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

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 investigate...

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Vydáno v:Journal of neurochemistry Ročník 116; číslo 3; s. 459 - 466
Hlavní autoři: Michelhaugh, Sharon K, Lipovich, Leonard, Blythe, Jason, Jia, Hui, Kapatos, Gregory, Bannon, Michael J
Médium: Journal Article
Jazyk:angličtina
Vydáno: Oxford, UK Blackwell Publishing Ltd 01.02.2011
Wiley-Blackwell
Témata:
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
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Shrnutí: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.
Bibliografie:http://dx.doi.org/10.1111/j.1471-4159.2010.07126.x
Joint first authors.
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ISSN:0022-3042
1471-4159
1471-4159
DOI:10.1111/j.1471-4159.2010.07126.x