title: Protein complex interactor analysis and differential activity of KDM3 subfamily members towards H3K9 methylation.
abstract: 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 histone demethylase 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 histone demethylase specificity and protein function at a systems level and are instrumental in identifying the more subtle differences between closely related proteins.
authors.affiliation: Developmental & Molecular Pathways, Novartis Institutes for Biomedical Research, Basel, Switzerland. brauchle@nyu.edu
authors.forename: Michael
authors.initials: M
authors.lastname: Brauchle
authors.forename: Zhiping
authors.initials: Z
authors.lastname: Yao
authors.forename: Rishi
authors.initials: R
authors.lastname: Arora
authors.forename: Sachin
authors.initials: S
authors.lastname: Thigale
authors.forename: Ieuan
authors.initials: I
authors.lastname: Clay
authors.forename: Bruno
authors.initials: B
authors.lastname: Inverardi
authors.forename: Joy
authors.initials: J
authors.lastname: Fletcher
authors.forename: Paul
authors.initials: P
authors.lastname: Taslimi
authors.forename: Michael G
authors.initials: MG
authors.lastname: Acker
authors.forename: Bertran
authors.initials: B
authors.lastname: Gerrits
authors.forename: Johannes
authors.initials: J
authors.lastname: Voshol
authors.forename: Andreas
authors.initials: A
authors.lastname: Bauer
authors.forename: Dirk
authors.initials: D
authors.lastname: Schübeler
authors.forename: Tewis
authors.initials: T
authors.lastname: Bouwmeester
authors.forename: Heinz
authors.initials: H
authors.lastname: Ruffner
mesh_terms: D015153:Blotting, Western; D017931:DNA Primers / Q000235:genetics; D044127:Epigenesis, Genetic / Q000502:physiology*; D057809:HEK293 Cells; D006657:Histones / Q000378:metabolism*; D006801:Humans; D047468:Immunoprecipitation; D056484:Jumonji Domain-Containing Histone Demethylases / Q000378:metabolism*; D013058:Mass Spectrometry; D008745:Methylation; D008856:Microscopy, Fluorescence; D010089:Oxidoreductases, N-Demethylating / Q000378:metabolism; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D017931:DNA Primers; D006657:Histones; C540922:SCAI protein, human; D014157:Transcription Factors; C520448:JMJD1C protein, human; D056484:Jumonji Domain-Containing Histone Demethylases; C530247:KDM3A protein, human; C438748:KDM3B protein, human; D010089:Oxidoreductases, N-Demethylating