TITLE:
Use of Synteny Conversion in Identification of Candidate Genes for Somitogenesis in Humans
AUTHORS:
Philip F. Giampietro, Cathy L. Raggio, Robert D. Blank
KEYWORDS:
Synteny; Candidate Genes; Vertebral Patterning Genes; Congenital Scoliosis; Idiopathic Scoliosis
JOURNAL NAME:
Open Journal of Orthopedics,
Vol.2 No.2,
June
22,
2012
ABSTRACT: Understanding the genetic component of scoliosis in humans has relied on the assumption that spine development is conserved across species. Since evolutionary conserved genes tend to lie within synteny blocks (HSBs) and genes which are not conserved lie within evolutionary breakpoint regions (EBRs), HSB analysis may be used to determine if spine development is conserved across species. We hypothesized that vertebral patterning genes are conserved in amniotes and their location is within stable or “syntenic” regions of chromosomes. Seventy seven patterning genes involved in Fgf, Wnt and Notch signaling pathways were analyzed to determine their location within HSBs or EBRs in the genomes of several amniotic species. The human genome was divided into 1 Mbp intervals and a comparison was made to determine whether these genes were preferentially localized within HSBs or EBRs associated with rapid evolution. The results indicate that genes associated with somite development in humans are preferentially located away from the EBRs: 0.014 genes in EBRs on genome average vs. 0.030 on average in other parts of the genome (p-value = 0.01). The concentration of vertebral patterning genes in HSBs, provides evidence that developmental pathways involved in vertebral morphogenesis are likely conserved across amniotes, consistent with their known function. These data support prior observations indicating that gene networks associated with major developmental processes such as neuronal, central nervous system, bone and blood vessel development, some mediated by Wnt and Notch signaling pathways, were less likely to be localized at EBRs.