Yoshihara Minako, Sato Tetsuya, Saito Daisuke, Ohara Osamu, Kuramoto Takashi, Suyama Mikita
Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan.
AMED-CREST, Japan Agency for Medical Research and Development, Fukuoka, 812-8582, Japan.
BMC Genet. 2017 Mar 29;18(1):29. doi: 10.1186/s12863-017-0497-3.
Head spot is one of the phenotypes identified in the KFRS4/Kyo rat strain. Although previous linkage analysis suggested that Ednrb, which is frequently involved in coat color variations in various animals, could be the gene responsible for this phenotype, no mutations have been identified in its coding region.
To identify mutations causative of this phenotype in KFRS4/Kyo, we analyzed target capture sequencing data that we recently generated. Our target capture method has a unique feature, i.e., it covers not only exonic regions but also conserved non-coding sequences (CNSs) among vertebrates; therefore, it has the potential to detect regulatory mutations. We identified a deletion of approximately 50 kb in length approximately 50 kb upstream of Ednrb. A comparative analysis with the epigenomic data in the corresponding region in humans and mice showed that one of the CNSs might be an enhancer. Further comparison with Hi-C data, which provide information about chromosome conformation, indicated that the putative enhancer is spatially close to the promoter of Ednrb, suggesting that it acts as an enhancer of Ednrb.
These in silico data analyses strongly suggest that the identified deletion in the intergenic region upstream of Ednrb, which might contain a melanocyte-specific enhancer, is the mutation causative of the head spot phenotype in the KFRS4/Kyo rat strain.
头部斑点是在KFRS4/Kyo大鼠品系中鉴定出的表型之一。尽管先前的连锁分析表明，在各种动物中经常参与毛色变异的内皮素受体B（Ednrb）可能是导致该表型的基因，但其编码区域未发现突变。
为了鉴定KFRS4/Kyo中导致该表型的突变，我们分析了最近生成的目标捕获测序数据。我们的目标捕获方法具有独特的特点，即它不仅覆盖外显子区域，还覆盖脊椎动物中的保守非编码序列（CNS）；因此，它有检测调控突变的潜力。我们在Ednrb上游约50 kb处鉴定出一个长度约为50 kb的缺失。与人类和小鼠相应区域的表观基因组数据进行比较分析表明，其中一个CNS可能是一个增强子。与提供染色体构象信息的Hi-C数据进一步比较表明，推定的增强子在空间上靠近Ednrb的启动子，表明它作为Ednrb的增强子发挥作用。
这些计算机数据分析强烈表明，在Ednrb上游基因间区域鉴定出的缺失可能包含一个黑素细胞特异性增强子，是KFRS4/Kyo大鼠品系中头部斑点表型的致病突变。
