Interaction of JMJD6 with single-stranded RNA

Integrated Department of Immunology, National Jewish Health, Denver, CO 80206.
Proceedings of the National Academy of Sciences (Impact Factor: 9.67). 08/2010; 107(33):14568-72. DOI: 10.1073/pnas.1008832107
Source: PubMed


JMJD6 is a Jumonji C domain-containing hydroxylase. JMJD6 binds alpha-ketoglutarate and iron and has been characterized as either a histone arginine demethylase or U2AF65 lysyl hydroxylase. Here, we describe the structures of JMJD6 with and without alpha-ketoglutarate, which revealed a novel substrate binding groove and two positively charged surfaces. The structures also contain a stack of aromatic residues located near the active center. The side chain of one residue within this stack assumed different conformations in the two structures. Interestingly, JMJD6 bound efficiently to single-stranded RNA, but not to single-stranded DNA, double-stranded RNA, or double-stranded DNA. These structural features and truncation analysis of JMJD6 suggest that JMJD6 may bind and modify single-stand RNA rather than the previously reported peptide substrates.

Download full-text


Available from: James Hagman,
  • Source
    • "JMJD6 serves as a histone arginine demethylase and interacts with the splicing factor U2 small nuclear RNA auxiliary factor 2 (U2AF65) to regulate alternative RNA splicing in the nucleus1415. X-ray crystallographic data show that JMJD6 interacts with single-stranded RNA16. Elevated expression of JMJD6 in breast cancer was associated with poor outcomes and JMJD6 was shown to drive breast cancer cell proliferation17. "
    [Show abstract] [Hide abstract]
    ABSTRACT: T cell functional exhaustion during chronic hepatitis B virus (HBV) infection may contribute to the failed viral clearance; however, the underlying molecular mechanisms remain largely unknown. Here we demonstrate that jumonji domain-containing protein 6 (JMJD6) is a potential regulator of T cell proliferation during chronic HBV infection. The expression of JMJD6 was reduced in T lymphocytes in chronic hepatitis B (CHB) patients, and this reduction in JMJD6 expression was associated with impaired T cell proliferation. Moreover, silencing JMJD6 expression in primary human T cells impaired T cell proliferation. We found that JMJD6 promotes T cell proliferation by suppressing the mRNA expression of CDKN3. Furthermore, we have identified platelet derived growth factor-BB (PDGF-BB) as a regulator of JMJD6 expression. PDGF-BB downregulates JMJD6 expression and inhibits the proliferation of human primary T cells. Importantly, the expression levels of JMJD6 and PDGF-BB in lymphocytes from CHB patients were correlated with the degree of liver damage and the outcome of chronic HBV infection treatment. Our results demonstrate that PDGF-BB and JMJD6 regulate T cell function during chronic HBV infection and may provide insights for the treatment strategies for CHB patients.
    Scientific Reports 09/2014; 4:6359. DOI:10.1038/srep06359 · 5.58 Impact Factor
  • Source
    • "It had been reported previously that Jmjd6 can bind to RNA in vitro (38). We therefore investigated whether Jmjd6 co-localises with nascent RNA in cells. "
    [Show abstract] [Hide abstract]
    ABSTRACT: The Fe(II) and 2-oxoglutarate dependent oxygenase Jmjd6 has been shown to hydroxylate lysine residues in the essential splice factor U2 auxiliary factor 65 kDa subunit (U2AF65) and to act as a modulator of alternative splicing. We describe further evidence for the role of Jmjd6 in the regulation of pre-mRNA processing including interactions of Jmjd6 with multiple arginine–serine-rich (RS)-domains of SR- and SR-related proteins including U2AF65, Luc7-like protein 3 (Luc7L3), SRSF11 and Acinus S′, but not with the bona fide RS-domain of SRSF1. The identified Jmjd6 target proteins are involved in different mRNA processing steps and play roles in exon dependent alternative splicing and exon definition. Moreover, we show that Jmjd6 modifies splicing of a constitutive splice reporter, binds RNA derived from the reporter plasmid and punctually co-localises with nascent RNA. We propose that Jmjd6 exerts its splice modulatory function by interacting with specific SR-related proteins during splicing in a RNA dependent manner.
    Nucleic Acids Research 08/2014; 42(12-12):7833-7850. DOI:10.1093/nar/gku488 · 9.11 Impact Factor
  • Source
    • "In endothelial cells, alternate splicing of VEGF receptor (Flt1) by U2AF65 promoted endothelial cell migration, and siRNA-mediated knockdown of JMJD6 in endothelial cells led to decreased migration [7]. Based on X-ray crystallographic data, it was predicted and shown that apart from its enzymatic activity, JMJD6 protein bound single-stranded RNA [8]. These diverse findings predict a range of versatile functions for JMJD6, at the transcriptional, splicing, posttranscriptional, and biochemical levels. "
    [Show abstract] [Hide abstract]
    ABSTRACT: We developed an analytic strategy that correlates gene expression and clinical outcomes as a means to identify novel candidate oncogenes operative in breast cancer. This analysis, followed by functional characterization, resulted in the identification of Jumonji Domain Containing 6 (JMJD6) protein as a novel driver of oncogenic properties in breast cancer. Through microarray informatics, Cox proportional hazards regression was used to analyze the correlation between gene expression and distant metastasis-free survival (DMFS) of patients in 14 independent breast cancer cohorts. JMJD6 emerged as a top candidate gene robustly associated with poor patient survival. Immunohistochemistry, siRNA-mediated silencing, and forced overexpression of JMJD6 in cell-based assays elucidated molecular mechanisms of JMJD6 action in breast cancer progression and shed light on the clinical breast cancer subtypes relevant to JMJD6 action. JMJD6 was expressed at highest levels in tumors associated with worse outcomes, including ER- and basal-like, Claudin-low, Her2-enriched, and ER+ Luminal B tumors. High nuclear JMJD6 protein was associated with ER negativity, advanced grade, and poor differentiation in tissue microarrays. Separation of ER+/LN- patients that received endocrine monotherapy indicated that JMJD6 is predictive of poor outcome in treatment-specific subgroups. In breast cancer cell lines, loss of JMJD6 consistently resulted in suppressed proliferation but not apoptosis, whereas forced stable overexpression increased growth. In addition, knockdown of JMJD6 in invasive cell lines, such as MDA-MB231, decreased motility and invasion, whereas overexpression in MCF-7 cells slightly promoted motility but did not confer invasive growth. Microarray analysis showed that the most significant transcriptional changes occurred in cell-proliferation genes and genes of the TGF-β tumor-suppressor pathway. High proliferation was characterized by constitutively high cyclin E protein levels. The inverse relation of JMJD6 expression with TGF-β2 could be extrapolated to the breast cancer cohorts, suggesting that JMJD6 may affect similar pathways in primary breast cancer. JMJD6 is a novel biomarker of tumor aggressiveness with functional implications in breast cancer growth and migration.
    Breast cancer research: BCR 05/2012; 14(3):R85. DOI:10.1186/bcr3200 · 5.49 Impact Factor
Show more