Understanding the regulatory genome
Understanding the regulatory genome
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DOI：
10.1387/ijdb.072428ma
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发表时间：
2009-01-01
影响因子：
0.7
通讯作者：
Manzanares, Miguel
中科院分区：
文献类型：
--
作者：
Alonso, M. Eva;Pernaute, Barbara;Manzanares, Miguel
多个物种的全基因组测序为我们提供了如何构建生物体并使其工作的指导书，以及在进化过程中如何产生多样性的详细历史。不幸的是，我们仍然只了解一小部分，那就是定位基因的位置并破译它们编码的蛋白质。下一步是了解正确数量的基因产物是如何在空间和时间中产生的，以获得一个功能齐全的生物体，从卵子到成虫。这就是所谓的调控基因组，这个术语是由埃里克·H·戴维森.在这篇综述中，我们从基因组的角度审视了我们对基因调控的了解，修改了当前计算机模拟、体外和体内方法来研究转录调控，并指出系统发育足迹作为调控指南的力量元件发现。每种方法的优点和局限性被认为是新兴的观点，只有大规模的研究和数据处理将让我们深入了解基因组调控系统的语言，并允许在基因组中发现调控代码。
The sequencing of the whole genome of multiple species provides us with the instruction book of how to build an organism and make it work, plus a detailed history of how diversity was generated during evolution. Unfortunately, we still understand only a small fraction, which is locating where genes are and deciphering the proteins they code for. The next step is to understand how the correct amount of gene products are produced in space and time to obtain a fully functioning organism, from the egg to the adult. This is what is known as the regulatory genome, a term coined by Eric H. Davidson. In this review, we examine what we know about gene regulation from a genomic point of view, revise the current in silico, in vitro and in vivo methodological approaches to study transcriptional regulation, and point to the power of phylogenetic footprinting as a guide to regulatory element discovery. The advantages and limitations of each approach are considered, with the emerging view that only large-scale studies and data-crunching will give us insight into the language of genomic regulatory systems, and allow the discovery of regulatory codes in the genome.