Epigenetic reprogramming events rewire transcription during the alternation of generations in Arabidopsis [Small RNA-Seq]

Alternation between morphologically distinct haploid and diploid life forms is a defining feature of most plant and algal life cycles, yet the underlying molecular mechanisms that govern these transitions remain unclear. Here, we explore the dynamic relationship between chromatin accessibility and epigenetic modifications during life form transitions in Arabidopsis. The diploid-to-haploid life form transition is governed by the loss of H3K9me2 and DNA demethylation of transposon-associated cis-regulatory elements. This event is associated with dramatic changes in chromatin accessibility and transcriptional reprogramming. In contrast, the global loss of H3K27me3 in the haploid form shapes a chromatin accessibility landscape that is poised to re-initiate the transition back to diploid life after fertilization. Hence, distinct epigenetic reprogramming events rewire transcription through major reorganization of the regulatory epigenome to guide the alternation of generations in flowering plants. Re-analysis of published pollen small RNA-seq [SRR1567670, SRR1567672,SRR6208912,SRR12067243,SRR12067244,SRR12067245] Adapter trimming was performed using cutadapt version 1.9. Reads were aligned to the Arabidopsis genome (TAIR10) using the STAR version 2.7 requiring zero mismatches and ≤ 100 multiple end-to-end alignments The resulting SAM files were used as input for readmapIO.py software (Schon et al., 2018) to reassign multimappers with a “rich-get-richer” algorithm. The output bedFiles were sorted, condensed and normalized for total genome matching reads. TAIR10 cDNA sequences (Arabidopsis_thaliana.TAIR10.cdna.all.fa.gz) *.bed: BED files of small RNAs