The defining DNA methylation signature of Floating-Harbor Syndrome

Abstract

Floating-Harbor syndrome (FHS) is an autosomal dominant genetic condition characterized by short stature, delayed osseous maturation, expressive language impairment, and unique facial dysmorphology. We previously identified mutations in the chromatin remodeling protein SRCAP (SNF2-related CBP Activator Protein) as the cause of FHS. SRCAP has multiple roles in chromatin and transcriptional regulation; however, specific epigenetic consequences of SRCAP mutations remain to be described. Using high resolution genome-wide DNA methylation analysis, we identified a unique and highly specific DNA methylation "epi-signature" in the peripheral blood of individuals with FHS. Both hyper and hypomethylated loci are distributed across the genome, preferentially occurring in CpG islands. Clonal bisulfite sequencing of two hypermethylated (FIGN and STPG2) and two hypomethylated (MYO1F and RASIP1) genes confirmed these findings. The identification of a unique methylation signature in FHS provides further insight into the biological function of SRCAP and provides a unique biomarker for this disorder.

Figure 1. Euclidean Hierarchical Cluster Analysis.

Hierarchical clustering of probes differentially methylated between FHS and controls demonstrating marked asymmetry of the 2 groups. Cases are represented in the columns and significant probes (p < 0.01) in the rows.

Figure 2. DNA methylation profiles in FHS.

Methylation level from 0 (not methylated) to 1 (100% methylated) is shown across regions with significantly altered methylation in FHS: hypermethylated regions (a) MYO1F and (b) RASIP1; and hypomethylated regions (c) FIGN and (d) STPG2. RefSeq genes and CpG islands tracks are annotated on top of the figures. The top image corresponds to methylation array data visualized using Genomic Browser Viewer (Partek). Red lines correspond to representative control sample data. Blue lines correspond to FHS individual data. The bottom image corresponds to average methylation based on bisulfite sequencing data. The red and blue lines indicate the average methylation for control and FHS patient sample, respectively. Dotted lines correlate chromosome location between top (array generated) and bottom (bisulfite sequence generated) images.

Figure 3. Methylation string diagrams of significantly altered regions in FHS individuals compared to controls.

String diagrams indicating methylation status across regions with significantly altered methylation in FHS: hypermethylated regions (a) MYO1F and (b) RASIP1, and hypomethylated regions (c) FIGN and (d) STPG2; for four FHS individuals (top) and two gender matched control samples (bottom). Each dot on the string indicates a CpG sequence, and potential site for methylation. Black dots indicate the CpG is methylated. Open dots indicate the CpG is un-methylated.