Genetius

The study combined long‑read whole‑genome assembly, multi‑omics profiling (DNA methylation, mRNA, ribosome‑associated transcripts, tRNA abundance, and protein levels) in two Arabidopsis thaliana accessions to evaluate how genomic information propagates through the Central Dogma. Codon usage in gene sequences emerged as the strongest predictor of both mRNA and protein abundance, while methylation, tRNA levels, and ribosome‑associated transcripts contributed little additional information under stable conditions.

The study reveals that a set of REPRODUCTIVE MERISTEM (REM) transcription factors, termed RIMs, are essential for directing RNA‑directed DNA methylation (RdDM) to CLSY3 targets in a sex‑specific manner in Arabidopsis reproductive tissues. Disruption of RIM DNA‑binding domains or their target motifs abolishes RdDM at these loci, demonstrating that genetic cues can guide de novo methylation patterns.

The study identifies four Arabidopsis REM transcription factors (VDD, VAL, REM12, REM13) that bind specific DNA sequences and, together with GDE1, recruit RNA polymerase IV to produce 24‑nt siRNAs that direct DNA methylation at designated loci. Loss of GDE1 causes Pol IV complexes to relocalize to sites bound by REM8, indicating that REM proteins provide sequence‑specific cues for epigenetic patterning.