Long-range expression effects of CNV: insights from Smith-Magenis and Potocki-Lupski syndrome mouse model

To study the effect of structural changes on expression, we assessed gene expression in genomic disorder mouse models. Both a microdeletion and its reciprocal microduplication mapping to mouse chromosome 11 (MMU11), which model the rearrangements present in Smith-Magenis (SMS) and Potocki-Lupski (PTLS) syndromes patients, respectively, have been engineered. We profiled the transcriptome of five different tissues affected in human patients in mice with 1n (Deletion/+), 2n (+/+), 3n (Duplication/+) and uniallelic 2n (Deletion/Duplication) copies of the same region in an identical genetic background. The most differentially expressed transcripts between the four studied genotypes were ranked. A highly significant propensity, are mapping to the engineered SMS/PTLS interval in the different tissues. A statistically significant overrepresentation of the genes mapping to the flanks of the engineered interval was also found in the top-ranked differentially expressed genes. A phenomenon efficient across multiple cell lineages and that extends along the entire length of the chromosome, tens of megabases from the breakpoints. These long-range effects are unidirectional and uncoupled from the number of copies of the copy number variation (CNV) genes. Thus, our results suggest that the assortment of genes mapping to a chromosome is not random. They also indicate that a structural change at a given position of the human genome may cause the same perturbation in particular pathways regardless of gene dosage. An issue that should be considered in appreciating the contribution of this class of variation to phenotypic features. Keywords: Genetic modification Comparisons of heterozygous mice carrying a duplication, Dp(11)17/+, a deletion, Df(11)17)/+, or both rearrangements, Df(11)17/Dp(11)17, with wild-type mice. Gene expression of at least two male individuals of each of the four genotypes were measured in hippocampus, cerebellum, testis, kidney and heart.为探究结构变异对基因表达的影响，本研究对基因组紊乱小鼠模型中的基因表达水平进行了评估。我们构建了两种基因工程模型：分别对应史密斯-马吉利综合征（Smith-Magenis Syndrome, SMS）与波托基-卢普斯基综合征（Potocki-Lupski Syndrome, PTLS）患者染色体重排的小鼠11号染色体（MMU11）区域的微缺失（microdeletion）及其互补微重复（microduplication）模型。在遗传背景完全一致的前提下，我们对携带4种不同拷贝数该区域的小鼠开展了转录组分析，分别为1拷贝（缺失/野生型，Deletion/+）、2拷贝（野生型，+/+）、3拷贝（重复/野生型，Duplication/+）以及单等位双拷贝（缺失/重复，Deletion/Duplication），涵盖了人类患者中受影响的5种不同组织。对4种基因型小鼠间差异表达最显著的转录本进行排序后发现，不同组织中的差异转录本均显著倾向于映射至工程构建的SMS/PTLS关联区域。此外，在排名靠前的差异表达基因中，映射至该工程区域侧翼的基因也呈现出显著的富集现象。这种长距离效应可高效作用于多种细胞谱系，且跨越断点两侧数十兆碱基的整条染色体区域。此类长距离效应具有单向性，且与拷贝数变异（Copy Number Variation, CNV）相关基因的拷贝数无关。据此本研究结果表明，染色体上基因的排布并非随机。同时研究还显示，人类基因组特定位置的结构变异，可通过干扰特定通路引发相同的表型扰动，而不受基因剂量的影响——这一问题在评估此类变异对表型特征的贡献时值得关注。关键词：基因修饰；携带重复变异Dp(11)17/+、缺失变异Df(11)17/+，或同时携带两种重排Df(11)17/Dp(11)17的杂合小鼠与野生型小鼠的对比分析。本研究对4种基因型小鼠各至少2只雄性个体的海马体、小脑、睾丸、肾脏及心脏组织进行了基因表达量检测。