Table_1_Bi-Functional Chicken Immunoglobulin-Like Receptors With a Single Extracellular Domain (ChIR-AB1): Potential Framework Genes Among a Relatively Stable Number of Genes Per Haplotype.XLSX

The leukocyte receptor complex (LRC) in humans encodes many receptors with immunoglobulin-like (Ig-like) extracellular domains, including the killer Ig-like receptors (KIRs) expressed on natural killer (NK) cells among others, the leukocyte Ig-like receptors (LILRs) expressed on myeloid and B cells, and an Fc receptor (FcR), all of which have important roles in the immune response. These highly-related genes encode activating receptors with positively-charged residues in the transmembrane region, inhibitory receptors with immuno-tyrosine based motifs (ITIMs) in the cytoplasmic tail, and bi-functional receptors with both. The related chicken Ig-like receptors (ChIRs) are almost all found together on a microchromosome, with over 100 activating (A), inhibitory (B), and bi-functional (AB) genes, bearing either one or two extracellular Ig-like domains, interspersed over 500–1,000 kB in the genome of an individual chicken. Sequencing studies have suggested rapid divergence and little overlap between ChIR haplotypes, so we wished to begin to understand their genetics. We chose to use a hybridization technique, reference strand-mediated conformational analysis (RSCA), to examine the ChIR-AB1 family, with a moderate number of genes dispersed across the microchromosome. Using fluorescently-labeled references (FLR), we found that RSCA and sequencing of ChIR-AB1 extracellular exon gave two groups of peaks with mobility correlated with sequence relationship to the FLR. We used this system to examine widely-used and well-characterized experimental chicken lines, finding only one or a few simple ChIR haplotypes for each line, with similar numbers of peaks overall. We found much more complicated patterns from a broiler line from a commercial breeder and a flock of red junglefowl, but trios of parents and offspring from another commercial chicken line show that the complicated patterns are due to heterozygosity, indicating a relatively stable number of peaks within haplotypes of these birds. Some ChIR-AB1 peaks were found in all individuals from the commercial lines, and some of these were shared with red junglefowl and the experimental lines derived originally from egg-laying chickens. Overall, this analysis suggests that there are some simple features underlying the apparent complexity of the ChIR locus.

人类白细胞受体复合物（leukocyte receptor complex, LRC）编码多种携带免疫球蛋白样（immunoglobulin-like, Ig样）胞外结构域的受体，包括表达于自然杀伤（natural killer, NK）细胞的杀伤细胞免疫球蛋白样受体（killer Ig-like receptors, KIRs）等类型、表达于髓系细胞与B细胞的白细胞免疫球蛋白样受体（leukocyte Ig-like receptors, LILRs），以及Fc受体（Fc receptor, FcR），上述受体均在免疫应答中发挥重要功能。这些同源性极高的基因分别编码跨膜区携带带正电荷残基的活化型受体、胞质尾区带有免疫酪氨酸基序（immuno-tyrosine based motifs, ITIMs）的抑制性受体，以及同时兼具两类功能的双功能受体。相关的鸡免疫球蛋白样受体（chicken Ig-like receptors, ChIRs）几乎全部聚集于一条微染色体上，在个体鸡基因组的500~1000 kb区间内，散布着超过100个分别携带单个或两个胞外Ig样结构域的活化型（A）、抑制型（B）及双功能型（AB）基因。测序研究提示ChIR单倍型（haplotypes）间存在快速分化且序列重叠度极低，因此我们着手解析其遗传学特征。我们选择采用杂交技术——参考链介导构象分析（reference strand-mediated conformational analysis, RSCA），对分散于该微染色体上、基因数量适中的ChIR-AB1家族进行研究。通过荧光标记参考链（fluorescently-labeled references, FLR），我们发现对ChIR-AB1胞外外显子进行RSCA与测序分析时，得到了两组迁移率与该荧光标记参考链的序列同源性相关的峰型。利用该体系，我们对多种广泛使用且特征明确的实验用鸡品系进行检测，结果显示每个品系仅存在1种或少数几种简单的ChIR单倍型，整体峰型数量相近。我们在商业育种场的肉鸡品系与一群红原鸡中观察到更为复杂的峰型，但来自另一商业鸡品系的亲本子代trio家系分析表明，此类复杂峰型源于杂合性，说明这些鸡的单倍型内峰型数量相对稳定。商业品系的所有个体均能检测到部分ChIR-AB1峰型，其中部分峰型与红原鸡以及最初源自蛋鸡的实验品系共享。总体而言，本分析表明，ChIR基因座看似复杂的特征背后，存在若干简单的核心规律。