Identification of Long stress-induced non-coding transcripts that have altered expression in cancer

Jessica M. Silva, Damon S. Perez, Jay R. Pritchett, Meredith L. Halling, Hui Tang, David I Smith

Research output: Contribution to journalArticle

64 Citations (Scopus)

Abstract

It has recently become clear that the transcriptional output of the human genome is far more abundant than previously anticipated, with the vast majority of transcripts not coding for protein. Utilizing whole-genome tiling arrays, we analyzed the transcription across the entire genome in both normal human bronchial epithelial cells (NHBE) and NHBE cells exposed to the tobacco carcinogen NNK. Our efforts focused on the characterization of non-coding transcripts that were greater than 300 nucleotides in length and whose expression was increased in response to NNK. We identified 12 Long Stress-Induced Non-coding Transcripts that we term LSINCTs. Northern blot analysis revealed that these transcripts were larger than predicted from the tiling array data. Quantitative real-time RT-PCR performed across a panel of normal cell lines indicates that these transcripts are more abundantly expressed in rapidly growing tissues or in tissues that are more prone to cellular stress. These transcripts that have increased expression after exposure to NNK also had increased expression in a number of lung cancer cell lines and also in many breast cancer cell lines. Collectively, our results identified a new class of long stress responsive non-coding transcripts, LSINCTs, which have increased expression in response to DNA damage induced by NNK. LSINCTs interestingly also have increased expression in a number of cancer-derived cell lines, indicating that the expression is increased in both, correlating cellular stress and cancer.

Original languageEnglish (US)
Pages (from-to)355-362
Number of pages8
JournalGenomics
Volume95
Issue number6
DOIs
StatePublished - Jun 2010

Fingerprint

Cell Line
Neoplasms
Epithelial Cells
Genome
Human Genome
Northern Blotting
Carcinogens
DNA Damage
Tobacco
Real-Time Polymerase Chain Reaction
Lung Neoplasms
Nucleotides
Breast Neoplasms
Proteins

Keywords

  • Breast cancer
  • Entire genome analysis
  • Long non-coding transcripts
  • Lung cancer
  • NNK(4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone)
  • Non-coding RNA
  • Stress induction
  • Tiling arrays

ASJC Scopus subject areas

  • Genetics

Cite this

Identification of Long stress-induced non-coding transcripts that have altered expression in cancer. / Silva, Jessica M.; Perez, Damon S.; Pritchett, Jay R.; Halling, Meredith L.; Tang, Hui; Smith, David I.

In: Genomics, Vol. 95, No. 6, 06.2010, p. 355-362.

Research output: Contribution to journalArticle

Silva, Jessica M. ; Perez, Damon S. ; Pritchett, Jay R. ; Halling, Meredith L. ; Tang, Hui ; Smith, David I. / Identification of Long stress-induced non-coding transcripts that have altered expression in cancer. In: Genomics. 2010 ; Vol. 95, No. 6. pp. 355-362.
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