Dissection of a Ciona regulatory element reveals complexity of cross-species enhancer activity.
Dissection of a Ciona regulatory element reveals complexity of cross-species enhancer activity.
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DOI：
10.1016/j.ydbio.2014.03.013
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发表时间：
2014-06-15
影响因子：
2.7
通讯作者：
Shimeld, Sebastian M.
中科院分区：
文献类型：
--
作者：
Chen, Wei-Chung;Pauls, Stefan;Bacha, Jamil;Elgar, Greg;Loose, Matthew;Shimeld, Sebastian M.
脊椎动物基因组共享许多保守的非编码元件，其中许多具有增强元件的功能，并且由于需要通过序列特异性转录因子的组合结合而被假设受到进化限制。相比之下，在脊椎动物和它们最接近的无脊椎动物亲属之间，很少能检测到这样的保守元素。尽管缺乏序列同一性，但跨物种转基因已经发现，在一些情况下，来自无脊椎动物的非编码DNA驱动转基因脊椎动物的报告基因表达，其模式与脊椎动物同源物的表达相似。这些情况被认为反映了在无脊椎动物和脊椎动物同源物的调控区域中存在保守的结合位点，这样两种调控元件都可以正确地解释反式激活环境。结合位点的洗牌被认为是序列保护缺失的原因；然而，这还没有经过实验验证。在这里，我们研究了Ciona ninteinalis βγ-晶体蛋白基因增强子活性的潜在基础，该基因驱动转基因脊椎动物晶状体中的表达，尽管Ciona谱系早于晶状体的进化。我们构建了一个脊椎动物晶状体发育的交互式基因调控网络（GRN），允许对网络相互作用进行稳健的编目，并保守网络组件和特征。我们发现少量的结合基序对于Ciona βγ-晶体蛋白的表达是必需的，并缩小了与这些基序结合的可能因素。其中一些位点与脊椎动物晶状体GRN的保守核心重叠，暗示这些位点具有跨物种功能。然而，当我们在转基因脊椎动物中测试这些基序时，它们被证明对于晶状体中的报告基因表达是必不可少的。这些结果表明，目前将跨物种增强子功能描述为依赖于保守结合位点的模型可能过于简单，合理的进化推断需要详细解剖潜在机制。在脊椎动物晶状体中也起作用的Ciona增强子中结合基序的分析。可能调控该增强子的候选转录因子的建立。构建晶状体发育的调控、互动基因调控网络。通过专门的网站向公众开放。跨物种转基因中结合基序功能的实验研究。
Vertebrate genomes share numerous conserved non-coding elements, many of which function as enhancer elements and are hypothesised to be under evolutionary constraint due to a need to be bound by combinations of sequence-specific transcription factors. In contrast, few such conserved elements can be detected between vertebrates and their closest invertebrate relatives. Despite this lack of sequence identity, cross-species transgenesis has identified some cases where non-coding DNA from invertebrates drives reporter gene expression in transgenic vertebrates in patterns reminiscent of the expression of vertebrate orthologues. Such instances are presumed to reflect the presence of conserved suites of binding sites in the regulatory regions of invertebrate and vertebrate orthologues, such that both regulatory elements can correctly interpret the trans-activating environment. Shuffling of binding sites has been suggested to lie behind loss of sequence conservation; however this has not been experimentally tested. Here we examine the underlying basis of enhancer activity for the Ciona intestinalis βγ-crystallin gene, which drives expression in the lens of transgenic vertebrates despite the Ciona lineage predating the evolution of the lens. We construct an interactive gene regulatory network (GRN) for vertebrate lens development, allowing network interactions to be robustly catalogued and conserved network components and features to be identified. We show that a small number of binding motifs are necessary for Ciona βγ-crystallin expression, and narrow down the likely factors that bind to these motifs. Several of these overlap with the conserved core of the vertebrate lens GRN, implicating these sites in cross species function. However when we test these motifs in a transgenic vertebrate they prove to be dispensable for reporter expression in the lens. These results show that current models depicting cross species enhancer function as dependent on conserved binding sites can be overly simplistic, with sound evolutionary inference requiring detailed dissection of underlying mechanisms. Analysis of binding motifs in a Ciona enhancer that also works in vertebrate lens. Establishment of candidate transcription factors that may regulate this enhancer. Construction of a curated, interactive gene regulatory network of lens development. Public accessibility of this via a dedicated web site. Experimental test of binding motif function in cross species transgenesis.
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影响因子：
3
作者：
Chen H;Sharp BM
通讯作者：
Sharp BM
影响因子：
14.9
作者：
Blanco E;Farré D;Albà MM;Messeguer X;Guigó R
通讯作者：
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影响因子：
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作者：
McEwen GK;Goode DK;Parker HJ;Woolfe A;Callaway H;Elgar G
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影响因子：
4.6
作者：
Imai, Kaoru S.;Stolfi, Alberto;Satou, Yutaka
通讯作者：
Satou, Yutaka
DOI：
10.1073/pnas.052024999
发表时间：
2002-05-14
影响因子：
11.1
作者：
Harafuji, N;Keys, DN;Levine, M
通讯作者：
Levine, M