Comprehensive Genomic Discovery of Non-Coding Transcriptional Enhancers in the African Malaria Vector Anopheles coluzzii.
Comprehensive Genomic Discovery of Non-Coding Transcriptional Enhancers in the African Malaria Vector Anopheles coluzzii.
复制标题
DOI：
10.3389/fgene.2021.785934
复制
发表时间：
2021
影响因子：
3.7
通讯作者：
Riehle MM
中科院分区：
文献类型：
--
作者：
Holm I;Nardini L;Pain A;Bischoff E;Anderson CE;Zongo S;Guelbeogo WM;Sagnon N;Gohl DM;Nowling RJ;Vernick KD;Riehle MM
真核基因组中几乎所有基因表达的调节都是由远端非编码转录增强子对近端基因启动子的作用介导的。由于缺乏定义的序列代码，无法通过生物信息学准确预测增强子位置，因此需要进行功能测定来直接检测它们。在这里，我们使用大规模并行报告分析，即自转录活性调节区测序（STARR-seq），生成了首个全面的按蚊（冈比亚物种复合体中的主要非洲疟疾载体）全基因组增强子图谱。该筛选是通过将来自布基纳法索的 60 个野生 A. coluzzii 的基因组 DNA 创建的报告文库转染到 A. coluzzii 4a3A 细胞中进行的，以便在同源细胞环境中功能查询自然群体的增强子活性。我们报告了 3,288 个活性基因组增强子的目录，这些增强子在三个生物重复中具有重要意义，其中 74% 位于基因间和内含子区域。 STARR-seq 增强子筛选不含染色质，因此可检测全面的增强子目录的固有活性，这些增强子在体内可能仅限于特定细胞类型或发育阶段。使用手动荧光素酶测定对增强子候选物的验证组进行测试，证实了 28 个候选物中的 26 个（93%）的增强子功能，其活性范围较基线高 2 至至少 16 倍。增强子仅占基因组的0.7%，并表现出独特的组成特征。与匹配的非增强子基因组对照相比，增强子区室显着富集了 15 个转录因子结合位点特征，并且显示出特定二核苷酸重复的分歧。 A. coluzzii 增强子的全基因组目录以简单的可搜索图形格式公开提供。该增强子目录对于连接遗传和表型变异、识别可用于载体操作的调控元件以及更好地定位染色体编辑以尽量减少对引入序列的外来调控影响具有重要意义。 重要性：了解非编码调控基因组在复杂疾病表型中的作用至关重要，但即使在特征明确的模式生物中，在巨大的非编码基因组中识别调控区域仍然是一个挑战。我们使用大规模测定来生成转录增强子的全基因组图谱。随着非编码调控变异在疟疾感染不同易感性中的作用的探索，重要的疟疾媒介——按蚊（Anopheles coluzzii）的这样一个目录将成为一个重要的研究工具，并作为研究这种重要的昆虫疾病媒介的公共资源。
Almost all regulation of gene expression in eukaryotic genomes is mediated by the action of distant non-coding transcriptional enhancers upon proximal gene promoters. Enhancer locations cannot be accurately predicted bioinformatically because of the absence of a defined sequence code, and thus functional assays are required for their direct detection. Here we used a massively parallel reporter assay, Self-Transcribing Active Regulatory Region sequencing (STARR-seq), to generate the first comprehensive genome-wide map of enhancers in Anopheles coluzzii, a major African malaria vector in the Gambiae species complex. The screen was carried out by transfecting reporter libraries created from the genomic DNA of 60 wild A. coluzzii from Burkina Faso into A. coluzzii 4a3A cells, in order to functionally query enhancer activity of the natural population within the homologous cellular context. We report a catalog of 3,288 active genomic enhancers that were significant across three biological replicates, 74% of them located in intergenic and intronic regions. The STARR-seq enhancer screen is chromatin-free and thus detects inherent activity of a comprehensive catalog of enhancers that may be restricted in vivo to specific cell types or developmental stages. Testing of a validation panel of enhancer candidates using manual luciferase assays confirmed enhancer function in 26 of 28 (93%) of the candidates over a wide dynamic range of activity from two to at least 16-fold activity above baseline. The enhancers occupy only 0.7% of the genome, and display distinct composition features. The enhancer compartment is significantly enriched for 15 transcription factor binding site signatures, and displays divergence for specific dinucleotide repeats, as compared to matched non-enhancer genomic controls. The genome-wide catalog of A. coluzzii enhancers is publicly available in a simple searchable graphic format. This enhancer catalogue will be valuable in linking genetic and phenotypic variation, in identifying regulatory elements that could be employed in vector manipulation, and in better targeting of chromosome editing to minimize extraneous regulation influences on the introduced sequences. Importance: Understanding the role of the non-coding regulatory genome in complex disease phenotypes is essential, but even in well-characterized model organisms, identification of regulatory regions within the vast non-coding genome remains a challenge. We used a large-scale assay to generate a genome wide map of transcriptional enhancers. Such a catalogue for the important malaria vector, Anopheles coluzzii, will be an important research tool as the role of non-coding regulatory variation in differential susceptibility to malaria infection is explored and as a public resource for research on this important insect vector of disease.
登录
查看更多内容
DOI：
10.1093/bioinformatics/btr064
发表时间：
2011-04-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Grant CE;Bailey TL;Noble WS
通讯作者：
Noble WS
影响因子：
3
作者：
Farley EJ;Eggleston H;Riehle MM
通讯作者：
Riehle MM
影响因子：
12.8
作者：
Gloss BS;Dinger ME
通讯作者：
Dinger ME
DOI：
10.1073/pnas.0905754106
发表时间：
2009-08-25
影响因子：
11.1
作者：
Cande, Jessica;Goltsev, Yury;Levine, Michael S.
通讯作者：
Levine, Michael S.
影响因子：
14.9
作者：
Bailey TL;Johnson J;Grant CE;Noble WS
通讯作者：
Noble WS