Institute of Molecular Biology of Barcelona, CSIC and Institute for Research in Biomedicine, IRB Barcelona, Barcelona, Spain.
Nucleic Acids Res. 2012 Oct;40(19):9493-505. doi: 10.1093/nar/gks773. Epub 2012 Aug 16.
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.
H3K4me3 是一种组蛋白修饰，在活性基因的转录起始位点（TSS）积累，已知对转录激活很重要。H3K4me3 在 TSS 处的调控方式及其对转录的实际分子基础在很大程度上仍未得到解答。为了解决这些问题，我们分析了 dKDM5/LID（果蝇中主要的 H3K4me3 去甲基化酶）对 H3K4me3 模式调控的贡献。ChIP-seq 结果表明，在发育基因中，dKDM5/LID 定位于 TSS 并调节 H3K4me3。dKDM5/LID 的靶基因转录水平高，并富含活跃的 RNApol II 和 H3K36me3，表明其对转录有正向贡献。表达谱分析表明，尽管较弱，但 dKDM5/LID 靶基因在 dKDM5/LID 耗竭后显著下调。此外，dKDM5/LID 耗竭导致 RNApol II 占据减少，特别是由启动子近端 Pol llo(ser5)形式。我们的研究结果还表明，ASH2 是一种进化上保守的因子，位于 TSS 处，是 H3K4me3 所必需的，它结合并正向调节 dKDM5/LID 的靶基因。然而，dKDM5/LID 和 ASH2 不能同时结合，分别识别富含 H3K4me3 和不富含 H3K4me3 的不同染色质状态。这些结果表明，在发育基因中，dKDM5/LID 和 ASH2 协调调节 TSS 处的 H3K4me3，这种动态调控有助于转录。
