RNA-seq and RT-qPCR data showing MDF role in RNA splicing and gene expression control in Arabidopsis

Plants respond to environmental stresses through controlled stem cell maintenance and meristem activity. One level of transcriptional control is RNA alternative splicing. However the mechanistic link between stress, meristem function and RNA splicing is poorly understood. The MERISTEM-DEFECTIVE (MDF)/DEFECTIVELY ORGANIZED TRIBUTARIES (DOT2) gene of Arabidopsis encodes a SR-related family protein, required for meristem function and leaf vascularization, and is the likely orthologue of the human SART1 and yeast snu66 splicing factors. MDF is required for the correct splicing and expression of key transcripts associated with root meristem function. We identified RSZ33 and ACC1, both known to regulate cell patterning, as splicing targets required for MDF function in the meristem. MDF expression is modulated by osmotic and cold stress, associated with differential splicing and specific isoform accumulation and shuttling between nucleus and cytosol, and acts in part via a splicing target SR34..., RNA extraction and sequencing
RNA was extracted from three independent biological replicates using 7-day-old seedlings (ca. 100 mg tissue) grown on half-strength MS10 medium using the Sigma-Aldrich Plant Total RNA Kit (catalog number STRN50), with the On-Column DNase I Digestion Set (catalog Number: DNASE10-1SET) to eliminate any residual DNA molecules. Plant tissue was ground in liquid nitrogen before incubation in a lysis solution containing 2-mercaptoethanol at 65°C for 3 minutes. The solid debris was removed by centrifuging and 14 000 x g and column filtration before RNA was captured onto a binding column using the supplied binding solution, which helps preventing polysaccharide and genomic DNA from clogging the column. Most DNA was removed by wash solutions, and any trace of residual DNA was removed by DNase on the column. Then purified RNA was eluted using RNAase-free water.
RNA sequencing from three biological replicate samples was carried out on an Illumina HiSeq 2500 System wit..., Excel files are provided.