Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura.
Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura.
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DOI：
10.1186/gb-2004-5-9-r61
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发表时间：
2004
期刊：
影响因子：
12.3
通讯作者：
Celniker SE
中科院分区：
文献类型：
--
作者：
Berman BP;Pfeiffer BD;Laverty TR;Salzberg SL;Rubin GM;Eisen MB;Celniker SE
在体内分析了果蝇基因组中的27个预测的基因调控区域，确认了15个活性增强子区域。与果蝇伪暗区序列的比较表明，结合位点簇的保守性可以准确地区分功能区域和非功能区域。 鉴定后生动物中控制转录的序列是基因组分析的主要目标。在以前的研究中，我们证明了搜索预测的转录因子结合位点簇可以发现活跃的调控序列，并确定了黑腹果蝇基因组的37个区域，这些区域具有高密度的预测结合位点，用于参与前后胚胎模式的5个转录因子。这些簇中有9个与已知的增强子重叠。在这里，我们报告的结果在体内功能分析的27个剩余的集群。我们产生了转基因苍蝇携带每个集群连接到一个基础的启动子和报告基因，并分析胚胎报告基因的表达。6个簇是相邻基因的增强子：giant、fushi tarazu、odd-skipped、nubbin、squeeze和pdm 2; 3个簇驱动与相邻基因无关的表达模式;其余18个簇似乎没有增强子活性。我们使用果蝇pseudobscura基因组来比较15个阳性预测和18个假阳性预测的进化模式。虽然一级序列的保守性不能区分真阳性和假阳性，但结合位点聚类的保守性可以准确地区分功能性结合位点簇和无功能的结合位点簇。我们将结合位点聚类的保守性纳入一个新的全基因组增强子筛选中，并预测了数百个新的调控序列，其中包括85个与胚胎模式基因相邻的序列。测量与功能密切相关的序列特征的保守性-例如结合位点聚类-比仅检查序列同一性的常用方法更好地利用了比较序列数据。
27 predicted gene-regulatory regions in the Drosophila melanogaster genome were analyzed in vivo, confirming 15 active enhancer regions. A comparison with Drosophila pseudoobscura sequences revealed that conservation of binding-site clusters accurately discriminates functional regions from non-functional ones. The identification of sequences that control transcription in metazoans is a major goal of genome analysis. In a previous study, we demonstrated that searching for clusters of predicted transcription factor binding sites could discover active regulatory sequences, and identified 37 regions of the Drosophila melanogaster genome with high densities of predicted binding sites for five transcription factors involved in anterior-posterior embryonic patterning. Nine of these clusters overlapped known enhancers. Here, we report the results of in vivo functional analysis of 27 remaining clusters. We generated transgenic flies carrying each cluster attached to a basal promoter and reporter gene, and assayed embryos for reporter gene expression. Six clusters are enhancers of adjacent genes: giant, fushi tarazu, odd-skipped, nubbin, squeeze and pdm2; three drive expression in patterns unrelated to those of neighboring genes; the remaining 18 do not appear to have enhancer activity. We used the Drosophila pseudoobscura genome to compare patterns of evolution in and around the 15 positive and 18 false-positive predictions. Although conservation of primary sequence cannot distinguish true from false positives, conservation of binding-site clustering accurately discriminates functional binding-site clusters from those with no function. We incorporated conservation of binding-site clustering into a new genome-wide enhancer screen, and predict several hundred new regulatory sequences, including 85 adjacent to genes with embryonic patterns. Measuring conservation of sequence features closely linked to function - such as binding-site clustering - makes better use of comparative sequence data than commonly used methods that examine only sequence identity.
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影响因子：
11.4
作者：
HOCH, M;SCHRODER, C;JACKLE, H
通讯作者：
JACKLE, H
DOI：
10.1073/pnas.231608898
发表时间：
2002-01-22
影响因子：
11.1
作者：
Berman, BP;Nibu, Y;Eisen, MB
通讯作者：
Eisen, MB
影响因子：
64.5
作者：
HIROMI, Y;KUROIWA, A;GEHRING, WJ
通讯作者：
GEHRING, WJ
影响因子：
3
作者：
Emberly, E;Rajewsky, N;Siggia, ED
通讯作者：
Siggia, ED
DOI：
10.1073/pnas.1233791100
发表时间：
2003-08-19
影响因子：
11.1
作者：
Calhoun, VC;Levine, M
通讯作者：
Levine, M