Data from: Root architecture shaping by the environment is orchestrated by dynamic gene expression in space and time

Shaping of root architecture is a quintessential developmental response
that involves the concerted action of many different cell types, is highly
dynamic and underpins root plasticity. To determine to what extent the
environmental regulation of lateral root development is a product of cell
type preferential activities, we tracked transcriptomic responses to two
different treatments that both change root development in Arabidopsis
thaliana, at an unprecedented level of temporal detail. We found that
individual transcripts are expressed with a very high degree of temporal
and spatial specificity, yet biological processes are commonly regulated,
in a mechanism we term response non-redundancy. Using causative gene
network inference to compare the genes regulated in different cell types
and during responses to nitrogen and a biotic interaction we found that
common transcriptional modules often regulate the same gene families, but
control different individual members of these families, specific to
response and cell type. This reinforces that the activity of a gene cannot
be defined simply as molecular function; rather, it is a consequence of
spatial location, expression timing and environmental responsiveness.

根系构型塑造是一种典型的发育响应，该过程依赖多种不同细胞类型的协同作用，具有高度动态性，并为根系可塑性提供基础支撑。为探究侧根发育的环境调控在多大程度上源于细胞类型偏好性活性，本研究以模式植物拟南芥（Arabidopsis thaliana）为对象，以空前精细的时间分辨率追踪了两种均能改变根系发育的不同处理下的转录组响应。研究发现，单个转录本的表达具有极强的时空特异性，但生物学过程却往往受到共同调控，我们将这种调控机制命名为响应非冗余性（response non-redundancy）。本研究通过因果基因网络推断，对比了不同细胞类型以及在氮响应和生物互作响应中受调控的基因，结果发现，常见的转录模块通常调控同一基因家族，但针对不同响应和细胞类型，会靶向该家族中的不同成员。这进一步表明，基因的活性不能仅通过分子功能来定义；实际上，其活性是空间定位、表达时序与环境响应性共同作用的结果。