A noncanonical role of roX RNAs in autosomal epigenetic repression [ChIP-seq]. A noncanonical role of roX RNAs in autosomal epigenetic repression [ChIP-seq]

Long noncoding RNAs known as roX (RNA on X) are crucial for male development in Drosophila, as their loss leads to male lethality from the late larval stages. While roX RNAs are recognized for their role in sex-chromosome dosage compensation, ensuring balanced expression of X-linked genes in both sexes, their potential influence on autosomal gene regulation remains unexplored. Using an integrative multi-omics approach, we revealed that roX RNAs not only govern the X chromosome but also target genes on autosomes that lack male-specific lethal (MSL) complex occupancy, together with Polycomb repressive complexes (PRCs). We observed that roX RNAs colocalize with MSL proteins on the X chromosome and PRC components on autosomes. Intriguingly, loss of roX function reduces X-chromosomal H4K16ac levels and autosomal H3K27me3 levels. Correspondingly, X-linked genes display reduced expression, whereas many autosomal genes exhibit elevated expression upon roX loss. Our findings propose a dual role for roX RNAs: activators of X-linked genes and repressors of autosomal genes, achieved through interactions with MSL and PRC complexes, respectively. This study uncovers the unconventional epigenetic repressive function of roX RNAs. Overall design: Genomic binding profiles of H3K27me3 in roX1 roX2 double knockout (roX-KO) male larvae and their wild type counterparts were generated by ChIP-seq.

以roX（X染色体上RNA，RNA on X）命名的长链非编码RNA（long noncoding RNAs，lncRNAs）对果蝇雄性发育至关重要，其缺失会导致雄性个体在幼虫晚期出现致死表型。既往研究证实roX RNA参与性染色体剂量补偿过程，以维持雌雄个体间X连锁基因的表达平衡，但其对常染色体基因调控的潜在影响尚未被探索。
本研究采用整合多组学策略，发现roX RNA不仅靶向调控X染色体，还可作用于未结合雄性特异性致死复合体（male-specific lethal complex，MSL）但存在多梳抑制复合体（Polycomb repressive complexes，PRCs）的常染色体基因。研究观察到，roX RNA与X染色体上的MSL蛋白以及常染色体上的PRC组分共定位。
值得注意的是，roX功能缺失会降低X染色体的H4K16ac（histone H4 lysine 16 acetylation，H4K16ac）水平与常染色体的H3K27me3（histone H3 lysine 27 trimethylation，H3K27me3）水平。相应地，X连锁基因的表达量下调，而roX缺失后多数常染色体基因的表达量则显著上调。
本研究提出roX RNA具备双重功能：分别通过与MSL复合体和PRC复合体相互作用，充当X连锁基因的激活因子与常染色体基因的抑制因子。本研究揭示了roX RNA非典型的表观遗传抑制功能。
总体实验设计：通过染色质免疫共沉淀测序（chromatin immunoprecipitation sequencing，ChIP-seq），获取了roX1 roX2双敲除（double knockout，roX-KO）雄性幼虫及其野生型对照的H3K27me3全基因组结合谱。