Tackling the characterization of canine chromosomal breakpoints with an integrated in-situ/in-silico approach: The canine PAR and PAB

Abstract

The domestic dog continues to represent an influential model organism for comparative biomedical research owing to the numerous genetic and pathophysiological similarities shared between human and dog diseases. The combined availability of a high-quality genome assembly and a 1 Mb-resolution genome-assembly integrated bacterial artificial chromosome (BAC) panel now provides the essential resources to combine cytogenetic and computational analyses to determine the precise locations of chromosome breakpoint regions within aberrant karyotypes. In this study we demonstrate the synergy of using a such a combined in-situ/in-silico approach to define chromosome breakpoints using the naturally occurring breakpoint present on all canine X chromosomes--the pseudoautosomal breakpoint (PAB). In so doing we have further characterized the canine pseudoautosomal region (PAR) to extend approximately 6.6 Mb from the telomeric end of CFA Xp and established that the canine PAB is contained within a 2 kb region. Our characterization of the canine PAR allowed for the comparative study of gene content across previously defined mammalian PARs and indicates that the canine PAB is contained with the gene Shroom2. The future application of the approach demonstrated in this study will prove useful when seeking to identify the genomic sequences surrounding recurrent chromosome breakpoints present in canine cancers.

The Pseudoautosomal Region and Sex Chromosome Aneuploidies in Domestic Species

“…, dog [Olivier et al, 1999;Young et al, 2008], horse [Shiue et al, 2000;Raudsepp and Chowdhary, 2008], bovidscaprids [Iannuzzi et al, 2000a;Di Meo et al, 2005;Das et al, 2009], pig [Quilter et al, 2002], cat [Murphy et al, 2007;Pearks Wilkerson et al, 2008], and alpaca [own unpublished data]. On the X chromosome, which is evolutionarily conserved among mammals [Ohno, 1967;Raudsepp et al, 2004a], the PAR is typically located at Xpter ( fig.…”

“…For example, sequence draft assembly of the dog X chromosome has been available since 2005 [Lindblad-Toh et al, 2005]. However, the canine PAB and, thus, the physical domain of the PAR was determined only recently [Young et al, 2008]. Notably, the canine PAR is ϳ 6.6 Mb in size, thus more than two times larger than human PAR1.…”

“…Notably, the canine PAR is ϳ 6.6 Mb in size, thus more than two times larger than human PAR1. It extends proximal to SHROOM2 and contains at least 34 protein coding genes (Ensembl: http://www.ensembl.org/ index.html) [Young et al, 2008]. Though sequence assembly for the cat X chromosome is not complete (Ensembl website; UCSC: http://genome.ucsc.edu/cgi-bin/ hgGateway), radiation hybrid mapping suggests that the cat PAB is also located between SHROOM2 and WWC3 genes [Murphy et al, 2007].…”

“…Taken together, the available information shows that viable XO individuals are relatively frequently found in species with small PARs, such as horses [Raudsepp and Chowdhary, 2008], humans [Ross et al, 2005] and mice [Perry et al, 2001], but are rare or absent in species where the PAR is substantially larger, as in cattle/ruminants [Van Laere et al, 2008;Das et al, 2009], dogs [Young et al, 2008], pigs, and alpacas [own unpublished data]. No similar correlation can be pointed out between the PAR size and the X chromosome trisomy in different species.…”

“…Thus, even though map data are available for the X chromosome, lack of information for the Y sets limitations to properly demarcate the PAR. Despite these difficulties, recent mapping efforts indicate that the PAR varies in size and gene content between eutherian species [Raudsepp and Chowdhary, 2008;Van Laere et al, 2008;Young et al, 2008;Das et al, 2009]. Given that PAR genes escape X inactivation [Bondy and Cheng, 2009], these differences might critically influence the genetic effects caused by changes in sex chromosome numbers.…”