Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm.
Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm.
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DOI：
10.1371/journal.pbio.0060027
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发表时间：
2008-02
期刊：
影响因子：
9.8
通讯作者：
Biggin MD
中科院分区：
文献类型：
--
作者：
Li XY;MacArthur S;Bourgon R;Nix D;Pollard DA;Iyer VN;Hechmer A;Simirenko L;Stapleton M;Luengo Hendriks CL;Chu HC;Ogawa N;Inwood W;Sementchenko V;Beaton A;Weiszmann R;Celniker SE;Knowles DW;Gingeras T;Speed TP;Eisen MB;Biggin MD
识别序列特异性调控因子结合的基因组区域对于破译控制后生动物转录的复杂DNA顺式调控密码和确定塑造动物形态发生的基因范围都是至关重要的。我们使用全基因组平铺阵列映射序列绑定在果蝇胚胎的六个母亲和间隙转录因子，启动前后图案。我们发现，这些序列特异性的DNA结合蛋白质结合的数量上不同的特异性，高度重叠的几个胚盘胚胎基因组区域的集合。特定的高和中等亲和力的体外识别序列的每一个因素是丰富的结合区。然而，这种富集不足以解释体内结合的模式，并且以上下文依赖的方式变化，表明高阶规则必须控制转录因子的靶向。更高度结合的区域包括已知响应这些因子的所有超过40个充分表征的增强子以及在胚胎发生的这个阶段具有模式化表达的在发育调节因子附近聚集的几百个推定的新的顺式调节模块和其他基因。新的目标包括大多数的microRNA（miRNA）转录胚盘，以及所有主要的合子转录背腹图案的基因，其表达，我们表明是定量调制的前后因素。除了这些高度结合的区域之外，还有数千个区域以较低水平可重复地结合。然而，这些结合不良的区域，总的来说，远比高度结合的区域更远离胚盘中转录的基因;优先发现于蛋白质编码序列中;并且比高度结合的区域保守性更低。总之，这些观察结果表明，许多这些结合不良的地区不参与早期胚胎的转录调控，和一个显着的比例可能是无功能的。令人惊讶的是，对于六个因子中的五个，它们的识别位点在进化上并不比直接侧翼DNA受到更明确的限制，即使在更高度结合和推测的功能区域中，这表明比较DNA序列分析在识别功能性转录因子靶点的能力方面是有限的。序列特异性DNA结合转录因子是动物中最大的一类调控蛋白，它决定基因在哪些细胞中表达，从而控制动物从单细胞发育为形态复杂的成体。理解这个过程是如何协调的取决于知道每个转录因子结合和调节的基因的数量和类型。使用免疫沉淀的体内交联染色质结合DNA微阵列杂交（ChIP/芯片），我们已经确定了6个转录因子的早期胚胎中的基因组结合位点，这些转录因子在果蝇的早期发育中起着至关重要的作用。我们发现，这些蛋白质与数千个基因组区域结合，这些区域接近一半的蛋白质编码基因。虽然这是一个更大的基因数量比这些因素通常被认为是调节，我们继续表明，而更高度结合的基因通常看起来是功能性的目标，许多基因结合在较低的水平似乎不受这些因素的调节。我们的结论不同于那些没有区分不同水平的DNA结合在体内使用类似的测定和谁一般假设，所有检测到的结合是功能性的其他群体。ChIP/芯片分析表明，序列特异性转录因子与果蝇胚胎中数千个基因组区域的重叠集结合，但大多数区域的结合水平较低，许多区域可能不是这些因子的功能靶标。
Identifying the genomic regions bound by sequence-specific regulatory factors is central both to deciphering the complex DNA cis-regulatory code that controls transcription in metazoans and to determining the range of genes that shape animal morphogenesis. We used whole-genome tiling arrays to map sequences bound in Drosophila melanogaster embryos by the six maternal and gap transcription factors that initiate anterior–posterior patterning. We find that these sequence-specific DNA binding proteins bind with quantitatively different specificities to highly overlapping sets of several thousand genomic regions in blastoderm embryos. Specific high- and moderate-affinity in vitro recognition sequences for each factor are enriched in bound regions. This enrichment, however, is not sufficient to explain the pattern of binding in vivo and varies in a context-dependent manner, demonstrating that higher-order rules must govern targeting of transcription factors. The more highly bound regions include all of the over 40 well-characterized enhancers known to respond to these factors as well as several hundred putative new cis-regulatory modules clustered near developmental regulators and other genes with patterned expression at this stage of embryogenesis. The new targets include most of the microRNAs (miRNAs) transcribed in the blastoderm, as well as all major zygotically transcribed dorsal–ventral patterning genes, whose expression we show to be quantitatively modulated by anterior–posterior factors. In addition to these highly bound regions, there are several thousand regions that are reproducibly bound at lower levels. However, these poorly bound regions are, collectively, far more distant from genes transcribed in the blastoderm than highly bound regions; are preferentially found in protein-coding sequences; and are less conserved than highly bound regions. Together these observations suggest that many of these poorly bound regions are not involved in early-embryonic transcriptional regulation, and a significant proportion may be nonfunctional. Surprisingly, for five of the six factors, their recognition sites are not unambiguously more constrained evolutionarily than the immediate flanking DNA, even in more highly bound and presumably functional regions, indicating that comparative DNA sequence analysis is limited in its ability to identify functional transcription factor targets. One of the largest classes of regulatory proteins in animals, sequence-specific DNA binding transcription factors determine in which cells genes will be expressed and so control the development of an animal from a single cell to a morphologically complex adult. Understanding how this process is coordinated depends on knowing the number and types of genes that each transcription factor binds and regulates. Using immunoprecipitation of in vivo crosslinked chromatin coupled with DNA microarray hybridization (ChIP/chip), we have determined the genomic binding sites in early embryos of six transcription factors that play a crucial role in early development of the fruit fly Drosophila melanogaster. We find that these proteins bind to several thousand genomic regions that lie close to approximately half the protein coding genes. Although this is a much larger number of genes than these factors are generally thought to regulate, we go on to show that whereas the more highly bound genes generally look to be functional targets, many of the genes bound at lower levels do not appear to be regulated by these factors. Our conclusions differ from those of other groups who have not distinguished between different levels of DNA binding in vivo using similar assays and who have generally assumed that all detected binding is functional. ChIP/chip analysis indicates that sequence-specific transcription factors bind to overlapping sets of thousands of genomic regions in Drosophila embryos, but most regions are bound at low levels and many may not be functional targets of these factors.
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影响因子：
64.5
作者：
Cawley, S;Bekiranov, S;Gingeras, TR
通讯作者：
Gingeras, TR
影响因子：
12.3
作者：
Berman BP;Pfeiffer BD;Laverty TR;Salzberg SL;Rubin GM;Eisen MB;Celniker SE
通讯作者：
Celniker SE
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：
7
作者：
Bieda, M;Xu, XQ;Farnham, PJ
通讯作者：
Farnham, PJ
影响因子：
11.4
作者：
Carr, A;Biggin, MD
通讯作者：
Biggin, MD