Robust Identification of Developmentally Active Endothelial Enhancers in Zebrafish Using FANS-Assisted ATAC-Seq.
Robust Identification of Developmentally Active Endothelial Enhancers in Zebrafish Using FANS-Assisted ATAC-Seq.
复制标题
DOI：
10.1016/j.celrep.2017.06.070
复制
发表时间：
2017-07-18
期刊：
影响因子：
8.8
通讯作者：
Lawson ND
中科院分区：
文献类型：
--
作者：
Quillien A;Abdalla M;Yu J;Ou J;Zhu LJ;Lawson ND
组织特异性和发育活性增强子的鉴定提供了对胚胎发生过程中控制基因表达的机制的见解。然而，这些调控元件的稳健检测仍然具有挑战性，特别是在脊椎动物基因组中。在这里，我们应用荧光激活细胞核分选（FANS），然后用高通量测序（ATAC-Seq）检测转座酶可降解染色质，以确定斑马鱼基因组中发育活跃的内皮增强子。来自Tg（fli 1a：egfp）y1转基因胚胎的核的ATAC-Seq揭示了核小体定位在整个基因组的转录起始位点处的预期模式以及与活性组蛋白修饰的关联。来自GFP阳性和阴性细胞核的ATAC-Seq的比较鉴定了超过5，000个对内皮细胞特异性的开放元件。这些元件侧接对血管发育具有重要功能的基因，并显示内皮特异性基因表达。重要的是，大多数测试的元素驱动斑马鱼胚胎中的内皮基因表达。因此，使用转基因斑马鱼胚胎的FANS-assisted ATAC-Seq为活性组织特异性增强子元件的全基因组鉴定提供了一种稳健的方法。
Identification of tissue-specific and developmentally active enhancers provides insights into mechanisms that control gene expression during embryogenesis. However, robust detection of these regulatory elements remains challenging, especially in vertebrate genomes. Here, we apply fluorescent activated nuclei sorting (FANS) followed by Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-Seq) to identify developmentally active endothelial enhancers in the zebrafish genome. ATAC-Seq of nuclei from Tg(fli1a:egfp)y1 transgenic embryos revealed expected patterns of nucleosomal positioning at transcriptional start sites throughout the genome and association with active histone modifications. Comparison of ATAC-Seq from GFP-positive and -negative nuclei identified more than 5,000 open elements specific to endothelial cells. These elements flanked genes functionally important for vascular development and that displayed endothelial-specific gene expression. Importantly, a majority of tested elements drove endothelial gene expression in zebrafish embryos. Thus, FANS-assisted ATAC-Seq using transgenic zebrafish embryos provides a robust approach for genome-wide identification of active tissue-specific enhancer elements.
登录
查看更多内容
影响因子：
64.8
作者：
Heintzman, Nathaniel D.;Hon, Gary C.;Hawkins, R. David;Kheradpour, Pouya;Stark, Alexander;Harp, Lindsey F.;Ye, Zhen;Lee, Leonard K.;Stuart, Rhona K.;Ching, Christina W.;Ching, Keith A.;Antosiewicz-Bourget, Jessica E.;Liu, Hui;Zhang, Xinmin;Green, Roland D.;Lobanenkov, Victor V.;Stewart, Ron;Thomson, James A.;Crawford, Gregory E.;Kellis, Manolis;Ren, Bing
通讯作者：
Ren, Bing
影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
4
作者：
Ferg, Marco;Armant, Olivier;Straehle, Uwe
通讯作者：
Straehle, Uwe
影响因子：
2.7
作者：
Aday AW;Zhu LJ;Lakshmanan A;Wang J;Lawson ND
通讯作者：
Lawson ND
影响因子：
16
作者：
Heinz S;Benner C;Spann N;Bertolino E;Lin YC;Laslo P;Cheng JX;Murre C;Singh H;Glass CK
通讯作者：
Glass CK