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Summary Root hair (RH) cells can elongate to several hundred times their initial size, and are an ideal model system for investigating cell size control. Their development is influenced by both endogenous and external signals, which are combined to form an integrative response. Surprisingly, a low‐temperature condition of 10°C causes increased RH growth inArabidopsisand in several monocots, even when the development of the rest of the plant is halted.Previously, we demonstrated a strong correlation between RH growth response and a significant decrease in nutrient availability in the growth medium under low‐temperature conditions. However, the molecular basis responsible for receiving and transmitting signals related to the availability of nutrients in the soil, and their relation to plant development, remain largely unknown.We have discovered two antagonic gene regulatory networks (GRNs) controlling RH early transcriptome responses to low temperature. One GNR enhances RH growth and it is commanded by the transcription factors (TFs)ROOT HAIR DEFECTIVE 6(RHD6),HAIR DEFECTIVE 6‐LIKE 2 and 4(RSL2‐RSL4) and a member of the homeodomain leucine zipper (HD‐Zip I) group I 16 (AtHB16). On the other hand, a second GRN was identified as a negative regulator of RH growth at low temperature and it is composed by the trihelix TFGT2‐LIKE1(GTL1) and the associated DF1, a previously unidentified MYB‐like TF (AT2G01060) and several members of HD‐Zip I group (AtHB3, AtHB13, AtHB20, AtHB23).Functional analysis of both GRNs highlights a complex regulation of RH growth response to low temperature, and more importantly, these discoveries enhance our comprehension of how plants synchronize RH growth in response to variations in temperature at the cellular level. 

Abstract Nitrate is a nutrient and signal that regulates gene expression. The nitrate response has been extensively characterized at the organism, organ, and cell‐type‐specific levels, but intracellular mRNA dynamics remain unexplored. To characterize nuclear and cytoplasmic transcriptome dynamics in response to nitrate, we performed a time‐course expression analysis after nitrate treatment in isolated nuclei, cytoplasm, and whole roots. We identified 402 differentially localized transcripts (DLTs) in response to nitrate treatment. Induced DLT genes showed rapid and transient recruitment of the RNA polymerase II, together with an increase in the mRNA turnover rates. DLTs code for genes involved in metabolic processes, localization, and response to stimulus indicating DLTs include genes with relevant functions for the nitrate response that have not been previously identified. Using single‐molecule RNA FISH, we observed early nuclear accumulation of theNITRATE REDUCTASE 1(NIA1) transcripts in their transcription sites. We found that transcription ofNIA1, a gene showing delayed cytoplasmic accumulation, is rapidly and transiently activated; however, its transcripts become unstable when they reach the cytoplasm. Our study reveals the dynamic localization of mRNAs between the nucleus and cytoplasm as an emerging feature in the temporal control of gene expression in response to nitrate treatment in Arabidopsis roots. 

Nitrate is a nutrient and a potent signal that impacts global gene expression in plants. However, the regulatory factors controlling temporal and cell type–specific nitrate responses remain largely unknown. We assayed nitrate-responsive transcriptome changes in five major root cell types of the Arabidopsis thaliana root as a function of time. We found that gene-expression response to nitrate is dynamic and highly localized and predicted cell type–specific transcription factor (TF)–target interactions. Among cell types, the endodermis stands out as having the largest and most connected nitrate-regulatory gene network. ABF2 and ABF3 are major hubs for transcriptional responses in the endodermis cell layer. We experimentally validated TF–target interactions for ABF2 and ABF3 by chromatin immunoprecipitation followed by sequencing and a cell-based system to detect TF regulation genome-wide. Validated targets of ABF2 and ABF3 account for more than 50% of the nitrate-responsive transcriptome in the endodermis. Moreover, ABF2 and ABF3 are involved in nitrate-induced lateral root growth. Our approach offers an unprecedented spatiotemporal resolution of the root response to nitrate and identifies important components of cell-specific gene regulatory networks.