Massively parallel functional dissection of mammalian enhancers in vivo.
Massively parallel functional dissection of mammalian enhancers in vivo.
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DOI：
10.1038/nbt.2136
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发表时间：
2012-02-26
影响因子：
46.9
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中科院分区：
文献类型：
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哺乳动物调控元件的遗传变异的功能后果知之甚少。我们报告在体内解剖三个哺乳动物肝脏增强在单核苷酸分辨率通过大规模并行报告分析。对于每个增强子，我们合成了> 100，000个突变单倍型的文库，与野生型具有2-3%的差异。每个单倍型与嵌入转录盒内的独特序列标签连接。我们将每个增强子文库引入小鼠肝脏，并通过转录标签的测序来测量单个单倍型的相对活性。线性回归得到了每个可能的单核苷酸变化对增强子活性的影响的高度可重复的估计。大多数突变的功能影响是适度的，约22%影响活性>1.2倍，仅约3%影响活性>2倍。这些结果表明，哺乳动物增强子对单核苷酸变化相对稳健。有几个，但不是所有的位置具有较高的影响显示纯化选择的证据，或与已知的肝脏相关的转录因子结合位点共定位，证明经验的高分辨率功能分析的价值。
The functional consequences of genetic variation in mammalian regulatory elements are poorly understood. We report the in vivo dissection of three mammalian liver enhancers at single nucleotide resolution via a massively parallelized reporter assay. For each enhancer, we synthesized a library of >100,000 mutant haplotypes with 2–3% divergence from wild-type. Each haplotype was linked to a unique sequence tag embedded within a transcriptional cassette. We introduced each enhancer library into mouse liver and measured the relative activities of individual haplotypes en masse by sequencing of the transcribed tags. Linear regression yielded highly reproducible estimates of the impact of every possible single nucleotide change on enhancer activity. The functional impact of most mutations was modest, with ~22% impacting activity by >1.2-fold, and only ~3% by >2-fold. These results suggest that mammalian enhancers are relatively robust to single nucleotide changes. Several, but not all positions with higher impact showed evidence for purifying selection, or co-localized with known liver-associated transcription factor binding sites, demonstrating the value of empirical high-resolution functional analysis.
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影响因子：
64.8
作者：
Ernst, Jason;Kheradpour, Pouya;Mikkelsen, Tarjei S.;Shoresh, Noam;Ward, Lucas D.;Epstein, Charles B.;Zhang, Xiaolan;Wang, Li;Issner, Robbyn;Coyne, Michael;Ku, Manching;Durham, Timothy;Kellis, Manolis;Bernstein, Bradley E.
通讯作者：
Bernstein, Bradley E.
影响因子：
9.8
作者：
ENCODE Project Consortium
通讯作者：
ENCODE Project Consortium
影响因子：
48
作者：
Hiatt, Joseph B.;Patwardhan, Rupali P.;Turner, Emily H.;Lee, Choli;Shendure, Jay
通讯作者：
Shendure, Jay
影响因子：
46.9
作者：
通讯作者：
--
影响因子：
7
作者：
Margulies, Elliott H.;Cooper, Gregory M.;Sidow, Arend
通讯作者：
Sidow, Arend