The H3K4 Demethylase Lid Associates with and Inhibits Histone Deacetylase Rpd3

Department of Biochemistry and Biophysics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7295. .
Molecular and Cellular Biology (Impact Factor: 4.78). 03/2009; 29(6):1401-10. DOI: 10.1128/MCB.01643-08
Source: PubMed


JmjC domain-containing proteins have been shown to possess histone demethylase activity. One of these proteins is the Drosophila histone H3 lysine 4 demethylase Little imaginal discs (Lid), which has been genetically classified as a Trithorax group protein. However, contrary to the supposed function of Lid in gene activation, the biochemical activity of this protein entails the removal of a histone mark that is correlated with active transcription. To understand the molecular mechanism behind the function of Lid, we have purified a Lid-containing protein complex from Drosophila embryo nuclear extracts. In addition to Lid, the complex contains Rpd3, CG3815/Drosophila Pf1, CG13367, and Mrg15. Rpd3 is a histone deacetylase, and along with Polycomb group proteins, which antagonize the function of Trithorax group proteins, it negatively regulates transcription. By reconstituting the Lid complex, we demonstrated that the demethylase activity of Lid is not affected by its association with other proteins. However, the deacetylase activity of Rpd3 is greatly diminished upon incorporation into the Lid complex. Thus, our finding that Lid antagonizes Rpd3 function provides an explanation for the genetic classification of Lid as a positive transcription regulator.

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    • "In this work, we analyze the contribution of dKDM5/LID to the regulation of the pattern of H3K4me3. Previous reports showed that dKDM5/LID is a component of various co-repressor complexes (32,33), which play a role in repression of NOTCH target genes (32,34). Similarly, several mammalian KDM5 isoforms associate with components of co-repressor complexes (35) and mediate repression (36–41). "
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    ABSTRACT: H3K4me3 is a histone modification that accumulates at the transcription-start site (TSS) of active genes and is known to be important for transcription activation. The way in which H3K4me3 is regulated at TSS and the actual molecular basis of its contribution to transcription remain largely unanswered. To address these questions, we have analyzed the contribution of dKDM5/LID, the main H3K4me3 demethylase in Drosophila, to the regulation of the pattern of H3K4me3. ChIP-seq results show that, at developmental genes, dKDM5/LID localizes at TSS and regulates H3K4me3. dKDM5/LID target genes are highly transcribed and enriched in active RNApol II and H3K36me3, suggesting a positive contribution to transcription. Expression-profiling show that, though weakly, dKDM5/LID target genes are significantly downregulated upon dKDM5/LID depletion. Furthermore, dKDM5/LID depletion results in decreased RNApol II occupancy, particularly by the promoter-proximal Pol llo(ser5) form. Our results also show that ASH2, an evolutionarily conserved factor that locates at TSS and is required for H3K4me3, binds and positively regulates dKDM5/LID target genes. However, dKDM5/LID and ASH2 do not bind simultaneously and recognize different chromatin states, enriched in H3K4me3 and not, respectively. These results indicate that, at developmental genes, dKDM5/LID and ASH2 coordinately regulate H3K4me3 at TSS and that this dynamic regulation contributes to transcription.
    Nucleic Acids Research 08/2012; 40(19):9493-505. DOI:10.1093/nar/gks773 · 9.11 Impact Factor
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    • "In addition to the acetyltransferase Tip60, MRG15 has been found in another complex that includes the deacetylase Rpd3 (Lee et al., 2009). We made germline clones of Rpd3 04556 and found that, rather than loss of H2AV, there was abundant -H2AV foci and evidence of a repair defect (Fig. S1). "
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    ABSTRACT: Ataxia telangiectasia-mutated (ATM) and ataxia telangiectasia-related (ATR) kinases are conserved regulators of cellular responses to double strand breaks (DSBs). During meiosis, however, the functions of these kinases in DSB repair and the deoxyribonucleic acid (DNA) damage checkpoint are unclear. In this paper, we show that ATM and ATR have unique roles in the repair of meiotic DSBs in Drosophila melanogaster. ATR mutant analysis indicated that it is required for checkpoint activity, whereas ATM may not be. Both kinases phosphorylate H2AV (γ-H2AV), and, using this as a reporter for ATM/ATR activity, we found that the DSB repair response is surprisingly dynamic at the site of DNA damage. γ-H2AV is continuously exchanged, requiring new phosphorylation at the break site until repair is completed. However, most surprising is that the number of γ-H2AV foci is dramatically increased in the absence of ATM, but not ATR, suggesting that the number of DSBs is increased. Thus, we conclude that ATM is primarily required for the meiotic DSB repair response, which includes functions in DNA damage repair and negative feedback control over the level of programmed DSBs during meiosis.
    The Journal of Cell Biology 10/2011; 195(3):359-67. DOI:10.1083/jcb.201104121 · 9.83 Impact Factor
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    • "Further analysis revealed that the distribution of KDM5B occupancy is highly correlated to the distribution of H3K36me3, a mark associated with actively transcribed genes, and that the demethylase is recruited to H3K36me3 though MRG15. Interestingly, the fly homologue of KDM5B, Lid, has also been found to interact with MRG15 (Lee et al, 2009). This leads to the proposal of an interesting model, in which the H3K4 demethylase crosstalks with transcription elongation-associated H3K36me3 through an Rpd3S-like histone deacetylase complex (Figure 1A). "
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    ABSTRACT: Recent discoveries of histone demethylases have shown that the dynamic regulation of histone methylation is important in differentiation and development. A paper in this issue of The EMBO Journal demonstrates that an H3K4me3 demethylase, KDM5B, is required for the regulation of self-renewal and pluripotency of embryonic stem (ES) cells by removing intragenic H3K4me3 and repressing cryptic transcription. © 2011 European Molecular Biology Organization | All Rights Reserved.
    The EMBO Journal 04/2011; 30(8):1420-1. DOI:10.1038/emboj.2011.99 · 10.43 Impact Factor
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