KdmB, a Jumonji Histone H3 Demethylase, Regulates Genome-Wide H3K4 Trimethylation and Is Required for Normal Induction of Secondary Metabolism in Aspergillus nidulans.
KdmB, a Jumonji Histone H3 Demethylase, Regulates Genome-Wide H3K4 Trimethylation and Is Required for Normal Induction of Secondary Metabolism in Aspergillus nidulans.
复制标题
KDMB是一种Jumonji组蛋白H3脱甲基酶，调节全基因组H3K4三甲基化，是在曲霉菌中正常诱导继发代谢所必需的。
DOI：
10.1371/journal.pgen.1006222
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发表时间：
2016-08
期刊：
影响因子：
4.5
通讯作者：
Strauss J
中科院分区：
文献类型：
--
作者：
Gacek-Matthews A;Berger H;Sasaki T;Wittstein K;Gruber C;Lewis ZA;Strauss J
组蛋白翻译后修饰（HPTMs）参与基于染色质的真菌次生代谢物生物合成（SMB）调控，其中相应的基因-通常以共调控簇的形式物理连接-在最佳生理条件下（营养丰富）沉默，但在营养受限时被激活。然而，HPTMs影响沉默和激活的确切分子机制仍有待更好地了解。在这里，我们通过定量质谱（LC-MS/MS）、全基因组染色质免疫沉淀（ChIP-seq）和转录网络分析（RNA-seq）的联合方法表明，沉默的麻豆SM簇的核心区域通常携带低水平的所有被测试的染色质修饰，并且这些SM簇的大部分都有异染色质标记。在二次代谢过程中，组蛋白标记通常与转录活性相关，如H3三甲基化赖氨酸-4 (H3K4me3)，即使在完全激活的情况下，也会在一些基因簇中建立，但并非所有基因簇都建立。KdmB是一种jarid1家族组蛋白H3赖氨酸去甲基化酶，预计除了具有催化作用的Jumonji结构域外，还包括一个BRIGHT结构域、一个锌指结构域和两个PHD结构域，它在体内靶向H3K4me3并使其去甲基化，并介导转录下调。在营养丰富（初级代谢）和营养限制（次级代谢）条件下，kdmB的缺失导致约1750个基因的转录增加。出乎意料的是，同样多的基因在kdmB缺失菌株中表现出表达减少，值得注意的是，该组中具有已知或预测的次生代谢物生物合成功能的基因显著富集。综上所述，该研究扩展了我们对多结构域KDM5组蛋白去甲基化酶的一般认识，并为真菌次生代谢物产生的染色质水平调控提供了新的细节。在这项工作中，我们通过蛋白质组学分析和ChIP-seq监测了在最佳生理条件（活跃生长）或较不利条件下培养的模式真菌中组蛋白H3的几个关键修饰的全基因组分布，这些修饰已知会促进次生代谢物（SM）的产生。当我们将活跃生长细胞中的染色质状态与转录活性联系起来时，我们发现沉默的SM基因簇的两侧有异色结构域，这可能有助于沉默，但簇的主体只携带任何研究标记的背景水平。在营养匮乏的条件下，激活标记入侵了一些，但到目前为止不是所有的转录簇，留下了这些区域如何在染色质水平上发生激活的问题。令人惊讶的是，大量这些基因簇实际上依赖于KdmB进行正常激活，未来看到这种蛋白质如何通过去除阳性H3K4m3标记来直接或间接地激活转录，这将是一件有趣的事情。
Histone posttranslational modifications (HPTMs) are involved in chromatin-based regulation of fungal secondary metabolite biosynthesis (SMB) in which the corresponding genes—usually physically linked in co-regulated clusters—are silenced under optimal physiological conditions (nutrient-rich) but are activated when nutrients are limiting. The exact molecular mechanisms by which HPTMs influence silencing and activation, however, are still to be better understood. Here we show by a combined approach of quantitative mass spectrometry (LC-MS/MS), genome-wide chromatin immunoprecipitation (ChIP-seq) and transcriptional network analysis (RNA-seq) that the core regions of silent A. nidulans SM clusters generally carry low levels of all tested chromatin modifications and that heterochromatic marks flank most of these SM clusters. During secondary metabolism, histone marks typically associated with transcriptional activity such as H3 trimethylated at lysine-4 (H3K4me3) are established in some, but not all gene clusters even upon full activation. KdmB, a Jarid1-family histone H3 lysine demethylase predicted to comprise a BRIGHT domain, a zinc-finger and two PHD domains in addition to the catalytic Jumonji domain, targets and demethylates H3K4me3 in vivo and mediates transcriptional downregulation. Deletion of kdmB leads to increased transcription of about ~1750 genes across nutrient-rich (primary metabolism) and nutrient-limiting (secondary metabolism) conditions. Unexpectedly, an equally high number of genes exhibited reduced expression in the kdmB deletion strain and notably, this group was significantly enriched for genes with known or predicted functions in secondary metabolite biosynthesis. Taken together, this study extends our general knowledge about multi-domain KDM5 histone demethylases and provides new details on the chromatin-level regulation of fungal secondary metabolite production. In this work we monitored by proteomic analysis and ChIP-seq the genome-wide distribution of several key modifications on histone H3 in the model fungus Aspergillus nidulans cultivated either under optimal physiological conditions (active growth) or less favourable conditions which are known to promote the production of secondary metabolites (SM). When we correlated the chromatin status to transcriptional activities in actively growing cells we found that the silenced SM gene clusters are flanked by heterochromatic domains presumably contributing to silencing but that the bodies of the clusters only carry background levels of any of the investigated marks. In nutrient-depleted conditions, activating marks were invading some, but by far not all transcribed clusters, leaving open the question how activation of these regions occurs at the chromatin level. Surprisingly, a large number of these gene clusters actually depend on KdmB for normal activation and it will be interesting to see in future how this protein thought to mainly act as repressor by removing positive H3K4m3 marks switches gears to activate transcription directly or indirectly.