Lechon Tamara, Kent Nicholas A, Murray James A H, Scofield Simon
School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK.
Sci Rep. 2025 Jan 2;15(1):240. doi: 10.1038/s41598-024-83985-1.
The Arabidopsis Knotted1-like homeobox (KNOX) gene SHOOT MERISTEMLESS (STM) encodes a homeodomain transcription factor that operates as a central component of the gene regulatory network (GRN) controlling shoot apical meristem formation and maintenance. It regulates the expression of target genes that include transcriptional regulators associated with meristem function, particularly those involved in pluripotency and cellular differentiation, as well as genes involved in hormone metabolism and signaling. Previous studies have identified KNOX-regulated genes and their associated cis-regulatory elements in several plant species. However, little is known about STM-DNA interactions in the regulatory regions of target genes in Arabidopsis. Here, we identify and map STM binding sites in the Arabidopsis genome using global ChIP-seq analysis to reveal potential directly-regulated STM target genes. We show that in the majority of target loci, STM binds within 1 kb upstream of the TSS, with other loci showing STM binding at more distal enhancer sites, and we reveal enrichment of DNA motifs containing a TGAC and/or TGAT core in STM-bound target gene cis-regulatory elements. We further demonstrate that many STM-bound genes are transcriptionally responsive to altered levels of STM activity, and show that among these, transcriptional regulators with key roles in meristem and hormone function are highly represented. Finally, we use a subset of these target genes to perform Bayesian network analysis to infer gene regulatory associations and to construct a refined GRN for STM-mediated control of meristem function.
拟南芥类 Knotted1 同源异型框（KNOX）基因无茎尖分生组织（STM）编码一种同源异型域转录因子，它是基因调控网络（GRN）的核心组成部分，控制着茎尖分生组织的形成和维持。它调控靶基因的表达，这些靶基因包括与分生组织功能相关的转录调节因子，特别是那些参与多能性和细胞分化的因子，以及参与激素代谢和信号传导的基因。先前的研究已经在几种植物物种中鉴定出 KNOX 调控的基因及其相关的顺式调控元件。然而，关于拟南芥靶基因调控区域中 STM 与 DNA 的相互作用知之甚少。在这里，我们使用全基因组染色质免疫沉淀测序（ChIP-seq）分析来鉴定和定位拟南芥基因组中的 STM 结合位点，以揭示潜在的直接受 STM 调控的靶基因。我们发现，在大多数靶基因座中，STM 结合在转录起始位点（TSS）上游 1 kb 范围内，其他基因座则显示 STM 在更远端的增强子位点结合，并且我们揭示了在 STM 结合的靶基因顺式调控元件中富含包含 TGAC 和/或 TGAT 核心的 DNA 基序。我们进一步证明，许多受 STM 结合的基因对 STM 活性水平的改变具有转录响应，并表明在这些基因中，在分生组织和激素功能中起关键作用的转录调节因子高度富集。最后，我们使用这些靶基因的一个子集进行贝叶斯网络分析，以推断基因调控关联，并构建一个优化的 GRN，用于 STM 介导的分生组织功能控制。
