## 3 Results  
### The Cerebellar Transcriptome Profile of ATM-Null Mice at 12 Months of Age  
As shown in Figure 1a, the global transcriptome analysis of cerebellar tissue was performed in four WT versus four ATM-null mice, aged in parallel until 12 months in pairs of identical sex. The genotype of analysed mice was controlled by breeding protocols, PCR from ear-punch DNA, RT-qPCR of _Atm_ mRNA and quantitative immunoblots of ATM protein (Figure 1b,c). For the selection of appropriate animals, the cerebellar weight of KO samples was normalised versus WT of the same sex, and KO tissues with weight reductions until 50% were chosen. The global transcriptome profile of the ATM-null cerebellum is documented in Table S1. To ensure data reproducibility among different organisms in this strongly affected tissue at advanced age, we compared our ATM-null mouse cerebellar transcriptome profile at age 12 months with a published [66] proteome survey of A T patient cerebellar post-mortem samples (although distortions by altered tissue composition at end-stage will generate artefacts, and mass-spectrometry will detect maximally some 10,000 among all existing proteins), annotating the consistent findings in Table S1 and compiling these factors in Table 1. The comparison of our 12-month-old ATM-null mouse cerebellar transcriptome profile with previous A-T patient cerebrospinal fluid proteome data [67] revealed parallel reductions for _Reln_, _Fat2_, _Omd_, _Cnt6_ (down) and _C4b_ (up). This transcriptome was then interrogated in the context of known ATM functions and phenotypes, as far as they are known in the current literature. Given the scarcity of 12-month-old ATM-null mice with cerebellar anomalies, and in view of the massive widespread transcriptome changes observed (which are probably a direct consequence of altered phosphorylation cascades that alert to membrane stress and modulate nuclear transcription), we also performed extensive validation work in stressed cell models to elucidate the role of prominent molecular events. For the factors with interspecies consistency and multi-omics reproducibility shown in Table 1, the transcript identity and average expression levels are shown in the first columns, followed by a heatmap of log2-fold-changes with up- (red colour) versus downregulations (blue), and false discovery rate _p_-values illustrated by a yellow colour. Prominent upregulation (grey) of neurofilament medium and light chain mRNAs (_Nefm_ and _Nefl_) reflect the axon pathology at this disease stage and presumably represent cellular efforts to compensate the progressive neurofilament loss that is known to occur in A-T [6], while other upregulates probably represent efforts to substitute dendritic loss (_Map2_, _Tubb3_, _Tubb2a_) and cell adhesion (e.g., _Ncan_). Expression downregulations (green) concerned exclusively synaptic factors (_Dypsl4_, _Slc17a7_, _Cadps2_, _Syne1_, _Stxbp5l_) and might be due to impaired differentiation. In Figure 2a, a volcano plot displays the overall distribution of transcript dysregulations with actual significance (FDR < 0.05, corresponding to \(p\) < 0.0017), identifying particularly relevant coding transcripts by their gene symbols. As a noteworthy finding, ATM depletion was responsible for significant downregulations of mostly non-coding transcripts, whereas the upregulations concerned almost exclusively coding transcripts. The strongest downregulated microRNA was miR-495 (log2 fold change, FC \(-\)3.85, \(p\) = 0.0002) as angiogenesis-hypoxia-autophagy-synaptic depression modulator [68; 69; 70; 71; 72; 73]. An even greater downregulation was detected for the non-coding RNA TC0500000412.mm.1 (FC \(-\)10.77, \(p\) = 6.30 \(\times\) 10\({}^{-7}\)) as a prime example for the massive impact of ATM-loss on non-coding RNAs in general. The cellular roles of TC0500000412.mm.1 are unknown at present. In Figure 2b, pie charts reflect this massive contrast between non-coding downregulations versus coding upregulations, providing absolute numbers and percentages.