Global analysis of the impact of environmental perturbation on cis-regulation of gene expression: BMP2, 2hr

Genetic variants altering cis-regulation of normal gene expression (cis-eQTLs) have been extensively mapped in human cells and tissues, but the extent to which environmental perturbation influences such traits has not been studied to date. We carried out large-scale induction experiments using primary human bone cells derived from 113 unrelated donors of Swedish origin harvested under 18 different conditions (seven treatments, two vehicles, each assessed at two time points). The treatments with the largest impact on the transcriptome, verified on two independent expression arrays, included BMP-2 (t=2h), dexamethasone (DEX) (t=24h), and PGE2 (t=24h). Using these treatments, we performed expression profiling for 18,144 RefSeq transcripts applying biological replicates of the complete study cohort (ntotal=782) and combined it with genome-wide SNP-genotyping data in order to map treatment-specific cis-eQTLs. We found that 93% of cis-eQTLs at 1% FDR were replicated in at least one additional treatment and in fact, on average only 1.4% of the cis-eQTLs were considered as treatment-specific at high confidence. The relative invariability of cis-regulation following perturbation was reiterated independently by genome-wide allelic expression tests where only a small proportion of variance could be attributed to treatment, though treatment-specific cis-regulatory effects were 2-6-fold more abundant among up-or downregulated genes. We further followed-up and validated the DEX-specific cis-regulation of the MYO6 and TNC loci and found top cis-regulatory variants located 180 and 250kb upstream of the transcription start sites, respectively. Our results suggest that, as opposed to tissue-specificity of cis-eQTLs, the interaction between cellular environment and cis-variants are relatively rare (~1.5%), but that detection of such specific interactions can be achieved by combination of functional genomic tools. Total RNA from cultured trabecular bone cells obtained from ~100 unrelated Caucasian donors treated under multiple different conditions and timepoints. Each sample represented by two or three biological replicates. This dataset includes samples treated with bone morphogenetic protein 2 (BMP2) for 2 hours.

能够改变正常基因表达顺式调控模式的遗传变异（cis-eQTLs，顺式表达数量性状位点）已在人类细胞与组织中得到广泛定位，但迄今为止，环境扰动对这类性状的影响程度仍未得到研究。本研究采用源自113名无亲缘关系瑞典供体的原代人骨细胞，在18种不同培养条件下（7种处理方式、2种载体对照，每种均设置两个时间点进行检测）开展了大规模诱导实验。经两套独立表达芯片验证后，对转录组影响最显著的处理方式包括骨形态发生蛋白2（BMP-2，t=2h）、地塞米松（DEX，t=24h）以及前列腺素E2（PGE2，t=24h）。本研究针对上述处理方式，利用全部研究队列的生物学重复样本（总样本量n_total=782）对18144条RefSeq转录本进行表达谱分析，并结合全基因组SNP基因分型数据，以定位处理特异性的顺式表达数量性状位点。研究发现，在1%错误发现率（FDR，false discovery rate）筛选下的顺式表达数量性状位点中，有93%可在至少一种其他处理中得到重复；实际上，平均仅1.4%的顺式表达数量性状位点可被高置信度认定为处理特异性位点。全基因组等位基因表达检测独立验证了扰动后顺式调控的相对稳定性：仅极小部分表达变异可归因于处理方式，但在表达上调或下调的基因中，处理特异性顺式调控效应的丰度是其他基因的2~6倍。本研究进一步针对地塞米松特异性的MYO6与TNC基因座顺式调控效应进行了追踪验证，分别在转录起始位点上游180kb与250kb处找到了核心顺式调控变异。本研究结果表明，与顺式表达数量性状位点的组织特异性不同，细胞环境与顺式变异之间的交互作用相对罕见（约1.5%），但通过整合功能基因组学工具可实现这类特异性交互作用的检测。本数据集的样本源自约100名无亲缘关系高加索供体的培养小梁骨细胞，经多种不同处理方式与时间点处理后提取总RNA；每个样本设置2~3个生物学重复。本数据集包含经骨形态发生蛋白2（BMP2）处理2小时的样本。