RNA-dependent chromatin localization of KDM4D lysine demethylase promotes H3K9me3 demethylation

Muhammad Zoabi, Prathamesh T. Nadar-Ponniah, Hanan Khoury-Haddad, Marko Usaj, Inbal Budowski-Tal, Tali Haran, Arnon Henn, Yael Mandel-Gutfreund, Nabieh Ayoub*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


The JmjC-containing lysine demethylase, KDM4D, demethylates di-and tri-methylation of histone H3 on lysine 9 (H3K9me3). How KDM4D is recruited to chromatin and recognizes its histone substrates remains unknown. Here, we show that KDM4D binds RNA independently of its demethylase activity. We mapped two non-canonical RNA binding domains: the first is within the N-terminal spanning amino acids 115 to 236, and the second is within the C-terminal spanning amino acids 348 to 523 of KDM4D. We also demonstrate that RNA interactions with KDM4D N-terminal region are critical for its association with chromatin and subsequently for demethylating H3K9me3 in cells. This study implicates, for the first time, RNA molecules in regulating the levels of H3K9 methylation by affecting KDM4D association with chromatin.

Original languageEnglish
Pages (from-to)13026-13038
Number of pages13
JournalNucleic Acids Research
Issue number21
StatePublished - 1 Dec 2014
Externally publishedYes


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