GSE116267
Global effects of SUPT4H1 RNAi on gene expression of HEK293 cells
SUPT4H1 is a transcription elongation factor comprising part of the RNA polymerase II complex. Recent studies propose a selective role for SUPT4H1 in transcription of repeat-containing transcripts; the translated products of which being a hallmark of neurodegeneration in disorders such as Huntington's Disease and C9orf72-amyotrophic lateral sclerosis. To investigate the potential of SUPT4H1 as a therapeutic target in repeat-associated neurodegeneration, we depleted SUPT4H1 by RNA interference in order to mimic pharmacological loss of function. Using RNA sequencing we assessed SUPT4H1-knockdown induced changes is both immortalized cells (HEK293t) as well as primary human fibroblasts. Diminished SUPT4H1 leads to a global reduction in cellular RNA. Overall design: siRNA-mediated knockdown of SUPT4H1 in HEK293 cells was performed.  Control experiments (HEK293 treatment with non-targeting siRNA) was compared to knockdown conditions for the assessement of global modulatory effects on cell RNA abundances after SUPT4H1 depletion. Ribosomal RNA was depleted before library preparation using Illumina's RiboZero Gold kit.  Three disitnct clonal cell lines were engineered and assayed: one expressing EGFP (control) and two expressing di-amino acid (DARP) repeats, fused to EGFP.  DARPs were encoded by an array of 71 G4C2 repeats as a model of C9orf72 ALS.