Gene expression in eukaryotic genomes is far more complex than previously thought. We understand how the process of transcription converts DNA information provided by genes into protein coding mRNAs. However, recent data show that transcription occurs mainly outside of genes, which is referred to as “pervasive transcription”. This raises the question: does pervasive transcription serve a purpose? Research in my addresses this question by focusing on gene regulation by pervasive transcription in yeast and plants. Perhaps surprisingly, we find that the process of pervasive transcription, rather than the generated long non-coding RNA (lncRNA), is often regulatory through co-transcriptional effects on chromatin structure. Gene repression by the act of pervasive transcription reconciles how the process of transcribing mysterious non-coding DNA sequences can function in regulation. I will present the latest case-studies of functional pervasive transcription in yeast and plants, but also present our ongoing efforts to map gene repression by the act of transcription using genomics approaches.