Facultative dosage compensation of developmental genes on autosomes in Drosophila and mammals [RIP-seq]

Haploinsufficiency and aneuploidy are two phenomena, where alteration of gene dosage causes severe cellular defects ultimately resulting in developmental failures and disease. One remarkable exception is the X chromosome, where copy number differences between males and females are buffered through the action of dosage compensation systems. In Drosophila, the Male-Specific Lethal complex (MSLc) mediates two-fold upregulation of the single male X chromosome via Histone H4 lysine 16 acetylation (H4K16ac). The evolutionary origin and conservation of this process orchestrated by MSL2, the only male-specific protein within the fly MSLc, have remained unclear. Here, we report that MSL2, in addition to its function on the X, targets dosage-sensitive autosomal genes involved in patterning and morphogenesis. We show that the precise regulation of these genes by MSL2 is required for proper development of the fly wing. This set of dosage sensitive genes maintained such regulation during evolution, as MSL2 binds and similarly regulates mouse orthologues via deposition of H4K16ac. We propose that MSL2-mediated H4K16ac is an evolutionarily conserved process mediating gene-by-gene dosage compensation across flies and mammals. Genome-wide RNA interaction profiles (FLASH; Fast cloning of RNA After some Sort of affinity purification for High-throughput sequencing) of MSL2 and MLE in Drosophila melanogaster third instar larvae. Males and females separated, 2 biological replicates each.

单倍体不足（Haploinsufficiency）与非整倍体（aneuploidy）是两类关键现象：基因剂量改变会引发严重的细胞缺陷，最终导致发育异常与疾病。X染色体是一个显著的例外，雌雄个体间的X染色体拷贝数差异可通过剂量补偿系统的作用得到缓冲。在果蝇（Drosophila）中，雄性特异性致死复合物（MSLc）通过组蛋白H4赖氨酸16乙酰化（H4K16ac）介导雄性单条X染色体的转录水平上调至原始水平的两倍。由果蝇MSLc中唯一的雄性特异性蛋白MSL2所调控的这一过程，其进化起源与保守性至今仍未阐明。本研究发现，MSL2除在X染色体上发挥调控功能外，还靶向参与模式构建与形态发生的剂量敏感型常染色体基因。我们证实，MSL2对这些基因的精准调控是果蝇翅膀正常发育的必要前提。这类剂量敏感基因在进化过程中保留了这一调控模式：MSL2可通过沉积H4K16ac结合小鼠同源基因，并对其进行类似的调控。我们提出，MSL2介导的H4K16ac修饰是一个进化保守的过程，可在果蝇与哺乳动物中实现逐基因的剂量补偿。本研究获取了黑腹果蝇（Drosophila melanogaster）三龄幼虫中MSL2与MLE的全基因组RNA相互作用谱（FLASH：亲和纯化后快速克隆RNA以进行高通量测序，Fast cloning of RNA After some Sort of affinity purification for High-throughput sequencing）。实验分为雌雄两组，每组设置2次生物学重复。