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Integrated Transcriptomic, In Silico, and In Vitro Characterization of lncRNA ENST00000615487.1 Reveals
Nataša Đokić1, Anastasija Bubanja1, Jelena Karanović1
1Gene Regulation in Cancer Group, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11000 Belgrade, Serbia.
Non-Coding RNA
|July 24, 2026
Summary
This study reveals that ENST00000615487.1, a long non-coding RNA (lncRNA), is downregulated in colorectal cancer (CRC). Its localization shifts from the nucleus to the cytoplasm in CRC cells, suggesting altered functions in colorectal carcinogenesis.
Area of Science:
- Molecular Biology
- Genomics
- Cancer Research
Background:
- Long non-coding RNAs (lncRNAs) play critical roles in tumor biology.
- The lncRNA ENST00000615487.1 (CTD-2396E7.11/AC010503.4) has been linked to various cancers, but its function in colorectal cancer (CRC) is not well understood.
Purpose of the Study:
- To investigate the expression, localization, and potential functions of ENST00000615487.1 in colorectal cancer (CRC).
- To utilize integrated in vitro and in silico methods for a comprehensive analysis.
Main Methods:
- In silico analysis using tools like CPC2, RNA Analyzer 3, UCSC Xena Browser, lncATLAS, lncLocator, iLoc-LncRNA, Fasim-LongTarget, miRDB, AnnoLnc2, STRING, and Enrichr.
- Experimental validation including PCR, qRT-PCR, and analysis of single-cell RNA sequencing data (GSE161277).
- Assessment of molecular characteristics, differential expression across tumor types, cell type-specific expression, subcellular localization, and potential molecular interactions.
Main Results:
- ENST00000615487.1 is a stable lncRNA with a structured secondary formation.
- Significant downregulation of ENST00000615487.1 was observed in CRC compared to normal colon tissues.
- The lncRNA is predominantly expressed in epithelial cells and shows a shift in localization from the nucleus in normal cells to the cytoplasm in CRC cells.
- Potential interactions were identified with genes like HIP1R and RPH3AL, miRNAs, and proteins involved in transcriptional regulation, RNA processing, and vesicular transport.
Conclusions:
- ENST00000615487.1 is a structurally stable lncRNA with context-dependent expression and localization in CRC.
- The observed shift in localization suggests a potential transition from nuclear transcriptional roles to cytoplasmic post-transcriptional functions during colorectal cancer development.
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