The Novel Gene CRNDE Encodes a Nuclear Peptide (CRNDEP) Which Is Overexpressed in Highly Proliferating Tissues

PLoS One. 2015 May 15;10(5):e0127475. doi: 10.1371/journal.pone.0127475. eCollection 2015.

Abstract

CRNDE, recently described as the lncRNA-coding gene, is overexpressed at RNA level in human malignancies. Its role in gametogenesis, cellular differentiation and pluripotency has been suggested as well. Herein, we aimed to verify our hypothesis that the CRNDE gene may encode a protein product, CRNDEP. By using bioinformatics methods, we identified the 84-amino acid ORF encoded by one of two CRNDE transcripts, previously described by our research team. This ORF was cloned into two expression vectors, subsequently utilized in localization studies in HeLa cells. We also developed a polyclonal antibody against CRNDEP. Its specificity was confirmed in immunohistochemical, cellular localization, Western blot and immunoprecipitation experiments, as well as by showing a statistically significant decrease of endogenous CRNDEP expression in the cells with transient shRNA-mediated knockdown of CRNDE. Endogenous CRNDEP localizes predominantly to the nucleus and its expression seems to be elevated in highly proliferating tissues, like the parabasal layer of the squamous epithelium, intestinal crypts or spermatocytes. After its artificial overexpression in HeLa cells, in a fusion with either the EGFP or DsRed Monomer fluorescent tag, CRNDEP seems to stimulate the formation of stress granules and localize to them. Although the exact role of CRNDEP is unknown, our preliminary results suggest that it may be involved in the regulation of the cell proliferation. Possibly, CRNDEP also participates in oxygen metabolism, considering our in silico results, and the correlation between its enforced overexpression and the formation of stress granules. This is the first report showing the existence of a peptide encoded by the CRNDE gene.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Amino Acids / genetics
  • Cell Line, Tumor
  • Cell Nucleus / genetics*
  • Cell Proliferation / genetics*
  • Epithelial Cells / metabolism
  • HeLa Cells
  • Humans
  • Intestinal Mucosa / metabolism
  • Male
  • Molecular Sequence Data
  • Open Reading Frames / genetics
  • Peptides / genetics*
  • RNA, Long Noncoding / genetics
  • RNA, Small Interfering / genetics
  • Spermatocytes / metabolism

Substances

  • Amino Acids
  • Peptides
  • RNA, Long Noncoding
  • RNA, Small Interfering

Grants and funding

This study was supported by the grants no. N N401 2361 34 and N N407 0272 38 of the Polish Ministry of Science and Higher Education. URL: (http://www.nauka.gov.pl/en/). Immunofluorescence imaging was performed in Multimodal Laboratory of Cell Adhesion and Motility in Nencki Institute of Experimental Biology PAS, supported by the NanoFun Project POIG.02.02.00-00-025/09. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.