Implications of COMT long-range interactions on the phenotypic variability of 22q11.2 deletion syndrome

Abstract

22q11.2 deletion syndrome (22q11DS) results from a hemizygous microdeletion on chromosome 22 and is characterized by extensive phenotypic variability. Penetrance of signs, including congenital heart, craniofacial, and neurobehavioral abnormalities, varies widely and is not well correlated with genotype. The three-dimensional structure of the genome may help explain some of this variability. The physical interaction profile of a given gene locus with other genetic elements, such as enhancers and co-regulated genes, contributes to its regulation. Thus, it is possible that regulatory interactions with elements outside the deletion region are disrupted in the disease state and modulate the resulting spectrum of symptoms. COMT, a gene within the commonly deleted ~3 Mb region has been implicated as a contributor to the neurological features frequently found in 22q11DS patients. We used this locus as bait in a 4C-seq experiment to investigate genome-wide interaction profiles in B lymphocyte and fibroblast cell lines derived from both 22q11DS and unaffected individuals. All normal B lymphocyte lines displayed local, conserved chromatin looping interactions with regions that are lost in atypical and distal deletions, which may mediate similarities between typical, atypical, and distal 22q11 deletion phenotypes. There are also distinct clusterings of cis interactions based on disease state. We identified regions of differential trans interactions present in normal, and lost in deletion-carrying, B lymphocyte cell lines. This data suggests that hemizygous chromosomal deletions such as 22q11DS can have widespread effects on chromatin organization, and may contribute to the inherent phenotypic variability.

Keywords: DiGeorge syndrome; chromosome conformation capture; genome organization; long-range interactions; schizophrenia.

Figure 1. (A) Diagram of deletions on chromosome 22q11.2. The common large deletion (green) encompasses the shorter nested deletion (green) and the region of atypical deletions (red). The region containing distal deletions is highlighted green. Locations of DGCR6, COMT, TBX1 and MAPK1 are shown. (B) COMT expression in 4 normal and 4 deletion B lymphocyte cell lines. **, P < 0.01. (C) 4C-seq local interaction profiles observed in 4 normal B lymphocyte cell lines. The bait locus COMT (red) is located in both the large typically deleted region and the shorter nested deletion (green bars). Normalized cis reads in the normal B cell line GM18056. Image generated from UCSC genome browser GRCh37/hg19. Significant regions displayed underneath deletions were obtained using a sliding window of 20 restriction sites and a z-score cutoff of 3. Red bars indicate interactions in the region comprising atypical deletions and blue bars indicate interactions in the distal deletion region. Locations of the predicted B lymphocyte, strong enhancers were extracted from the Broad chromatin state segmentation track. (D) Hierarchical clustering by cis interactions profiles. Each square represents a pairwise comparison of the similarity between each cell line using Pearson correlation between the vectors of intrachromosomal z scores assigned using a sliding window of 20 restriction sites.

Figure 2. Differential trans interactions. (A) Ideograms of chromosomes with regions interacting with COMT in all 4 normal B lymphocyte cell lines and ≤ 1 22q11DS B lymphocyte cell lines are depicted by orange bars. Heat map represents known gene density. Region defined as 20 consecutive overlapping windows of 100 restriction sites, sliding by 1 site. (B) Magnified view of 1 selected differentially interacting region on chromosome 4. Significant COMT interacting windows (gray bars) are present in all normal and none of the 22q11DS B lymphocyte cell lines. The transcription start site of SORCS2 a bipolar disorder, and schizophrenia associated gene (red) is highlighted. Image generated from UCSC genome browser GRCh37/hg19 and Ideographica software.