Novosibirsk State University, Russian Federation.
Institute of Cytology and Genetics, Russian Federation.
J Exp Bot. 2018 Jan 4;69(2):329-339. doi: 10.1093/jxb/erx254.
The phytohormone auxin regulates virtually every developmental process in land plants. This regulation is mediated via de-repression of DNA-binding auxin response factors (ARFs). ARFs bind TGTC-containing auxin response cis-elements (AuxREs), but there is growing evidence that additional cis-elements occur in auxin-responsive regulatory regions. The repertoire of auxin-related cis-elements and their involvement in different modes of auxin response are not yet known. Here we analyze the enrichment of nucleotide hexamers in upstream regions of auxin-responsive genes associated with auxin up- or down-regulation, with early or late response, ARF-binding domains, and with different chromatin states. Intriguingly, hexamers potentially bound by basic helix-loop-helix (bHLH) and basic leucine zipper (bZIP) factors as well as a family of A/T-rich hexamers are more highly enriched in auxin-responsive regions than canonical TGTC-containing AuxREs. We classify and annotate the whole spectrum of enriched hexamers and discuss their patterns of enrichment related to different modes of auxin response.
植物激素生长素几乎调节陆地植物的所有发育过程。这种调节是通过去阻遏 DNA 结合生长素反应因子（ARF）来介导的。ARF 结合含有 TGTC 的生长素反应顺式元件（AuxRE），但越来越多的证据表明，生长素反应调控区域中还存在其他顺式元件。生长素相关顺式元件的组合及其在不同的生长素反应模式中的参与尚不清楚。在这里，我们分析了与生长素上调或下调、早期或晚期反应、ARF 结合结构域以及不同染色质状态相关的生长素反应基因上游区域中核苷酸六聚体的富集情况。有趣的是，潜在地由碱性螺旋-环-螺旋（bHLH）和碱性亮氨酸拉链（bZIP）因子以及一系列 A/T 富含六聚体结合的六聚体在生长素反应区域中的富集程度高于典型的含有 TGTC 的 AuxRE。我们对整个富集六聚体进行分类和注释，并讨论它们与不同的生长素反应模式相关的富集模式。
