Ubiquitin-dependent degrons are so named because they are implicated in the polyubiquitination process for targeting a protein to the proteasome.^[15][16] In some cases, the degron itself serves as the site for polyubiquitination as is seen in TAZ and β-catenin proteins.^[17] Because the exact mechanism by which a degron is involved in a protein's polyubiqutination is not always known, degrons are classified as ubiquitin-dependent if their removal from the protein leads to less ubiquitination or if their addition to another protein leads to more ubiquitination.^[18][19]

In contrast, ubiquitin-independent degrons are not necessary for the polyubiquitination of their protein. For example, the degron on IκBα, a protein involved in the regulation of the immune system, was not shown to be involved in ubiquitination since its addition to green fluorescent protein (GFP) did not increase ubiquitination.^[1] However, a degron can only hint at the mechanism by which a protein is degraded^[20] and so identifying and classifying a degron is only the first step in understanding the degradation process for its protein.

In order to identify a portion of a protein as a degron, there are often three steps performed.^[1][19][20] First, the degron candidate is fused to a stable protein, such as GFP, and protein abundances over time are compared between the unaltered protein and the fusion (as shown in green).^[21] If the candidate is in fact a degron, then the abundance of the fusion protein will decrease much faster than that of the unaltered protein.^[9][10][11] Second, a mutant form of the degron's protein is designed such that it lacks the degron candidate. Similar to before, the abundance of the mutant protein over time is compared to that of the unaltered protein (as shown in red). If the deleted degron candidate is in fact a degron, then the mutant protein abundance will decrease much slower than that of the unaltered protein.^[9][10][11] Recall that degrons are often referred to as “ubiquitin-dependent” or “ubiquitin-independent” The third step performed is often done after one or both of the previous two steps, because it serves to identify the ubiquitin dependence or lack thereof of a previously identified degron. In this step, protein A and A’ (identical in every way except the presence of degron in A’) will be examined. Note that mutation or fusion procedures could be performed here, so either A is a protein like GFP and A’ is a fusion of GFP with the degron (as shown in green) or A’ is the degron's protein and A is a mutant form without the degron (as shown in Red.) The amount of ubiquitin bound to A and to A’ will be measured.^[1][7][20] A significant increase in the amount of ubiquitin in A’ as compared to A will suggest that the degron is ubiquitin-dependent.^[1][9]

• N-end rule
• Proteasome
• proteolysis