Abiotic stress mediated modulation of chromatin landscape in Arabidopsis thaliana

This dataset include figures and supplementary material for the manuscript entitled "Abiotic stress mediated modulation of chromatin landscape in Arabidopsis thaliana" to be published in Journal of Experimental Botany special issue focused on Chromatin.

Supplementary File 1: Table describing read count, mapping percentage and genome coverage from each sample in FAIRE-seq and DNase-seq.

Supplementary File 2: List of DHSs obtained from control and stress subjected samples.

Supplementary File 3: List of FIRs obtained from control and stress subjected samples.

Supplementary File 4: List of uniquely merged OCRs with respective chromatin accessibility score in cold, heat, salt and drought stress.

Supplementary File 5: List of GO terms enriched in nrOCRs, SRCRs, and SACRs.

Supplementary File 6: List of GO terms enriched in overlapping nrOCRs, SRCRs, and SACRs.

Supplementary File 7: List of digital footprints (DFPs) obtained from nrOCRs regions of control-cold, control-heat, control-salt and control-drought pairs.

Supplementary File 8: Annotation details of the chromatin regions which were either found to be in state of accessible (CAS > 0.2) or inaccessible (CAS < -0.2) upon exposure to all of the stresses studied (heat, cold, salt and drought stress).

Supplementary Fig S1: Overlap of DHSs in control sample of present study with previously published studies.

A Venn diagram showing overlap of DNase hypersensitive sites (DHSs) found in control sample of present study and Zhang et al 2010 (A) and Sullivan et al 2014 (B). The statistical significance of overlap is calculate using hypergeometric Fischer`s exact test.

Supplementary Fig S2: Genomic locations of DHSs and FIRs

A line diagram representing the genomic location of unique DHSs and FIRs over each chromosome. DHSs/FIRs identified from each sample were merged to generate unique non-redundant subset of DHSs/FIRs before plotting over genome.

Supplementary Fig S3: Validation of correlation between OCRs and gene expression using microarray.

Box plot representing expression of genes (log10(normalised expression)) whose various structual elements fall in OCRs.

Supplementary Fig S4: First exons are highly enriched in both DHSs and FIRs

 A bar plot showing presence of uFIRs, uDHSs, and ovOCRs in various positions of exon in Arabidopsis genes. The X-axis represent the exon number whereas Y-axis represent the fraction of OCRs found in each exon number.

Supplementary Fig S5: Validation of correlation between Ha-SACRs/Ha-SRCRs and gene expression using microarray.

Relative expression of genes (log2 fold change) corresponding to Ha-SACRs (Top) and (Ha-SRCRs (bottom) in cold (A), heat (B), salt (C) and drought (D) stress are plotted as box plot (p- value from Mann-Whitney test). To further compare RNA-seq data of salt stress with microarray, RNA-seq data was down-sampled to include genes which were also present in microarray data (E).

Supplementary Fig S6: Genomic location of SACRs and SRCRs found in Drought sample.

A snapshot of Integrative Genome Viewer (IGV) showing genomic location of stress activated chromatin regions (SACRs) and stress repressed chromatin region (SRCRs) in drought sample. The location of the centromere on each chromosome is shown as green bar IGV track.