). Pool of libraries for n = 4 independent experiments. c, Individual UMI-4C profile trends from four individual experiments of doxycycline-induced HNF1A overexpression in HASTER+ / + and HASTERΔP/ΔP EndoC-βH3 cells. In a-c shades represent estimated binomial standard deviation centered on the profile trend. d, HNF1A promoter – E interaction frequencies from individual replicates (n = 4 independent experiments). Interaction frequencies were measured at a 5 kb region centered on E highlighted with a green shade. Box plots show medians and interquartile ranges; whiskers, 1.5 times the interquartile ranges. e, Human islet chromatin marks showing the position of enhancers in the vicinity of HNF1A. f, HASTER+ / + or HASTERΔP1/ΔP1 clone #1 cells carrying targeted deletions in C (ΔC), E (ΔE) or sgGFP as control (WT). HASTER+ / + control and E deletion are identical to Fig. 7e. ΔC and ΔE were polyclonal deletions. Results are expressed as fold-differences relative to the parental HASTER+ / + or HASTERΔP1/ΔP1 cells. This showed that ΔC has no effect on HASTER or HNF1A, ΔE had significant effects on HASTER but did not significantly affect HNF1A in wild type cells, yet showed a significant HNF1A reduction in HASTERΔP1/ΔP1 cells. This is shown in cartoon form in the right panel, whereby E predominantly enhances HASTER transcription, but enhances HNF1A in the absence of HASTER. Pool of n = 3 independent experiments with 3 pairs of sgRNAs for each deletion. TBP-normalized mean expression ± s.d.; two-tailed Student’s t-test.
