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RNA-Seq of Flp-In T-REx 293, two clones of CRISPR-Cas9 mediated knockout of CASC3 and further CASC3 depletion via small interfering RNAs

ABSTRACT: We report two knockouts of the CASC3 (Barentsz, MLN51) gene and further depletion of gene expression with small interfering RNAs (siRNAs). CASC3 is a component of the exon-junction complex (EJC) which is deposited upstream of splice junctions on the mRNA. The EJC core and peripheral interacting factors are involved in RNA splicing, export, translation and nonsense-mediated decay. Contrasting to the other factors that form the exon-junction complex, CASC3 individual role on these processes was relatively poorly understood in the literature. To further elucidate the role of CASC3 in these processes we have established 2 different CRISPR-Cas9 genetic knockouts (KO) of CASC3. We extracted the total RNA by using the NucleoSpin RNA Plus kit (Macherey-Nagel), and performed ribosomal depletion and strand-specific library preparation with the TruSeq Stranded Total RNA protocol with Ribo-Zero Gold. Sequencing of the KO clones as well as the KO clones treated with CASC3 siRNA was carried out with the Illumina NovaSeq6000 sequencer with 2×100bp, targeting approximately 50 million read-pairs per sample. By studying the RNA-Seq of the 4 conditions, one with minimal CASC3 expression (condition H) or and three with complete depletion of the protein expression (conditions H-KD, T, T-KD), we observed the up-regulation of known and novel nonsense mediated decay substrates, thus establishing CASC3 as a critical factor for efficient nonsense mediated decay of certain transcripts.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Homo sapiens

SUBMITTER: Thiago Britto Borges

PROVIDER: E-MTAB-8461 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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