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A systematic comparison of enzymatic activity and protein interaction analysis of the KDM3 histone demethylase subfamily.

Brauchle, Michael, Yao, Zhiping, Arora, Rishi, Clay, Ieuan, Inverardi, Bruno, Gerrits, Bertran, Voshol, Johannes, Bauer, Andreas, Schuebeler, Dirk, Bouwmeester, Antonius, Ruffner, Heinz and Thigale, Sachin (2013) A systematic comparison of enzymatic activity and protein interaction analysis of the KDM3 histone demethylase subfamily. PLOS ONE, 8 (4). e60549. ISSN 1932-6203


Histone modifications play an important role in chromatin organization and gene regulation, and their interpretation is referred to as epigenetic control. The methylation levels of several lysine residues in histone tails are tightly controlled, and JmjC domain-containing proteins are one class of broadly expressed enzymes catalyzing methyl group removal. However, several JmjC proteins remain uncharacterized, gaps persist in understanding substrate recognition, and the integration of JmjC proteins into signaling pathways is just emerging. The KDM3 subfamily is an evolutionarily conserved group of HDM proteins, thought to share lysine substrate specificity. Here we use a systematic approach to compare KDM3 subfamily members. We show that full-length KDM3A and KDM3B are H3K9me1/2 histone demethylases whereas we fail to observe histone demethylase activity for JMJD1C using immunocytochemical and biochemical approaches. Structure-function analyses revealed the importance of a single amino acid in KDM3A implicated in the catalytic activity towards H3K9me1/2 that is not conserved in JMJD1C. Moreover, we use quantitative proteomic analyses to identify subsets of the interactomes of the 3 proteins. Specific interactor candidates were identified for each of the three KDM3 subfamily members. Importantly, we find that SCAI, a known transcriptional repressor, interacts specifically with KDM3B. Taken together, we identify substantial differences in the biology of KDM3 histone demethylases, namely enzymatic activity and protein-protein interactions. Such comparative approaches pave the way to a better understanding of KDM specificity and protein function at a systems level and are instrumental in identifying the more subtle differences between closely related proteins.

Item Type: Article
Date Deposited: 13 Oct 2015 13:14
Last Modified: 04 Jul 2016 23:46