Discovery of stimulation-responsive immune enhancers with CRISPR activation.
Discovery of stimulation-responsive immune enhancers with CRISPR activation.
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DOI：
10.1038/nature23875
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发表时间：
2017-09-07
期刊：
影响因子：
64.8
通讯作者：
Marson A
中科院分区：
文献类型：
--
作者：
Simeonov DR;Gowen BG;Boontanrart M;Roth TL;Gagnon JD;Mumbach MR;Satpathy AT;Lee Y;Bray NL;Chan AY;Lituiev DS;Nguyen ML;Gate RE;Subramaniam M;Li Z;Woo JM;Mitros T;Ray GJ;Curie GL;Naddaf N;Chu JS;Ma H;Boyer E;Van Gool F;Huang H;Liu R;Tobin VR;Schumann K;Daly MJ;Farh KK;Ansel KM;Ye CJ;Greenleaf WJ;Anderson MS;Bluestone JA;Chang HY;Corn JE;Marson A
大多数与人类常见疾病相关的遗传变异都与增强子、非编码元件有关，这些元件形成细胞类型特异性转录程序和对细胞外信号的反应。为了了解非编码基因序列变异导致疾病的机制，需要系统地绘制功能增强子及其生物学背景。功能增强子可以通过基因组序列破坏来绘制，但这种方法仅限于在所研究的特定细胞环境中必需的增强子子集。我们假设，即使增强子目前在被测细胞中没有活性，向增强子募集强转录激活子也足以驱动靶基因表达。在这里，我们描述了一个发现平台，可以识别独立于刺激暴露的靶基因的刺激反应增强子。我们使用平片CRISPR激活（CRISPRa）在两个关键自身免疫风险位点（CD69和IL2RA）周围的大基因组区域（超过100千碱基）合成招募转录激活子。我们确定了几种具有刺激应答增强子染色质特征的crispr应答元件，包括含有自身免疫风险变体的IL2RA增强子。使用工程小鼠模型，我们发现疾病相关Il2ra增强子的序列扰动并没有完全阻断Il2ra的表达，而是延迟了响应特定细胞外信号的基因激活时间。增强子缺失使幼稚T细胞向促炎T辅助（TH17）细胞状态倾斜，并远离调节性T细胞状态。这种综合方法识别功能增强子，并揭示与人类免疫功能障碍相关的非编码变异如何改变环境特异性基因程序。
The majority of genetic variants associated with common human diseases map to enhancers, non-coding elements that shape cell-type-specific transcriptional programs and responses to extracellular cues. Systematic mapping of functional enhancers and their biological contexts is required to understand the mechanisms by which variation in non-coding genetic sequences contributes to disease. Functional enhancers can be mapped by genomic sequence disruption, but this approach is limited to the subset of enhancers that are necessary in the particular cellular context being studied. We hypothesized that recruitment of a strong transcriptional activator to an enhancer would be sufficient to drive target gene expression, even if that enhancer was not currently active in the assayed cells. Here we describe a discovery platform that can identify stimulus-responsive enhancers for a target gene independent of stimulus exposure. We used tiled CRISPR activation (CRISPRa) to synthetically recruit a transcriptional activator to sites across large genomic regions (more than 100 kilobases) surrounding two key autoimmunity risk loci, CD69 and IL2RA. We identified several CRISPRa-responsive elements with chromatin features of stimulus-responsive enhancers, including an IL2RA enhancer that harbours an autoimmunity risk variant. Using engineered mouse models, we found that sequence perturbation of the disease-associated Il2ra enhancer did not entirely block Il2ra expression, but rather delayed the timing of gene activation in response to specific extracellular signals. Enhancer deletion skewed polarization of naive T cells towards a pro-inflammatory T helper (TH17) cell state and away from a regulatory T cell state. This integrated approach identifies functional enhancers and reveals how non-coding variation associated with human immune dysfunction alters context-specific gene programs.
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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：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
14.8
作者：
通讯作者：
--
影响因子：
64.5
作者：
Hnisz D;Abraham BJ;Lee TI;Lau A;Saint-André V;Sigova AA;Hoke HA;Young RA
通讯作者：
Young RA
DOI：
10.1126/science.1222794
发表时间：
2012-09-07
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Maurano MT;Humbert R;Rynes E;Thurman RE;Haugen E;Wang H;Reynolds AP;Sandstrom R;Qu H;Brody J;Shafer A;Neri F;Lee K;Kutyavin T;Stehling-Sun S;Johnson AK;Canfield TK;Giste E;Diegel M;Bates D;Hansen RS;Neph S;Sabo PJ;Heimfeld S;Raubitschek A;Ziegler S;Cotsapas C;Sotoodehnia N;Glass I;Sunyaev SR;Kaul R;Stamatoyannopoulos JA
通讯作者：
Stamatoyannopoulos JA