Section of Cell and Developmental Biology, University of California San Diego, Gilman Drive, La Jolla, CA 92093-0130, USA.
Genome Biol. 2009 Feb 11;10(2):R17. doi: 10.1186/gb-2009-10-2-r17.
Organisms are able to anticipate changes in the daily environment with an internal oscillator know as the circadian clock. Transcription is an important mechanism in maintaining these oscillations. Here we explore, using whole genome tiling arrays, the extent of rhythmic expression patterns genome-wide, with an unbiased analysis of coding and noncoding regions of the Arabidopsis genome.
As in previous studies, we detected a circadian rhythm for approximately 25% of the protein coding genes in the genome. With an unbiased interrogation of the genome, extensive rhythmic introns were detected predominantly in phase with adjacent rhythmic exons, creating a transcript that, if translated, would be expected to produce a truncated protein. In some cases, such as the MYB transcription factor AT2G20400, an intron was found to exhibit a circadian rhythm while the remainder of the transcript was otherwise arrhythmic. In addition to several known noncoding transcripts, including microRNA, trans-acting short interfering RNA, and small nucleolar RNA, greater than one thousand intergenic regions were detected as circadian clock regulated, many of which have no predicted function, either coding or noncoding. Nearly 7% of the protein coding genes produced rhythmic antisense transcripts, often for genes whose sense strand was not similarly rhythmic.
This study revealed widespread circadian clock regulation of the Arabidopsis genome extending well beyond the protein coding transcripts measured to date. This suggests a greater level of structural and temporal dynamics than previously known.
生物能够通过内部振荡器即生物钟来预测日常环境的变化。转录是维持这些振荡的重要机制。在这里，我们使用全基因组平铺阵列，在不考虑 Arabidopsis 基因组的编码和非编码区域的情况下，探索了全基因组范围内的节律表达模式的程度。
与之前的研究一样，我们检测到基因组中约 25%的蛋白质编码基因具有昼夜节律。通过对基因组进行无偏分析，检测到大量的节律性内含子，主要与相邻的节律性外显子相协调，从而产生一种如果翻译的话，预计会产生截短蛋白的转录本。在某些情况下，例如 MYB 转录因子 AT2G20400，内含子表现出昼夜节律，而其余的转录本则无节律。除了几个已知的非编码转录本，包括 microRNA、反式作用短干扰 RNA 和小核仁 RNA 外，还检测到超过一千个基因间区域受到生物钟的调节，其中许多区域没有预测的功能，无论是编码还是非编码。近 7%的蛋白质编码基因产生节律性反义转录本，通常是针对那些 sense 链没有类似节律的基因。
这项研究揭示了 Arabidopsis 基因组中广泛的生物钟调节，超出了迄今为止测量的蛋白质编码转录本的范围。这表明存在比以前已知的更大的结构和时间动态。
