Olivier Loudet

To fully understand gene regulation, it is necessary to have a thorough understanding of both the transcriptome and the enzymatic and RNA-binding activities that shape it. While many RNA-Seq-based tools have been developed to analyze the transcriptome, most only consider the abundance of sequencing reads along annotated patterns (such as genes). These annotations are typically incomplete, leading to errors in the differential expression analysis. To address this issue, we present DiffSegR - an R package that enables the discovery of transcriptome-wide expression differences between two biological conditions using RNA-Seq data. DiffSegR does not require prior annotation and uses a multiple changepoints detection algorithm to identify the boundaries of differentially expressed regions in the per-base log2 fold change. In a few minutes of computation, DiffSegR could rightfully predict the role of chloroplast ribonuclease Mini-III in rRNA maturation and chloroplast ribonuclease PNPase in (3′/5′)-degradation of rRNA, mRNA and tRNA precursors as well as intron accumulation. We believe DiffSegR will benefit biologists working on transcriptomics as it allows access to information from a layer of the transcriptome overlooked by the classical differential expression analysis pipelines widely used today. DiffSegR is available at https://aliehrmann.github.io/DiffSegR/index.html.

SUMMARY Soil water uptake by roots is a key component of plant water homeostasis contributing to plant growth and survival under ever‐changing environmental conditions. The water transport capacity of roots (root hydraulic conductivity; L p r ) is mostly contributed by finely regulated Plasma membrane Intrinsic Protein (PIP) aquaporins. In this study, we used natural variation of Arabidopsis for the identification of quantitative trait loci (QTLs) contributing to L p r . Using recombinant lines from a biparental cross (Cvi‐0 x Col‐0), we show that the gene encoding class 2 Sucrose‐Non‐Fermenting Protein kinase 2.4 (SnRK2.4) in Col‐0 contributes to >30% of L p r by enhancing aquaporin‐dependent water transport. At variance with the inactive and possibly unstable Cvi‐0 SnRK2.4 form, the Col‐0 form interacts with and phosphorylates the prototypal PIP2;1 aquaporin at Ser121 and stimulates its water transport activity upon coexpression in Xenopus oocytes and yeast cells. Activation of PIP2;1 by Col‐0 SnRK2.4 in yeast also requires its protein kinase activity and can be counteracted by clade A Protein Phosphatases 2C. SnRK2.4 shows all hallmarks to be part of core abscisic acid (ABA) signaling modules. Yet, long‐term (>3 h) inhibition of L p r by ABA possibly involves a SnRK2.4‐independent inhibition of PIP2;1. SnRK2.4 also promotes stomatal aperture and ABA‐induced inhibition of primary root growth. The study identifies a key component of L p r and sheds new light on the functional overlap and specificity of SnRK2.4 with respect to other ABA‐dependent or independent SnRK2s.