Mining Affymetrix microarray data for long non-coding RNAs: altered expression in the nucleus accumbens of heroin abusers

• Published in: Journal of neurochemistry Vol. 116; no. 3; pp. 459 - 466
• Main Authors: Michelhaugh, Sharon K, Lipovich, Leonard, Blythe, Jason, Jia, Hui, Kapatos, Gregory, Bannon, Michael J
• Format: Journal Article
• Language: English
• Published: Oxford, UK Blackwell Publishing Ltd 01.02.2011; Wiley-Blackwell
• Subjects: Abundance; Addictive behaviors; Adult and adolescent clinical studies; Analgesics, Opioid - adverse effects; Biological and medical sciences; Brain; Brain Chemistry - drug effects; Brain Chemistry - genetics; Central nervous system; Central neurotransmission. Neuromudulation. Pathways and receptors; Computational neuroscience; Data Mining - methods; Data processing; DNA microarrays; Drug abuse; Drug addiction; Fundamental and applied biological sciences. Psychology; Gene expression; Gene Expression Regulation - drug effects; Gene Expression Regulation - genetics; Genetic Markers - drug effects; Genetic Markers - physiology; Heroin; Heroin - adverse effects; Heroin Dependence - genetics; Heroin Dependence - metabolism; Humans; lncRNA; MALAT1; Medical sciences; MEG3; MIAT; NEAT1; non-coding RNA; Nucleus accumbens; Nucleus Accumbens - drug effects; Nucleus Accumbens - metabolism; Oligonucleotide Array Sequence Analysis - methods; Organelles; Polymerase chain reaction; Polymerase Chain Reaction - methods; Psychology. Psychoanalysis. Psychiatry; Psychopathology. Psychiatry; Reward; Ribonucleic acid; RNA; RNA, Untranslated - biosynthesis; RNA, Untranslated - drug effects; RNA, Untranslated - genetics; Up-Regulation - drug effects; Up-Regulation - genetics; Vertebrates: nervous system and sense organs; Human; MEG3; Drug addiction; Central nervous system; IncRNA; Basal ganglion; Substance abuse; MIAT; Gene expression; NEAT1; Encephalon; Nucleus accumbens; Coding; MALAT1
• ISSN: 0022-3042; 1471-4159; 1471-4159
• DOI: 10.1111/j.1471-4159.2010.07126.x

J. Neurochem. (2011) 116, 459-466. ABSTRACT: Although recent data suggest that some long non-coding RNAs (lncRNAs) exert widespread effects on gene expression and organelle formation, lncRNAs as a group constitute a sizable but poorly characterized fraction of the human transcriptome. We investigated whether some human lncRNA sequences were fortuitously represented on commonly used microarrays, then used this annotation to assess lncRNA expression in human brain. A computational and annotation pipeline was developed to identify lncRNA transcripts represented on Affymetrix U133 arrays. A previously published dataset derived from human nucleus accumbens was then examined for potential lncRNA expression. Twenty-three lncRNAs were determined to be represented on U133 arrays. Of these, dataset analysis revealed that five lncRNAs were consistently detected in samples of human nucleus accumbens. Strikingly, the abundance of these lncRNAs was up-regulated in human heroin abusers compared to matched drug-free control subjects, a finding confirmed by quantitative PCR. This study presents a paradigm for examining existing Affymetrix datasets for the detection and potential regulation of lncRNA expression, including changes associated with human disease. The finding that all detected lncRNAs were up-regulated in heroin abusers is consonant with the proposed role of lncRNAs as mediators of widespread changes in gene expression as occur in drug abuse.