Root Hair Single Cell Type Specific Profiles of Gene Expression and Alternative Polyadenylation Under Cadmium Stress

Abstract

Transcriptional networks are tightly controlled in plant development and stress responses. Alternative polyadenylation (APA) has been found to regulate gene expression under abiotic stress by increasing the heterogeneity at mRNA 3′-ends. Heavy metals like cadmium pollute water and soil due to mining and industry applications. Understanding how plants cope with heavy metal stress remains an interesting question. The Arabidopsis root hair was chosen as a single cell model to investigate the functional role of APA in cadmium stress response. Primary root growth inhibition and defective root hair morphotypes were observed. Poly(A) tag (PAT) libraries from single cell types, i.e., root hair cells, non-hair epidermal cells, and whole root tip under cadmium stress were prepared and sequenced. Interestingly, a root hair cell type-specific gene expression under short term cadmium exposure, but not related to the prolonged treatment, was detected. Differentially expressed poly(A) sites were identified, which largely contributed to altered gene expression, and enriched in pentose and glucuronate interconversion pathways as well as phenylpropanoid biosynthesis pathways. Numerous genes with poly(A) site switching were found, particularly for functions in cell wall modification, root epidermal differentiation, and root hair tip growth. Our findings suggest that APA plays a functional role as a potential stress modulator in root hair cells under cadmium treatment.

The Position and Complex Genomic Architecture of Plant T-DNA Insertions Revealed by 4SEE

“…Along with annotating T-DNA insertions, 4SEE uncovered chromosomal inversion in SALK_011436 and chromosomal translocations associated with T-DNA insertions in the ADF8p:NTF/ACT2p:BirA line. This line is widely used to isolate specific cell-types [30][31][32][33][34][35]. Structural analysis genomic loci flanking these insertions by 4C-seq validated these rearrangements and unraveled their complexity.…”

“…Unlike T-DNA insertions used for genetic perturbation of endogenous genes, less attention is paid to mapping their exact positions when they are used for transgene expression. Therefore, as a test case, we aimed to annotate by 4SEE the T-DNA insertions in a widely used transgene bearing the INTACT system for affinity purification of nuclei (see [30][31][32][33][34][35]). This plant was generated by introducing a T-DNA expressing the nuclear targeting fusion (NTF) synthetic protein under the control of the ACTIN DEPOLYMERIZING FACTOR 8 (ADF8) promoter (ADF8p:NTF) into a transgenic line expressing the E. coli biotin ligase BirA from the constitutive ACTIN2 (ACT2) promoter (ACT2p:BirA).…”

Alternative Polyadenylation in response to temperature stress contributes to gene regulation in Populus trichocarpa

“…In recent years, the APA mediated gene regulation is found to play an important role in stress responses. Notably, abiotic stresses can induce APA events to generate distinct transcript isoforms in diverse plant species [14][15][16]. For example, in Arabidopsis, hypoxia has been found to induce the usage of non-canonical (e.g.…”

Alternative Polyadenylation and Salicylic Acid Modulate Root Responses to Low Nitrogen Availability

“…Although polyadenylation typically occurs at the end of the 3 -UTR (and actually defines it), polyadenylation may also occur within introns, protein-coding regions, and 5 -UTRs, which are termed as non-canonical. The levels of mRNA isoforms with non-canonical polyadenylation increase in response to abiotic stresses [12][13][14], suggesting a role of these non-canonical mRNA isoforms during the plant response to these stresses. For example, in Arabidopsis, an increase in mRNA isoforms with 3 ends in coding regions and 5 -UTRs is seen in response to hypoxia [14].…”