Genetic and Genomic Analyses of Drosophila melanogaster Models of Chromatin Modification Disorders

Switch/Sucrose Non-Fermentable (SWI/SNF)-related intellectual disability disorders (SSRIDDs) and Cornelia de Lange syndrome are rare syndromic neurodevelopmental disorders with overlapping clinical phenotypes. SSRIDDs are associated with the BAF (Brahma‐Related Gene‐1 Associated Factor) complex, whereas CdLS is a disorder of chromatin modification associated with the cohesin complex. Here, we used RNA interference in Drosophila melanogaster to reduce expression of six genes (brm, osa, Snr1, SMC1, SMC3, vtd) orthologous to human genes associated with SSRIDDs and CdLS. These fly models exhibit changes in sleep, activity, startle behavior (a proxy for sensorimotor integration) and brain morphology. Whole genome RNA sequencing identified 9,657 differentially expressed genes (FDR < 0.05), 156 of which are differentially expressed in both sexes in SSRIDD- and CdLS-specific analyses, including Bap60, which is orthologous to SMARCD1, a SSRIDD-associated BAF component. k-means clustering reveals genes co-regulated within and across SSRIDD and CdLS fly models. RNAi-mediated reduction of expression of six genes co-regulated with focal genes brm, osa, and/or Snr1 recapitulated changes in behavior of the focal genes. Based on the assumption that fundamental biological processes are evolutionarily conserved, Drosophila models can be used to understand underlying molecular effects of variants in chromatin-modification pathways and may aid in discovery of drugs that ameliorate deleterious phenotypic effects. RNAseq (post rRNA depletion) of whole body Drosophila melanogaster, sexes separately, in the genetic background TRiP (y1, sc1, v1, sev21) (control), where mutant samples have ubiquitous Ubi156-GAL4-mediated UAS-GAL4 system knockdown of brm, osa, Snr1, SMC1, SMC3, and vtd. Three biological replicates per sex per line.

Switch/Sucrose Non-Fermentable (SWI/SNF)相关智力障碍疾病（SSRIDD）与科妮莉亚·德兰格综合征（Cornelia de Lange Syndrome, CdLS）均为具有重叠临床表型的罕见综合征性神经发育障碍。其中SSRIDD与BAF（Brahma相关基因1关联因子，Brahma‐Related Gene‐1 Associated Factor）复合物相关，而CdLS则是一类与黏连蛋白复合物（cohesin complex）相关的染色质修饰疾病。
本研究利用黑腹果蝇（Drosophila melanogaster）中的RNA干扰（RNA interference, RNAi）技术，下调6个与人类SSRIDD和CdLS相关基因同源的果蝇基因（brm、osa、Snr1、SMC1、SMC3、vtd）的表达。上述果蝇模型出现了睡眠模式、活动水平、惊跳行为（作为感觉运动整合的替代指标）以及大脑形态的异常改变。全基因组RNA测序（RNA-seq）共鉴定出9657个差异表达基因（错误发现率（False Discovery Rate, FDR） < 0.05），其中156个在SSRIDD和CdLS特异性分析的雌雄个体中均存在差异表达，包括与SSRIDD相关BAF复合物组分SMARCD1同源的Bap60。K均值（k-means）聚类分析显示，在SSRIDD与CdLS果蝇模型内部及跨模型间存在共调控基因。对与核心基因brm、osa和/或Snr1存在共调控关系的6个基因进行RNAi介导的表达下调，可重现核心基因所诱导的行为改变。
基于“基础生物学过程在进化上具有保守性”的假设，黑腹果蝇模型可用于解析染色质修饰通路变异的潜在分子效应，或有助于筛选可改善有害表型的候选药物。
本数据集为经核糖体RNA去除（post rRNA depletion）的黑腹果蝇全转录组RNA测序数据，实验分别设置雌雄两组，所有样本的遗传背景为TRiP品系（y¹, sc¹, v¹, sev²¹）作为对照组；突变样本采用泛在表达的Ubi156-GAL4介导的UAS-GAL4系统，分别敲低brm、osa、Snr1、SMC1、SMC3和vtd基因。每个品系的每个性别均设置3个生物学重复。