Degradome sequencing

The degradome encompasses the entire set of proteases that are expressed at a specific time in a given biological material, including tissues, cells, organisms, and biofluids.

[4] Degradome sequencing is a complex process which includes multiple steps such as isolating RNA fragments in a given sample as well as ligation and reverse transcription to form complementary DNA (cDNA) strands.

[7] The applications of degradome sequencing include identifying microRNA (miRNA) targets, establishing mRNA methods of decay, and finding novel non-coding RNA fragments.

[21] In this study, researchers developed a model in which biologists could use data derived from degradome sequencing to determine the effect of transcriptional and/or post-transcriptional regulation on patterns of gene expression in plants.

In particular, this model applies degradome sequencing data to establish the method by which small RNAs (sRNAs) mature and guide the process of targeted gene regulation.

In particular, degradome sequencing data can be used to track non-coding RNA (ncRNA) processing signals which would be a valuable tool if expanded to include animal-based research.

Given the established role of extracellular proteases in promoting tumor development and growth across different tissues, degradome sequencing also holds important implications for discovering novel therapeutic targets for cancer treatments.

Additionally, this study revealed that environmental factors, such as nutrient and oxygen abundance, affect the extent to which breast cancer cells rely on specific proteases identified via degradome sequencing.

[9] The results of this study were validated by using individual knockdown constructs in mice which functionally diminished the proteases of interest and affected the expression of breast cancer cells.

These results indicate the high degree of reliability of degradome sequencing in identifying proteases involved in the growth of breast cancer cell lines in mouse models.

A schematic for the methodology of degradome sequence and constructing an improved degradome library via miRNA induced cleavage, reverse transcription, second strand synthesis, PCR, and sample pooling and sequencing.
This image demonstrates the complexity of degradome sequencing data when used for the application of microRNA re-annotation. Degradome sequencing has allowed for the identification of mature miRNAs highlighted in green and the processing sites supported by degradome signals, indicated by arrows on the predicted secondary structure of the miRNA precursor.
A novel model proposed for microRNA processing involving base-to-loop and loop-to-base mechanisms based on the abundant distribution data provided by degradome sequencing.
The generation of two phenotypically distinct breast cancer cell lines in mice, each of which is targeted by degradomes. Thus, degradome sequencing was used to identify and distinguish proteases important for breast cancer cell growth (A) and proteases only important under specific environmental conditions (B).