A comprehensive annotation and differential expression analysis of short and long non-coding RNAs in 16 bat genomes

Nelly Mostajo Berrospi; Marie Lataretu; Sebastian Krautwurst; Florian Mock; Daniel Desirò; Kevin Lamkiewicz; Maximilian Collatz; Andreas Schoen; Friedemann Weber; Manja Marz; Martin Hölzer

Based on the small RNA-Seq comparison of mock and virus-infected (Clone 13) samples 24 h post infection (Weber-2019), we found several miRNAs (Rfam-and mirDeep2-based) and snoRNAs to be differentially expressed ( Fig. 4 and details in Files S2.13). In general, replicates of virus-infected and IFN-treated samples 24 h post infection tend to cluster together only based on the expression profiles of small ncRNAs (mainly miRNAs) ( Fig. 4A and B ). Most differences can be observed between the 24 h virus-infected and all other samples, that seem to show no clearly distinguishable expression pattern. Interestingly, at 6 h post infection, we see replicates clustering together regardless of their treatment (mock, IFN, Clone 13). Thus, after only 6 h, few miRNAs are differentially expressed and therefore the samples of each replicate (mock, IFN, Clone 13) cluster together, because they have the same passaging history but the passaging history in between the replicates differ 36 . After 24 h, more and more miRNAs are significantly differentially expressed and the samples can be better distinguished based on their treatment ( Fig. 4A and B) . We observed that, in general, miRNAs tend to be down-regulated (Fig 4B; upper half) , while snoRNAs tend to be up-regulated (lower half) after 24 h of Clone 13 infection compared to mock. For example, we found a novel miRNA (MLUGD00000002094 in our annotation; predicted by mirDeep2; Tab. S7) located in an intron of the protein-coding gene SEMA3G, significantly down-regulated (log 2 fc=-2.56) during Clone 13 infection (Fig. 4C and D) . Based on Rfam alignments we further found a histone 3'-UTR stem-loop (RF00032), an RNA element involved in nucleocytoplasmic transport of the histone mRNAs, significantly down-regulated during infection. For the same comparison of mock and virus-infected samples at 24 h, the rRNAdepleted data set (Hölzer-2019) revealed several DE lncRNAs. For example, we found a lncRNA potentially transcribed in an intron of MX1 (MLUGL00000039178) up-regulated (log 2 fc=3.36) during infection. Another lncRNA (MLUGL00000087396), we found potentially transcribed as a part of two exons of the PLAT protein-coding gene and down-regulated (log 2 fc = -1.67) during viral infection (see details in Files S2.11).