Peking-Yale Joint Center of Plant Molecular Genetics and Agrobiotechnology, National Laboratory of Protein Engineering and Plant Genetic Engineering, School of Life Sciences, Peking University, Beijing 100871, China.
Plant J. 2011 Feb;65(3):346-58. doi: 10.1111/j.1365-313X.2010.04426.x. Epub 2010 Dec 30.
LONG HYPOCOTYL 5 (HY5) is a basic leucine zipper transcription factor (TF) that functions downstream of multiple families of photoreceptors. Mutations in the HY5 gene cause a myriad of aberrant phenotypes in Arabidopsis, including elongated hypocotyl, reduced accumulation of pigments, halted chloroplast development in greening hypocotyls, altered root morphology, and defective hormonal and stimulus responses. HY5 thus acts as an integrator that links various gene networks to coordinate plant development. Here we report the experimental mapping of HY5-mediated gene networks in Arabidopsis by integrating genomic loci occupied by HY5 and HY5-dependent gene expression profiles. Our results indicate that HY5 binds to over 9000 genes, detectably affecting the expression of over 1100 genes, either positively or negatively. Further, HY5 indirectly regulate many other genes through sub-networks mediated by other regulators. In particular, HY5 regulates eight miRNA genes that in turn control the transcript abundance of specific target genes. Over-expressing HY5-targeted miR408 resulted in phenotypes that are opposite to the hy5 mutants. Together, our results reveal both transcriptional and post-transcriptional components of the HY5-mediated gene networks.
长日下胚轴 5（HY5）是一个基本亮氨酸拉链转录因子（TF），它在多个光受体家族下游发挥作用。HY5 基因突变在拟南芥中引起了许多异常表型，包括下胚轴伸长、色素积累减少、绿苗下胚轴中叶绿体发育停滞、根系形态改变以及激素和刺激反应缺陷。因此，HY5 作为一个整合因子，将各种基因网络联系起来，协调植物的发育。在这里，我们通过整合 HY5 结合的基因组位点和 HY5 依赖的基因表达谱，报告了 HY5 介导的拟南芥基因网络的实验作图。我们的结果表明，HY5 结合了超过 9000 个基因，可检测地影响超过 1100 个基因的表达，无论是正向还是负向。此外，HY5 通过其他调节剂介导的子网络间接调节许多其他基因。特别是，HY5 调节了八个 miRNA 基因，这些基因反过来又控制特定靶基因的转录丰度。过表达 HY5 靶向的 miR408 导致的表型与 hy5 突变体相反。总之，我们的结果揭示了 HY5 介导的基因网络的转录和转录后成分。
