RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan.
Department of Crops and Soil Sciences, Washington State University, Pullman, WA, 99164, USA.
BMC Plant Biol. 2022 Aug 15;22(1):399. doi: 10.1186/s12870-022-03737-z.
SUPPRESSOR OF PHYTOCHROME B-4 #3 (SOB3) is a member of the AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED (AHL) family of transcription factors that are involved in light-mediated growth in Arabidopsis thaliana, affecting processes such as hypocotyl elongation. The majority of the research on the AHLs has been conducted in continuous light. However, there are unique molecular events that promote growth in short days (SD) compared to constant light conditions. Therefore, we investigated how AHLs affect hypocotyl elongation in SD. Firstly, we observed that AHLs inhibit hypocotyl growth in SD, similar to their effect in constant light. Next, we identified AHL-regulated genes in SD-grown seedlings by performing RNA-seq in two sob3 mutants at different time points. Our transcriptomic data indicate that PHYTOCHROME INTERACTING FACTORS (PIFs) 4, 5, 7, and 8 along with PIF-target genes are repressed by SOB3 and/or other AHLs. We also identified PIF target genes that are repressed and have not been previously described as AHL-regulated, including PRE1, PIL1, HFR1, CDF5, and XTR7. Interestingly, our RNA-seq data also suggest that AHLs activate the expression of growth repressors to control hypocotyl elongation, such as HY5 and IAA17. Notably, many growth-regulating and other genes identified from the RNA-seq experiment were differentially regulated between these two sob3 mutants at the time points tested. Surprisingly, our ChIP-seq data suggest that SOB3 mostly binds to similar genes throughout the day. Collectively, these data suggest that AHLs affect gene expression in a time point-specific manner irrespective of changes in binding to DNA throughout SD.
拟南芥光形态建成抑制因子 B-4#3（SOB3）是 AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED（AHL）家族转录因子的成员，该家族参与光介导的生长，影响拟南芥下胚轴伸长等过程。大多数关于 AHL 的研究都是在连续光照下进行的。然而，与连续光照条件相比，短日照（SD）中存在促进生长的独特分子事件。因此，我们研究了 AHL 如何影响 SD 中下胚轴的伸长。首先，我们观察到 AHL 在 SD 中抑制下胚轴生长，与它们在连续光照中的作用相似。接下来，我们通过在两个 sob3 突变体中在不同时间点进行 RNA-seq，确定了 SD 中生长的幼苗中受 AHL 调控的基因。我们的转录组数据表明，PHYTOCHROME INTERACTING FACTORS（PIFs）4、5、7 和 8 以及 PIF 靶基因受 SOB3 和/或其他 AHL 调控。我们还鉴定了受 SOB3 和/或其他 AHL 调控的 PIF 靶基因，这些基因受到抑制且之前未被描述为 AHL 调控，包括 PRE1、PIL1、HFR1、CDF5 和 XTR7。有趣的是，我们的 RNA-seq 数据还表明，AHL 激活生长抑制剂的表达来控制下胚轴伸长，例如 HY5 和 IAA17。值得注意的是，从 RNA-seq 实验中鉴定的许多生长调节基因和其他基因在测试的时间点在这两个 sob3 突变体之间存在差异调节。令人惊讶的是，我们的 ChIP-seq 数据表明 SOB3 主要在一天中的相似时间点结合到相似的基因上。总的来说，这些数据表明，AHL 以时间点特异性的方式影响基因表达，而与 SD 中 DNA 结合的变化无关。
