Context-Dependent Function of Long Noncoding RNA PURPL in Transcriptome Regulation during p53 Activation

Author:

Hartford, Corrine Corrina R

Shrestha, Roshan L

Pongor, Lorinc

Zhao,Yongmei

Chen, Xiongfong

Fromont,Caroline

Chaudhary, Ritu

Li, Xiao Ling

Pasterczyk, Katherine R

Kumar, Ravi

Muys, Bruna R

Tsitsipatis, Dimitrios

Chari,Raj

Gorospe, Myriam

Aladjem, Mirit I

Khan, Javed

Basrai, Munira A

Grammatikakis, Ioannis

Lal, Ashish [ORCID]
Author Address

NCI, Regulatory RNAs & Canc Sect, Genet Branch, Ctr Canc Res CCR,NIH, Bethesda, MD 20892 USA NCI, Yeast Genome Stabil Sect, Genet Branch, NIH, Bethesda, MD 20892 USA NCI, Dev Therapeut Branch, CCR, NIH, Bethesda, MD 20892 USA NCI, Sequencing Facil Bioinformat Grp, Bioinformat & Computat Sci Directorate, Frederick Natl Lab Canc Res, Frederick, MD 21701 USA NCI, Sequencing Facil, Canc Res Technol Program, Frederick Natl Lab Canc Res, Frederick, MD 21701 USA H Lee Moffitt Canc Ctr & Res Inst, Dept Head & Neck Endocrine Oncol, Tampa, FL USA NIA, Lab Genet & Genom, NIH, Baltimore, MD 20892 USA NCI, Genome Modificat Core, Frederick Natl Lab Canc Res, Frederick, MD 21701 USA NCI, Oncogen Sect, Genet Branch, CCR,NIH, Bethesda, MD 20892 USA

Abstract:

PURPL is a p53-induced lncRNA that suppresses basal p53 levels. Here, we investigated PURPL upon p53 activation in liver cancer cells, where it is expressed at significantly higher levels than other cell types. Using isoform sequencing, we discovered novel PURPL transcripts that have a retained intron and/or previously unannotated exons. To determine PURPL function upon p53 activation, we performed transcriptome sequencing (RNA-Seq) after depleting PURPL using CRISPR interference (CRISPRi), followed by Nutlin treatment to induce p53. Strikingly, although loss of PURPL in untreated cells altered the expression of only 7 genes, loss of PURPL resulted in altered expression of ~800 genes upon p53 activation, revealing a context-dependent function of PURPL. Pathway analysis suggested that PURPL is important for fine-tuning the expression of specific genes required for mitosis. Consistent with these results, we observed a significant decrease in the percentage of mitotic cells upon PURPL depletion. Collectively, these data identify novel transcripts from the PURPL locus and suggest that PURPL delicately moderates the expression of mitotic genes in the context of p53 activation to control cell cycle arrest.

See More

Author Address