RNA-seq analysis reveals significant transcriptome changes in huntingtin-null human neuroblastoma cells

To investigate the transcriptional role of normal Htt, we first knocked out Htt in the human neuroblastoma SH-SY5Y cell line using the CRISPR (clustered regularly interspaced short palindromic repeats)-Cas9 (CRISPR-associated protein 9) gene editing approach. We then performed RNA-seq analysis on two indepedent Htt-null stable cell lines and wild type SH-SY5Y cells to probe the global transcriptome changes induced by Htt deletion. Conclusion: Htt has a widespread effect on gene transcription. Functional analysis of the differentially expressed genes (DEGs) using various bioinformatic tools revealed irregularities in pathways related to cell communication and signaling, and more specifically those related to neuron development, neurotransmission and synaptic signaling. Overall design: RNA profiles of two independent HttKO cell lines and the parental wildtype SH-SY5Y cells