Journal: NPJ Genomic Medicine

Article Title: Distinguishing benign from pathogenic duplications involving GPR101 and VGLL1 -adjacent enhancers in the clinical setting with the bioinformatic tool POSTRE

doi: 10.1038/s41525-025-00548-7

Figure Lengend Snippet: A Visualization of the S22 duplication using the UCSC genome browser. The image was obtained through the adjustment (zoom in) of a UCSC link available from the POSTRE output. The duplicated area is highlighted in orange. The session also depicts bigwigs of H3K27ac ChIP-seq and ATAC-seq data from anterior pituitary, TAD maps from hESC, and highlights POSTRE-predicted active enhancers with green vertical lines. It can be appreciated that the entire VGLL1 -TAD—particularly the region surrounding the gene, including enhancer e5—exhibits strong H3K27ac enrichment, in clear contrast to the GPR101 -TAD, where acetylation levels remain uniformly low across the locus. B Overview of the VGLL1 -adjacent enhancers. According to the POSTRE enhancer calling pipeline, five enhancers, that we named e1-e5 (e1: chrX:135,626,976-135,627,240, e2: chrX:135,628,829-135,629,196, e3: chrX:135,631,401-135,631,758, e4: chrX:135,633,336-135,633,961, e5: chrX:135,659,670-135,660,230), are predicted. Four are located within VGLL1 and one (e5) is 25 kb telomeric to the gene. C Barplot of the mean H3K27ac levels at the e1-e5 enhancers (calculated from H3K27ac ChIP-seq bigwigs considering a window of +-500bp with respect to the enhancer coordinates). Higher H3K27ac levels are indicators of stronger enhancer activity .

Article Snippet: ChIP-seq profiling of the H3K27ac histone mark was performed on an additional normal adult anterior pituitary sample using the ChIP-IT High Sensitivity kit (Cat. No. V13-53040, Active Motif,) and a polyclonal anti-H3K27ac antibody (Cat. No. 39135, Active Motif).

Techniques: ChIP-sequencing, Activity Assay

Journal: NPJ Genomic Medicine

Article Title: Distinguishing benign from pathogenic duplications involving GPR101 and VGLL1 -adjacent enhancers in the clinical setting with the bioinformatic tool POSTRE

doi: 10.1038/s41525-025-00548-7

Figure Lengend Snippet: A–D show a schematic representation of genomic configurations at the X-LAG locus showing TAD boundaries (red hexagons), pituitary-active enhancers (green ovals), and GPR101 -associated duplications (adapted from Daly et al. , with permission). For each configuration, a linear genomic view (left) and the corresponding TAD model (right) are shown. A Normal locus configuration with a zoom-in on the VGLL1 region showing the VGLL1 -intronic enhancer (a cluster of four elements, e1-e4), and the VGLL1 distal enhancer (e5), marked by ATAC-seq and H3K27ac peaks. GPR101 and the pituitary-active VGLL1 enhancers are separated by a TAD boundary, forming a distinct GPR101 -TAD (gray) adjacent to a pituitary enhancer-containing TAD (green). The size and position of GPR101 -associated duplications are indicated below. B Intra-TAD duplications involving GPR101 that preserve the TAD boundary incorporate an additional GPR101 copy within the original TAD (yellow), maintaining its separation from pituitary enhancers. C Inter-TAD duplications spanning GPR101 and the TAD boundary, but not the pituitary enhancers, result in neo-TAD formation (orange) that preserves the insulation of GPR101 from pituitary enhancers. D Pathogenic inter-TAD duplications spanning GPR101 and encompassing both the TAD boundary and pituitary enhancers form a neo-TAD (blue) that establishes ectopic chromatin contacts between GPR101 and pituitary enhancers, resulting in GPR101 misexpression and X-LAG.

Article Snippet: ChIP-seq profiling of the H3K27ac histone mark was performed on an additional normal adult anterior pituitary sample using the ChIP-IT High Sensitivity kit (Cat. No. V13-53040, Active Motif,) and a polyclonal anti-H3K27ac antibody (Cat. No. 39135, Active Motif).

Techniques: Insulation