Cryptic unstable transcripts (CUTs) are a subset of non-coding RNAs (ncRNAs) that are produced from intergenic and intragenic regions. CUTs were first observed in S. cerevisiae yeast models and are found in most eukaryotes. Some basic characteristics of CUTs include a length of around 200–800 base pairs, a 5' cap, poly-adenylated tail, and rapid degradation due to the combined activity of poly-adenylating polymerases and exosome complexes. CUT transcription occurs through RNA Polymerase II and initiates from nucleosome-depleted regions, often in an antisense orientation. To date, CUTs have a relatively uncharacterized function but have been implicated in a number of putative gene regulation and silencing pathways. Thousands of loci leading to the generation of CUTs have been described in the yeast genome. Additionally, stable uncharacterized transcripts, or SUTs, have also been detected in cells and bear many similarities to CUTs but are not degraded through the same pathways. Discovery and characterization Regions of non-coding RNA were mapped in several early experiments examining S. cerevisiae using a tiling array approach, which indicated that a large amount of transcriptional activity could be attributed to the intergenic region of the genome. These detected transcripts are not readily observed in the mRNA population because they are rapidly targeted for degradation in both the nucleus and cytoplasm. However, CUTs can be examined in yeast mutants with compromised exosome enzyme capability, which allows for transcripts to accumulate and enables their study and characterization. In 2009, the Steinmetz and Jacquier laboratories performed a series of high-resolution transcriptome maps, further characterizing the widespread distribution and location of non-coding transcripts within eukaryotes. CUTs were found to comprise around 13% of all mapped transcripts. Degradation pathways As CUTs cannot be observed at appreciable levels in wild-type S. cerevisiae, a large component of their early study has focused on their degradation. To date, two main pathways have been identified: the recruitment of a degrading exosome via the Nrd1-Nab3-Sen1 protein complex assisted by TRAMP, and termination due to the poly-adenylating capability of the Pap1p complex. In addition to these two main pathways, 5' processing enzymes such as Xrn1 have also been shown to participate in CUT degradation. Many of these findings were generated by observing Δrrp6 cells, a knock-out mutant for the exosome enzyme which has heightened levels of cryptic transcripts mapped to transgenic regions. In fact, deletion of the RRP6 subunit has served as one of the earliest and most frequently used