Cryptic unstable transcripts (CUTs) are a subset of non-coding RNAs (ncRNAs) that are produced from intergenic and intragenic regions.
[1][3] CUT transcription occurs through RNA Polymerase II and initiates from nucleosome-depleted regions, often in an antisense orientation.
[9] 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.
[1] 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,[4][11] further characterizing the widespread distribution and location of non-coding transcripts within eukaryotes.
[2] 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.
[2] 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.
Additionally, serial analysis of gene expression has demonstrated that the location of CUT 3' ends can be found in close proximity to the start features of ORFs in both sense and antisense configurations,[11] indicating that the end of CUT sequences lay within the 5' promoter region of expressed proteins.
Like CUTs, SUT transcription start sites are also found at nucleosome free regions[4] and are associated with the promoters of protein coding genes.
[20] Spt6 is responsible for restoring normal chromatin structure following transcription from RNA polymerase II, and yeast cells with compromised Spt6 function have been found to produce an increased number of CUTs.
[21] For instance, RNA polymerase II has been observed to bind incorrectly to the interior initiation region of the FLO8 gene in spt6 mutants, allowing for cryptic transcription to occur due to an erroneous nucleosome distribution.
These antisense TY1 transcripts reduce TY1 transposition activity in a trans manner and mitigates its expression,[5] indicating a potential role for CUTs and SUTs in epigenetics.