LINC01021 Attenuates Expression and Affects Alternative Splicing of a Subset of p53-Regulated Genes

Area of Science:

• Molecular Biology
• Cancer Research
• Genomics

Background:

• The p53-inducible long non-coding RNA LINC01021 influences sensitivity to DNA-damaging chemotherapeutics in colorectal cancer (CRC) cell lines.
• Understanding LINC01021's role in the p53 transcriptional program is crucial for CRC treatment strategies.

Purpose of the Study:

• To comprehensively analyze how LINC01021 affects the p53-induced transcriptional program in CRC.
• To investigate the impact of abrogating LINC01021's p53-inducibility on gene expression and splicing.

Main Methods:

• CRISPR/Cas9 was used to delete the p53 binding site in the LINC01021 promoter in SW480 CRC cells.
• RNA-sequencing (RNA-Seq) was performed after ectopic p53 activation.
• RNA affinity purification followed by mass spectrometry identified LINC01021-associated proteins.

Main Results:

• Loss of LINC01021 p53-inducibility increased the number of regulated mRNAs by ~1.8-fold after p53 activation.
• Direct p53 target genes (e.g., NOXA, FAS) showed stronger induction when LINC01021 inducibility was lost.
• Alternative splicing of specific mRNAs (e.g., ARHGAP12, HSF2, LYN) was observed upon loss of LINC01021 p53-inducibility.
• Mass spectrometry identified RNA binding proteins involved in pre-mRNA splicing as LINC01021 interaction partners.

Conclusions:

• LINC01021 appears to restrict the extent and strength of p53-mediated transcriptional changes.
• This regulation occurs via context-dependent control of expression and splicing of a subset of p53-regulated genes.