We recently identified the chromatin regulator FACT (Facilitates Chromatin Transcription) as a cellular reprogramming barrier in C. elegans and H. sapiens (Kolundzic et al., 2018). FACT is a heterodimer consisting of the histone-binding protein SPT-16 and either HMG-3 or HMG-4 (SSRP1 in H. sapiens) in C. elegans. Ectopic overexpression of the ASE neuron fate-inducing Zn-finger transcription factor (TF) CHE-1 in FACT depleted C. elegans, enables germ cells to express the reporter
gcy-5p::gfp, which is specific for the glutamatergic ASER neuron. These germ cells also display morphological changes, including axo-dendritic like projections and expression of pan-neuronal markers such as
rab-3 or
unc-119, indicating a conversion to neuron-like cells. We report now the identification of a previously uncharacterized pseudogene, F55A3.7, which shares more than 90% sequence homology with the FACT subunit-encoding gene
spt-16. Strikingly, the
ok1829 deletion allele of F55A3.7 allows germ cell conversion upon broad CHE-1 overexpression, mimicking the knock-down effect of other FACT members. We could detect the transcript of F55A3.7 using RT-PCR, confirming its expression, but no protein production from a 3xFLAG CRISPR knock-in allele, suggesting that F55A3.7 transcripts are non-coding. F55A3.7 acts in trans, as we can rescue the mutant phenotype by expressing the WT transcript in the
ok1829 mutant background. We performed qRT-PCR of dissected gonads to check for germline-specific transcript levels of the mother gene
spt-16 in the
ok1829 mutant background, as reduced levels of
spt-16 would be the simplest explanation for the germline conversion phenotype. However, germ-line specific transcript levels of
spt-16 (as well as of other FACT subunits) were unaltered, suggesting that the non-coding RNA F55A3.7 acts through other gene regulatory pathways. To reveal how it safeguards the germ cell identity, we performed germline-specific ATAC-seq and RNA-seq and used the gathered data to perform an enhancer/suppressor RNAi screen.