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Related Experiment Video

Updated: Jun 10, 2026

In Vivo Modeling of the Morbid Human Genome using Danio rerio

In Vivo Modeling of the Morbid Human Genome using Danio rerio

Published on: August 24, 2013

Interaction of JMJD6 with single-stranded RNA.

Xia Hong¹, Jianye Zang, Janice White

¹Integrated Department of Immunology, National Jewish Health, Denver, CO 80206.

Proceedings of the National Academy of Sciences of the United States of America

|August 4, 2010

Summary

The Jumonji C domain-containing hydroxylase JMJD6 binds RNA. Structural and biochemical data reveal JMJD6 may modify single-stranded RNA, challenging previous findings on peptide substrates.

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RNA-Associated Chromatin DNA-DNA Interaction Method

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Published on: April 30, 2026

Area of Science:

Biochemistry
Structural Biology
Molecular Biology

Background:

JMJD6 is a Jumonji C (JmjC) domain-containing hydroxylase involved in various cellular processes.
It has been previously characterized as a histone arginine demethylase or a U2AF65 lysyl hydroxylase.
Understanding JMJD6's precise function requires detailed structural and substrate-binding information.

Purpose of the Study:

To elucidate the structure of JMJD6 in complex with its cofactor, alpha-ketoglutarate.
To identify novel structural features and potential substrate-binding sites of JMJD6.
To investigate the substrate specificity of JMJD6, particularly its interaction with nucleic acids.

Main Methods:

X-ray crystallography was used to determine the structures of JMJD6 with and without alpha-ketoglutarate.
Biochemical assays were performed to assess JMJD6 binding to various forms of RNA and DNA.
Truncation analysis was employed to identify key regions involved in substrate interaction.

Main Results:

The crystal structures revealed a novel substrate-binding groove and two positively charged surfaces within JMJD6.
A stack of aromatic residues near the active site showed conformational flexibility.
JMJD6 demonstrated efficient binding to single-stranded RNA (ssRNA) but not to single-stranded DNA (ssDNA), double-stranded RNA (dsRNA), or double-stranded DNA (dsDNA).

Conclusions:

The structural and biochemical findings suggest that JMJD6's primary role may involve binding and modifying single-stranded RNA.
These results challenge the previously reported functions of JMJD6 as a peptide-modifying enzyme.
Further investigation into JMJD6's RNA-binding and modifying capabilities is warranted.