The transcriptional regulator CBP has defined spatial associations within interphase nuclei
The transcriptional regulator CBP has defined spatial associations within interphase nuclei
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DOI：
10.1371/journal.pcbi.0020139
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发表时间：
2006-10-01
影响因子：
4.3
通讯作者：
Hendzel, Michael J.
中科院分区：
文献类型：
--
作者：
McManus, Kirk J.;Stephens, David A.;Hendzel, Michael J.
越来越清楚的是，核大分子和大分子复合物通过结合相互作用被划分成明显的三维有序结构。然而，这种顺序似乎并不确定的程度，染色质和非染色质结构保持严格的3-D排列。相反，细胞核内的空间秩序似乎符合随机而不是确定性的空间关系。当试图描述参与基因组调控的蛋白质之间的空间关系时，组织的随机性就变得特别成问题。CREB结合蛋白（CBP）是一种这样的转录调节因子，当通过共聚焦显微镜观察时，揭示了一种高度点状的染色模式，包括分布在核体积内的数百个单独的病灶。常染色质序列的标记具有相似的模式。令人惊讶的是，在大多数情况下，没有观察到预测的转录因子和染色质序列之间的一对一关系。因此，要了解不一致的空间关系是否是非随机的和潜在的生物学重要性，有必要开发统计方法。在这项研究中，我们报告了这种方法的发展，并将其应用于了解CBP在介导染色质修饰和转录调控中的作用。我们使用最近邻距离测量和概率分析来研究CBP和其他富含转录因子、染色质和剪接因子的核亚区室之间的空间关系。我们的研究结果表明，CBP与其他核亚室的空间关联的顺序。我们观察到CBP和RNA聚合酶II富集灶和SC 35斑点之间的关系比新生RNA或特定乙酰化组蛋白更密切。此外，我们发现CBP有一个显着更高的概率接近其已知的体内底物组蛋白H4赖氨酸5相比，密切相关的H4赖氨酸12。这项研究表明，复杂的关系不描述共定位存在于间期核，可以表征和量化。CBP的亚核分布很难与染色质组织是调节转录的蛋白质的核组织的唯一决定因素的模型相一致，但与空间关联和核功能之间的密切联系是一致的。
It is becoming increasingly clear that nuclear macromolecules and macromolecular complexes are compartmentalized through binding interactions into an apparent three-dimensionally ordered structure. This ordering, however, does not appear to be deterministic to the extent that chromatin and nonchromatin structures maintain a strict 3-D arrangement. Rather, spatial ordering within the cell nucleus appears to conform to stochastic rather than deterministic spatial relationships. The stochastic nature of organization becomes particularly problematic when any attempt is made to describe the spatial relationship between proteins involved in the regulation of the genome. The CREB-binding protein (CBP) is one such transcriptional regulator that, when visualised by confocal microscopy, reveals a highly punctate staining pattern comprising several hundred individual foci distributed within the nuclear volume. Markers for euchromatic sequences have similar patterns. Surprisingly, in most cases, the predicted one-to-one relationship between transcription factor and chromatin sequence is not observed. Consequently, to understand whether spatial relationships that are not coincident are nonrandom and potentially biologically important, it is necessary to develop statistical approaches. In this study, we report on the development of such an approach and apply it to understanding the role of CBP in mediating chromatin modification and transcriptional regulation. We have used nearest-neighbor distance measurements and probability analyses to study the spatial relationship between CBP and other nuclear subcompartments enriched in transcription factors, chromatin, and splicing factors. Our results demonstrate that CBP has an order of spatial association with other nuclear subcompartments. We observe closer associations between CBP and RNA polymerase II-enriched foci and SC35 speckles than nascent RNA or specific acetylated histones. Furthermore, we find that CBP has a significantly higher probability of being close to its known in vivo substrate histone H4 lysine 5 compared with the closely related H4 lysine 12. This study demonstrates that complex relationships not described by colocalization exist in the interphase nucleus and can be characterized and quantified. The subnuclear distribution of CBP is difficult to reconcile with a model where chromatin organization is the sole determinant of the nuclear organization of proteins that regulate transcription but is consistent with a close link between spatial associations and nuclear functions.