Distinct and shared molecular targets and functions of ALS-associated TDP-43, FUS, and TAF15 revealed by comprehensive multi-system integrative analyses [CLIP-Seq]. Mus musculus

TDP-43, FUS, and TAF15 are implicated in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia. We integrate CLIP-seq and RNA Bind-N-Seq technologies to discover that TAF15 binds to ~4,900 RNAs enriched for GGUA motifs. In the mouse brain, TAF15 and FUS, but not TDP-43, exhibit strikingly similar RNA binding profiles, yet they alter the expression of distinct mRNA populations upon their individual depletions. TAF15 has a minimal role in alternative splicing and instead affects RNA turnover, consistent with an enrichment of TAF15 binding sites in 3’ untranslated regions. In human stem cell-derived motor neurons, loss of both TAF15 and FUS affected mRNAs distinct from those altered by loss of either protein alone, revealing redundant roles for TAF15 and FUS in maintaining mRNA levels. Furthermore, concomitant rather than individual depletion of TAF15 and FUS more closely resembles RNA profiles of motor neurons derived from FUS R521G ALS patients or from late-stage, sporadic ALS patients. Our study reveals convergent and divergent mechanisms by which FUS, TAF15 and TDP-43 affects RNA metabolism in neurological disease. Overall design: RNA-seq, CLIP-seq and arrays in mouse and human against TAF15 knockdowns This Series represents CLIP-seq sample(s).

TDP-43、FUS与TAF15均与肌萎缩侧索硬化症（amyotrophic lateral sclerosis, ALS）及额颞叶痴呆相关。我们整合交联免疫沉淀测序（CLIP-seq）与RNA Bind-N-Seq技术，发现TAF15可结合约4900个富集GGUA基序的RNA分子。在小鼠脑组织中，TAF15与FUS（而非TDP-43）展现出极为相似的RNA结合谱，但二者在单独敲低后，会分别调控不同mRNA群体的表达水平。TAF15在可变剪接中仅发挥极微弱的作用，转而影响RNA周转过程，这与其结合位点在3'非翻译区（3' untranslated region, 3'UTR）中的富集特征相一致。在人类干细胞诱导的运动神经元中，同时敲低TAF15与FUS所影响的mRNA，与单独敲低任一蛋白所改变的mRNA均存在差异，这揭示了TAF15与FUS在维持mRNA水平上具有功能冗余性。此外，相较于单独敲低TAF15与FUS，同时敲低二者所得到的RNA谱，与FUS R521G突变型ALS患者来源的运动神经元，或晚期散发性ALS患者来源的运动神经元的RNA谱更为相似。本研究揭示了FUS、TAF15及TDP-43在神经系统疾病中调控RNA代谢的趋同与分化机制。实验整体设计：在小鼠与人类样本中针对TAF15敲低模型开展RNA测序（RNA-seq）、CLIP-seq及基因芯片检测。本数据集系列包含CLIP-seq样本。