Mining Affymetrix microarray data for long non-coding RNAs: altered expression in the nucleus accumbens of heroin
Sharon K Michelhaugh1, Leonard Lipovich, Jason Blythe
1Department of Pharmacology, Wayne State University School of Medicine, Detroit, Michigan, USA. skmichel@wayne.edu
Journal of Neurochemistry
|December 7, 2010
Summary
Long non-coding RNAs (lncRNAs) were detected in human brain tissue. Their abundance increased in heroin abusers, suggesting a role in drug abuse and gene expression changes.
Area of Science:
- Genomics
- Neuroscience
- Molecular Biology
Background:
- Long non-coding RNAs (lncRNAs) are a significant but understudied component of the human transcriptome.
- lncRNAs are known to influence gene expression and organelle formation.
Purpose of the Study:
- To identify lncRNAs represented on commonly used microarrays.
- To assess lncRNA expression in the human brain, specifically in nucleus accumbens.
- To investigate changes in lncRNA expression associated with heroin abuse.
Main Methods:
- Development of a computational pipeline to identify lncRNA transcripts on Affymetrix U133 arrays.
- Analysis of a previously published dataset from human nucleus accumbens.
- Validation of detected lncRNA expression using quantitative PCR.
Main Results:
- Twenty-three lncRNAs were found to be represented on U133 arrays.
- Five lncRNAs were consistently detected in human nucleus accumbens samples.
- All five detected lncRNAs showed increased abundance in heroin abusers compared to controls, confirmed by qPCR.
Conclusions:
- Existing microarray datasets can be utilized to detect and study lncRNA expression.
- lncRNA dysregulation may play a role in the molecular changes associated with human drug abuse.
- The findings support the proposed function of lncRNAs in mediating widespread gene expression alterations.
