Small ubiquitin-like modifier (SUMO) modification of transcription factors is generally associated with repression. Reverse genetic analysis of SUMO-1, and -2 conserved residues emphasized the importance of dual charge reversals in abrogating the critical role of SUMO-2 K33, K35, and K42 in repression. GST-SUMO-2-affinity chromatography followed by liquid chromatography (LC)-MS analysis identified proteins that appeared to bind preferentially to WT SUMO-2 versus SUMO-2 K33E and K35E. LSD1, NXP-2, KIAA0809 (ARIP4), SAE2, RanGAP1, PELP1, and SETDB1 bound to SUMO-2 and not to SUMO-2 K33E, K42E, or K35E and K42E. Although LSD1 is a histone lysine demethylase, and histone H3K4 was demethylated at a SUMO-2-repressed promoter, neither overexpression of a dominant-negative LSD1 nor LSD1 depletion with RNA interference affected SUMO-2-mediated repression, indicating that LSD1 is not essential for repression, in this context. When tethered to a promoter by fusion to Gal4, NXP-2 repressed transcription, consistent with a role for NXP-2 in SUMO-mediated repression. SUMO-2-associated proteins identified in this study may contribute to SUMO-dependent regulation of transcription or other processes.regulation ͉ repressor ͉ ubiquitin-like S mall ubiquitin-like modifier (SUMO) is a ubiquitin-like protein that is reversibly covalently attached to lysines in target proteins, resulting in altered protein function, localization, or stability. SUMO modification of corepressors, coactivators, histones, histone-modifying enzymes, or sequence-specific transcription factors usually down-regulates transcription. For example, mutation so as to prevent SUMO modification increases transcription-factor activity associated with Elk-1, Sp3, c-myb, c-jun, AP2, or the p300 N terminus (1-5). In contrast to SUMO, ubiquitin modification is more frequently associated with proteasome-dependent degradation or activation of transcription. In fact, activation of transcription by the VP16 activation domain, in yeast, requires an E3 ubiquitin ligase (6). Addition of a SUMO consensus acceptor site to the Gal4-VP16 activation domain reduces transcription 10-fold (7). Thus, ubiquitin and SUMO modifications can have opposite effects on transcription.Despite these differences, SUMO-1, -2, and -3 are ubiquitinlike proteins and have ubiquitin-like structures. SUMO-2 and -3 are 95% identical and are 46% and 48%, respectively, identical to SUMO-1. In contrast, SUMO-1, -2, and -3 share only 18% identity with ubiquitin (Fig. 1). The differences in primary sequence and their role in the opposing transcriptional properties of SUMO and ubiquitin are being elucidated. SUMO interaction with histone deacetylases has been proposed as one mechanism of repression (1, 8). However, an unbiased directed screen to identify candidate SUMO-associated repressors has not been undertaken.The objective of our experiments was to identify proteins whose association with SUMO-2 depends on SUMO-2 residues required for repression. Such proteins would be candidate SUMO corepressors. We have u...