Attachment of ubiquitin or ubiquitin-like (Ubl) modifiers, such as the small ubiquitin-related modifier SUMO, is a posttranslational modification (PTM) that reversibly regulates the function and the stability of target proteins. The SUMO paralogs SUMO1 and SUMO2/3, although sharing a common conjugation pathway, seem to play different roles in the cell. Many regulatory mechanisms, which contribute to SUMO-paralog-specific modification, have emerged. We have recently found that cell environment affects SUMO-paralog-specific sumoylation of HDAC1, whose conjugation to SUMO1 and not to SUMO2 facilitates its protein turnover. Here, we describe how to identify SUMO-paralog-specific conjugation of HDAC1 and how the different expression of SUMO E3 ligases in the cell plays an important role in this mechanism.