Long non-coding transcription has emerged as a major player in the stress response of plants. However, it is still a bit of an enigma why plants and other eukaryotes use such a substantial amount of energy transcribing non-coding DNA sequences. With the adaptation of Native Elongation Transcript sequencing (NET-seq) to Arabidopsis, we have been able to start seeing all the non-coding transcription events that occur across the genome. We found that many genes have antisense transcription, i.e. transcription of the complementary strand of a gene. Interestingly, antisense transcription is prevalent at transcription factor loci. These transcription factor genes are often responsive to different kinds of stresses, hinting at an important role for antisense transcription in the response and acclimation to stress. Further, by comparing NET-seq and RNA-seq, we found that transcription factors with antisense transcription have specific RNA biology features compared to genes without. Here, I will discuss these antisense transcripts and their role in regulating the coding transcription.