In vitro identification and in silico utilization of interspecies sequence similarities using GeneChip technology.-猫眼课题宝

DOI：

10.1186/1471-2164-6-62

发表时间：

2005-05-04

期刊：

BMC genomics

影响因子：

4.4

通讯作者：

中科院分区：

生物学2区

文献类型：

作者：

Grigoryev DN;Ma SF;Simon BA;Irizarry RA;Ye SQ;Garcia JG

来源链接：

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1156887/?report=classic

大型动物模型(犬、羊等)的基因组方法具有挑战性，因为这些物种的基因组信息不足，并且缺乏相应的微阵列平台。为了解决这个问题，我们推测保守的物种间遗传序列可以通过跨物种杂交来实验检测。Affymetrix平台的探针冗余使您可以灵活地选择相关物种之间具有较高序列相似性的单个探针进行基因表达分析。用人类HG-U133A基因芯片(U133A)构建了40个犬类样本的基因表达谱。由于物种间的遗传差异，U133A探针组只检测到14±2%的犬类转录本，而40份人类样本的图谱检测到49%±6%的转录本。然而，当这些探针组被解构成单独的探针并检查每个探针的性能时，我们发现47%的人类探针能够在犬组织中找到它们的靶标并产生可检测的杂交信号。因此，我们将基因表达分析限制在这些探针上，并观察到已识别的犬类转录本数量增加了60%。通过将我们的限制性跨物种杂交分析鉴定的转录本与新的Affymetrix犬基因芯片®的肺总mRNA杂交鉴定的转录本进行比较，验证了这些结果。基因表达分析的实验鉴定和对具有可检测杂交信号的探针的限制大大提高了犬与人杂交的转录本检测，表明利用基因芯片技术进行近缘物种的杂交具有广泛应用的可能性。

Genomic approaches in large animal models (canine, ovine etc) are challenging due to insufficient genomic information for these species and the lack of availability of corresponding microarray platforms. To address this problem, we speculated that conserved interspecies genetic sequences can be experimentally detected by cross-species hybridization. The Affymetrix platform probe redundancy offers flexibility in selecting individual probes with high sequence similarities between related species for gene expression analysis. Gene expression profiles of 40 canine samples were generated using the human HG-U133A GeneChip (U133A). Due to interspecies genetic differences, only 14 ± 2% of canine transcripts were detected by U133A probe sets whereas profiling of 40 human samples detected 49 ± 6% of human transcripts. However, when these probe sets were deconstructed into individual probes and examined performance of each probe, we found that 47% of human probes were able to find their targets in canine tissues and generate a detectable hybridization signal. Therefore, we restricted gene expression analysis to these probes and observed the 60% increase in the number of identified canine transcripts. These results were validated by comparison of transcripts identified by our restricted analysis of cross-species hybridization with transcripts identified by hybridization of total lung canine mRNA to new Affymetrix Canine GeneChip®. The experimental identification and restriction of gene expression analysis to probes with detectable hybridization signal drastically increases transcript detection of canine-human hybridization suggesting the possibility of broad utilization of cross-hybridizations of related species using GeneChip technology.