Intergenic DNA, or junk DNA as its more colloquially known, was once thought of as “extra” DNA strands that play no role in the transcriptional process. However, in recent years, it has been shown that Junk DNA is actually transcribed into Junk RNA which is not tranlasted into protein (unlike their non-junk counterparts). In fact, researchers have demonstrated that Junk RNA is actually created by upstream transcription which occurs when the transcriptional process moves both upstream and downstream from the DNA promoter region. Since coding RNA is created from the downstream process, upstream transcription results in non-translatable RNA.
In a new study published in Nature this week, researchers at MIT described a mechanism by which cells initiate but then halt the copying of RNA in the non-protein coding direction while allowing the downstream activity to continue unhindered. In this model, the poly-A-tail, along with a factor known as U1 snRNP, work together to halt the upstream copying of RNA and actually chop up “Junk RNA” before it becomes too long.
For further reading see MIT biologists reveal how cells control the direction in which the genome is read