Temporal changes in the transcriptome (RNA-seq) and genome-wide chromatin accessibility (ATAC-seq) after Sinorhizobium meliloti LCO treatment, in Medicago truncatula roots

The extend of chromatin accessibility changes and its consequent impact on the transcriptional control of rhizobial infection, colonization, and nodule development, remain unknown. This understanding requires that the dynamic behavior of gene expression and chromatin accessibility be quantified. Thus, we uncovered the gene regulatory network in response to LCOs in M. truncatula roots by quantifying temporal changes in the transcriptome (RNA-seq) and genome-wide chromatin accessibility (ATAC-seq) after Sinorhizobium meliloti LCO treatment. Overall design: Seeds of M. truncatula wild-type reference accession Jemalong A17 were sterilized and germinated in 1% agar plates, including 1µM GA3. Plates were stored at 4°C for three days in the dark and placed at room temperature overnight for germination. Seedlings were grown vertically for five days on a modified Fahraeus medium with no nitrogen, in a growth chamber (24°C, 16 h light/8h dark cycle, 70 µmol m-2 s-1 photosynthetic photon flux). LCOs were purified from Sinorhizobium meliloti strain 2011. Next, seedling roots were immersed in a solution of purified LCOs (10-8 M) or 0.005% ethanol (control) for 1 h. Roots were cut and immediately used for nuclei extraction and generation of ATAC-seq libraries, or snap-frozen in liquid nitrogen for posterior RNA isolation and sequencing. Roots were collected at 0 h (control), 15 min, 30 min, 1 h, 2 h, 4 h, 8 h after LCOs treatment. Roots from seven plants were pooled for each of three biological replicates used in RNA sequencing, while roots from 15 plants were pooled for one replicate used in ATAC-seq, in each time point of the experiment.