The Interleaved Genome

Eukaryotic genomes are pervasively transcribed but until recently this noncoding transcription was considered to be simply noise. Noncoding transcription units overlap with genes and genes overlap other genes, meaning genomes are extensively interleaved. Experimental interventions reveal high degrees of interdependency between these transcription units, which have been co-opted as gene regulatory mechanisms. The precise outcome depends on the relative orientation of the transcription units and whether two overlapping transcription events are contemporaneous or not, but generally involves chromatin-based changes. Thus transcription itself regulates transcription initiation or repression at many regions of the genome.

TrendsMethods such as PRO-seq and NET-seq, map the activity of RNA polymerases at base pair resolution throughout eukaryotic genomes. When applied to RNA polymerase II, this reveals a great deal of transcription in addition to that producing pre-mRNA.In gene-rich regions, both strands of DNA are often pervasively transcribed. Transcription occurs upstream, downstream, and antisense to genes and may span several genes.Pervasive transcription has the potential to activate or repress neighbouring genes by altering DNA supercoiling or changing the structure and composition of the chromatin.Genomes are extensively interleaved by overlapping transcription meaning that transcription itself can control transcription initiation or repression.An interleaved genome is highly plastic. Altering gene expression at one gene in cluster can result in a new functional transcription unit over a different region of the cluster.