Ji Min Lee,^1,7 Jason S. Lee,^1,7 Hyunkyung Kim,^1,7 Kyeongkyu Kim,¹ Hyejin Park,² Ji-Young Kim,³ Seung Hoon Lee,⁴ Ik Soo Kim,¹ Joomyung Kim,¹ Minkyoung Lee,¹ Chin Ha Chung,¹ Sang-Beom Seo,³ Jong-Bok Yoon,⁴ Eunyoung Ko,⁵ Dong-Young Noh,⁵ Keun Il Kim,⁶ Kyeong Kyu Kim,² and Sung Hee Baek^1,*

¹Department of Biological Sciences, Creative Research Initiatives Center for Chromatin Dynamics, Seoul National University, Seoul 151-742, South Korea
²Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, South Korea
³Department of Life Science, Chung-Ang University, Seoul 156-756, South Korea
⁴Department of Biochemistry and Translational Research Center for Protein Function Control, Yonsei University, Seoul 120-749, South Korea
⁵Department of Surgery and Cancer Research Institute, Seoul National University College of Medicine, Seoul 110-744, South Korea
⁶Department of Biological Sciences, Sookmyung Women’s University, Seoul 140-742, South Korea
⁷These authors contributed equally to this work
^*Correspondence
http://dx.doi.org/10.1016/j.molcel.2012.09.004

Summary
Ubiquitination plays a major role in protein degradation. Although phosphorylation-dependent ubiquitination is well known for the regulation of protein stability, methylation-dependent ubiquitination machinery has not been characterized. Here, we provide evidence that methylation-dependent ubiquitination is carried out by damage-specific DNA binding protein 1 (DDB1)/cullin4 (CUL4) E3 ubiquitin ligase complex and a DDB1-CUL4-associated factor 1 (DCAF1) adaptor, which recognizes monomethylated substrates. Molecular modeling and binding affinity studies reveal that the putative chromo domain of DCAF1 directly recognizes monomethylated substrates, whereas critical binding pocket mutations of the DCAF1 chromo domain ablated the binding from the monomethylated substrates. Further, we discovered that enhancer of zeste homolog 2 (EZH2) methyltransferase has distinct substrate specificities for histone H3K27 and nonhistones exemplified by an orphan nuclear receptor, RORα. We propose that EZH2-DCAF1/DDB1/CUL4 represents a previously unrecognized methylation-dependent ubiquitination machinery specifically recognizing methyl degron; through this, nonhistone protein stability can be dynamically regulated in a methylation-dependent manner.