Multi-omic analysis of gametogenesis reveals a novel signature at the promoters and distal enhancers of active genes. Multi-omic analysis of gametogenesis reveals a novel signature at the promoters and distal enhancers of active genes

Epigenetic regulation of gene expression is tightly controlled by the dynamic modification of histones by chemical groups, the diversity of which has largely expanded over the past decade with the discovery of lysine acylations, catalyzed from acyl-coenzymes A. Here, we investigated the dynamics of lysine acetylation and crotonylation on histones H3 and H4 during mouse spermatogenesis. Lysine crotonylation appeared to be of significant abundance compared to acetylation, particularly on Lys27 of histone H3 (H3K27cr) that accumulates in sperm in a cleaved form of H3. We identified the genomic localization of H3K27cr and studied its effects on transcription compared to the classical active mark H3K27ac at promoters and distal enhancers. The presence of both marks was strongly associated with highest gene expression. Assessment of their co-localization with transcription regulators (SLY, SOX30) and chromatin-binding proteins (BRD4, BORIS and CTCF) indicated systematic highest binding when both active marks were present and different selective binding when present alone at chromatin. H3K27cr and H3K27ac finally mark the building of some sperm super-enhancers. This integrated analysis of omics data provides an unprecedented level of understanding of gene expression regulation by H3K27cr in comparison to H3K27ac, and reveals both synergistic and specific actions of each histone modification.

基因表达的表观遗传调控（epigenetic regulation）严格依赖于化学基团对组蛋白的动态修饰；过去十年间，随着酰基辅酶A（acyl-coenzymes A）介导的赖氨酸酰基化（lysine acylations）的发现，这类修饰的多样性得到了极大拓展。本研究探究了小鼠精子发生过程中组蛋白H3与H4上的赖氨酸乙酰化（lysine acetylation）及巴豆酰化（crotonylation）的动态变化。相较于乙酰化修饰，赖氨酸巴豆酰化的丰度更为显著，尤其是组蛋白H3赖氨酸27位巴豆酰化（H3K27cr），该修饰以剪切型组蛋白H3的形式在精子中积累。我们对H3K27cr的基因组定位进行了鉴定，并以经典活性标记H3K27乙酰化（H3K27ac）作为对照，研究了二者在启动子与远端增强子区域对转录的调控效应。当两种活性标记同时存在时，与最高水平的基因表达显著相关。通过分析其与转录调控因子SLY、SOX30以及染色质结合蛋白BRD4、BORIS、CTCF的共定位情况，我们发现当两种活性标记同时存在时，这些蛋白的结合水平系统性达到最高；而当染色质上仅存在单一修饰时，则呈现出不同的选择性结合模式。最终，H3K27cr与H3K27ac共同参与标记部分精子超级增强子（super-enhancers）的构建。本研究通过整合组学数据（omics data）开展分析，在对比H3K27ac的前提下，前所未有地深入解析了H3K27cr对基因表达的调控机制，并揭示了两种组蛋白修饰兼具协同效应与特异性的生物学功能。