Concentration of Double Strand Break Specification Signatures in Autism Associated Genes

Thursday, May 17, 2012
Sheraton Hall (Sheraton Centre Toronto)
9:00 AM
A. Omaiye1, N. Doan2, T. A. Deisher2 and S. D. Solares3, (1)Seattle University, Seattle, WA, (2)Sound Choice Pharmaceutical Institute, Seattle, WA, (3)University of Maryland , College Park, MD

Study of autism spectrum disorder (ASD) on an individual basis has identified over 350 genes associated with it, and hundreds of diverse de novo deletions and duplications have been identified in up to 10% of simplex ASD, indicating environmental influences on the genetics of ASD. Altered double strand break (DSB) formation and repair pathways may be a commonality among the diverse genetic mutations that have been documented in ASD.  Much of what is known about DSB hotspots comes from studies of meiotic recombination (MR). A haplotype map of the human genome has identified specific regions where MR crossover occurs most-readily, termed “MR hotspots”, and 41% of these hotspots are associated with a degenerate 13 mer sequence that binds to the hotspot specification protein PRDM9.


To determine the expression of constrained 13 mer sequences and whether they are concentrated in autism associated genes.


A list of all autism associated genes (aags) was obtained by combining the AutDB and ACGMap databases. The entire nucleotide sequence of each chromosome was downloaded from UCSC’s FTP site, and the exon positions for each of their genes were obtained from UCSC’s table browser. Then, meiotic recombination hotspot locations were obtained from the International HapMap Project and were changed from build 35 into build 37 with the UCSC LiftOver tool. An algorithm was written to generate all 1024 specific 13 mer sequences and their reversed complements, and these were then located on the chromosomes and their specific genes using NCBI’s stand-alone Blast, version 2.2.24. Multiple overlaying softwares were written to match the 13mer locations from Blast with MR hotspot locations on aags and all genes under chromosomal and exon levels. 


According to AutDB and ACGMap, the X-chromosome has the most aags, while chromosome 21 has the least aags. Chromosome 7 is used to validate results from the X-chromosome and chromosome 21. Hence, the study focuses on those three chromosomes.

The overlaying results show that aags have a higher concentration of MR hotspots, as well as number of constrained 13 mer, in comparison to all genes across each chromosome studied. However, there are consistently more hotspots with at least one 13 mer in all genes as opposed to aags. Results are summarized in the table below.

% Genes Containing 


% Hotspots Associated

With 13 mer

% Genes Containing

13 mer

X-Chromosome all genes 14 67 65
aags 45 39 95
Chromosome 7 all genes 26 77 77
aags 63 54 97
Chromosome 21 all genes 25 96 69
aags 100 100 100


The 13 mer motifs and MR hotspots are more concentrated on aags than total genes on the studied chromosomes. This concentration can potentially increase the risk of faulty DSBs leading to mutations associated with autism. The lower concentration of hotspots containing 13 mers may indicate that DSB formation is potentially regulated by other genetic factors, such as flanking sequences. Further investigation on other factors throughout the whole genome will provide a deeper understanding of DSB formation on aags.

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