Distinct and shared functions of ALS-associated TDP-43, FUS, and TAF15 revealed by comprehensive multi-system integrative analyses [RNA-Seq_mouse]

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.

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（frontotemporal dementia）密切相关。本研究整合了紫外交联免疫沉淀测序（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。在小鼠脑组织中，TAF15与FUS（而非TDP-43）展现出高度相似的RNA结合谱，但二者在单独敲除后，会分别调控不同mRNA群体的表达水平。TAF15在可变剪接中的作用极为有限，而是主要影响RNA周转过程，这与TAF15结合位点在3'非翻译区的富集特征相一致。在人类干细胞诱导的运动神经元中，同时敲除TAF15与FUS所影响的mRNA，与单独敲除任一蛋白所改变的mRNA均存在显著差异，这揭示了TAF15与FUS在维持mRNA水平上具有冗余功能。此外，与单独敲除TAF15和FUS相比，同时敲除二者的RNA表达谱更接近于FUS R521G突变型ALS患者，或晚期散发性ALS患者来源的运动神经元的RNA谱。本研究阐明了FUS、TAF15及TDP-43通过趋同与分化的双重机制，影响神经系统疾病中的RNA代谢过程。