TDP-43 oligomerization and RNA binding are codependent but their loss elicits distinct pathologies

Using the Flp-In T-REx technology, single copies of an N-terminally green fluorescent protein (GFP)-tagged TDP-43 coding sequence under the control of a doxycycline-inducible promoter were introduced into the HEK293 cells. The isogenic cell line named WT harboured the wild type form of the TDP-43 coding sequence. The isogenic cell line named 6M harboured point mutations that disrupt TDP-43 oligomerization as described in Afroz et al. (Nat Commun. 8, 45;2017). Finally, the isogenic cell line named RBDM harbored point mutations that disrupt TDP-43 oligomerization as described in Buratti et al. (J. Biol. Chem. 276, 36337) and Luvasky et al. (Nat Struct Mol Biol. 20, 1443 ; 2013). The expression was induced by doxycycline, cells were harvested and RNA extracted. For each of the three cell lines, four biological samples were paired-end sequenced on an Illumina HISEQ 2000 sequencer with two technical replicates each (total of 48 FASTQ-Files)