Systematic identification of cis-regulatory sequences active in mouse and human embryonic stem cells.
Systematic identification of cis-regulatory sequences active in mouse and human embryonic stem cells.
复制标题
在小鼠和人类胚胎干细胞中的顺式调节序列的系统鉴定。
DOI：
10.1371/journal.pgen.0030145
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发表时间：
2007-08
期刊：
影响因子：
4.5
通讯作者：
Ramalho-Santos, Miguel
中科院分区：
文献类型：
--
作者：
Grskovic, Marica;Chaivorapol, Christina;Gaspar-Maia, Alexandre;Li, Hao;Ramalho-Santos, Miguel
了解多能细胞的转录调控具有重要意义，并将极大地指导胚胎干细胞的分化或对体细胞重新编程。我们首先分析了小鼠胚胎干细胞和原始生殖细胞的转录图谱，并在体外和体内鉴定了在多能细胞中上调的基因。这些基因在转录、染色质重塑、细胞周期和DNA修复中具有丰富的作用。我们开发了一种新的计算算法CompMoby，它将不同基因组之间对齐和未对齐的序列分析与概率分割模型相结合，以系统地预测调控基因表达的短DNA基序。CompMoby被用来确定在多能细胞中上调的基因中保守的过度表达基序。我们发现，这些基序在未分化的小鼠胚胎干细胞和胚胎生殖细胞中以序列特异性的方式优先激活，并且它们可以在内源性启动子的背景下作为增强子。重要的是，这些基序的活性在人类ES细胞中是保守的。我们进一步证明，转录因子NF-Y与其中一个基序特异结合，在ES细胞分化过程中差异表达，是ES细胞增殖所必需的。这项研究为多能细胞的转录调控网络提供了新的见解。我们的结果表明，这种系统化的方法可以广泛应用于理解哺乳动物物种的转录网络。胚胎干细胞有两个显著的特性：它们可以非常迅速地增殖，它们可以分化出人体所有类型的细胞。了解胚胎干细胞中的基因活性是如何调节的，这将是迈向治疗应用的重要一步。基因的活性由被称为转录因子的蛋白质调节，转录因子与一段DNA序列结合，充当开关。我们确定了在小鼠胚胎干细胞中活跃但在分化细胞中不活跃的基因。我们推测，如果这些基因具有相似的活性模式，它们可能受到相同的转录因子的调控。因此，我们开发了一种计算方法，可以获取基因活动的信息，并预测可能起开关作用的DNA序列。使用这种方法，我们发现了新的DNA开关，可以调节小鼠和人类胚胎干细胞的基因活性。此外，我们还鉴定了一种转录因子，它与其中一个DNA开关结合，对胚胎干细胞的快速增殖非常重要。我们的方法揭示了胚胎干细胞的遗传调控，并将广泛适用于基因活性如何在其他感兴趣的细胞类型中调控的问题。
Understanding the transcriptional regulation of pluripotent cells is of fundamental interest and will greatly inform efforts aimed at directing differentiation of embryonic stem (ES) cells or reprogramming somatic cells. We first analyzed the transcriptional profiles of mouse ES cells and primordial germ cells and identified genes upregulated in pluripotent cells both in vitro and in vivo. These genes are enriched for roles in transcription, chromatin remodeling, cell cycle, and DNA repair. We developed a novel computational algorithm, CompMoby, which combines analyses of sequences both aligned and non-aligned between different genomes with a probabilistic segmentation model to systematically predict short DNA motifs that regulate gene expression. CompMoby was used to identify conserved overrepresented motifs in genes upregulated in pluripotent cells. We show that the motifs are preferentially active in undifferentiated mouse ES and embryonic germ cells in a sequence-specific manner, and that they can act as enhancers in the context of an endogenous promoter. Importantly, the activity of the motifs is conserved in human ES cells. We further show that the transcription factor NF-Y specifically binds to one of the motifs, is differentially expressed during ES cell differentiation, and is required for ES cell proliferation. This study provides novel insights into the transcriptional regulatory networks of pluripotent cells. Our results suggest that this systematic approach can be broadly applied to understanding transcriptional networks in mammalian species. Embryonic stem cells have two remarkable properties: they can proliferate very rapidly, and they can give rise to all of the body's cell types. Understanding how gene activity is regulated in embryonic stem cells will be an important step towards therapeutic applications. The activity of genes is regulated by proteins called transcription factors, which bind to stretches of DNA sequences that act as on or off switches. We identified genes that are active in mouse embryonic stem cells but not in differentiated cells. We reasoned that if these genes have similar patterns of activity, they may be regulated by the same transcription factors. We therefore developed a computational approach that takes information on gene activity and predicts DNA sequences that may act as switches. Using this approach, we discovered new DNA switches that regulate gene activity in mouse and human embryonic stem cells. Furthermore, we identified a transcription factor that binds to one of these DNA switches and is important for the rapid proliferation of embryonic stem cells. Our approach sheds light on the genetic regulation of embryonic stem cells and will be broadly applicable to questions of how gene activity is regulated in other cell types of interest.
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影响因子：
14.9
作者：
GuhaThakurta D
通讯作者：
GuhaThakurta D
影响因子：
56.9
作者：
BLACKWELL, TK;KRETZNER, L;WEINTRAUB, H
通讯作者：
WEINTRAUB, H
影响因子：
4.1
作者：
Coustry, F;Sinha, S;de Crombrugghe, B
通讯作者：
de Crombrugghe, B
影响因子：
7
作者：
Curwen, V;Eyras, E;Clamp, M
通讯作者：
Clamp, M
DOI：
10.1073/pnas.180265397
发表时间：
2000-08-29
影响因子：
11.1
作者：
Bussemaker, HJ;Li, H;Siggia, ED
通讯作者：
Siggia, ED