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PMID: 16809370 Published · ppublish English Journal Article Review

Microarrays and the microscope: balancing throughput with resolution.

The Journal of physiology ·Vol. 575 ·No. Pt 2 ·2006-09-01 ·Pages 353-9

Coppola G, Geschwind DH

Abstract

The cellular complexity of the brain is a major issue in the planning, execution and interpretation of microarray studies. Recent technical advances allow for high-throughput study of specific cell populations and circuits. Here we review representative examples of currently available methods that allow high resolution and specificity in brain microarray studies, while maintaining the goal of comprehensive, high-throughput analysis.

MeSH Terms
Animals Brain/cytology,physiology Diagnostic Imaging Gene Expression Profiling Gene Expression Regulation/genetics,physiology Genetic Markers Humans Microscopy, Fluorescence Neurons/cytology,physiology Oligonucleotide Array Sequence Analysis
Chemicals
Genetic Markers
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Coppola Giovanni
Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA.
Geschwind Daniel H
References (66)
66 references, click to expand
  1. Options available for profiling small samples: a review of sample amplification technology when combined with microarray profiling.
    Nucleic Acids Res. 2006;34(3):996-1014 PMID: 16473852
  2. Identification of ciliated sensory neuron-expressed genes in Caenorhabditis elegans using targeted pull-down of poly(A) tails.
    Genome Biol. 2005;6(2):R17 PMID: 15693946
  3. Presenilin-1-dependent transcriptome changes.
    J Neurosci. 2005 Feb 9;25(6):1571-8 PMID: 15703411
  4. Neuronal subtype-specific genes that control corticospinal motor neuron development in vivo.
    Neuron. 2005 Jan 20;45(2):207-21 PMID: 15664173
  5. DNA microarray analysis of functionally discrete human brain regions reveals divergent transcriptional profiles.
    Neurobiol Dis. 2003 Nov;14(2):240-50 PMID: 14572446
  6. Single-cell molecular biology.
    Nat Neurosci. 2001 Nov;4 Suppl:1155-6 PMID: 11687821
  7. Shift in the ratio of three-repeat tau and four-repeat tau mRNAs in individual cholinergic basal forebrain neurons in mild cognitive impairment and Alzheimer's disease.
    J Neurochem. 2006 Mar;96(5):1401-8 PMID: 16478530
  8. Selection and validation of microarray candidate genes from subregions and subnuclei of the brain.
    Methods. 2003 Dec;31(4):290-300 PMID: 14597313
  9. A primary culture system for functional analysis of C. elegans neurons and muscle cells.
    Neuron. 2002 Feb 14;33(4):503-14 PMID: 11856526
  10. A gene expression atlas of the central nervous system based on bacterial artificial chromosomes.
    Nature. 2003 Oct 30;425(6961):917-25 PMID: 14586460
  11. Expression profiles of multiple genes in single neurons of Alzheimer's disease.
    Proc Natl Acad Sci U S A. 1998 Aug 4;95(16):9620-5 PMID: 9689130
  12. Divergence between motoneurons: gene expression profiling provides a molecular characterization of functionally discrete somatic and autonomic motoneurons.
    Physiol Genomics. 2006 Feb 14;24(3):276-89 PMID: 16317082
  13. Gene expression profiles of laser-captured adjacent neuronal subtypes.
    Nat Med. 1999 Jan;5(1):117-22 PMID: 9883850
  14. Gene expression tomography.
    Physiol Genomics. 2002 Feb 28;8(2):159-67 PMID: 11875194
  15. Gene discovery in genetically labeled single dopaminergic neurons of the retina.
    Proc Natl Acad Sci U S A. 2004 Apr 6;101(14):5069-74 PMID: 15047890
  16. Microarray identification of FMRP-associated brain mRNAs and altered mRNA translational profiles in fragile X syndrome.
    Cell. 2001 Nov 16;107(4):477-87 PMID: 11719188
  17. The problem of neuronal cell types: a physiological genomics approach.
    Trends Neurosci. 2006 Jun;29(6):339-45 PMID: 16714064
  18. Analysis of gene expression in single live neurons.
    Proc Natl Acad Sci U S A. 1992 Apr 1;89(7):3010-4 PMID: 1557406
  19. Identification of thermosensory and olfactory neuron-specific genes via expression profiling of single neuron types.
    Curr Biol. 2004 Dec 29;14(24):2245-51 PMID: 15620651
  20. Noncoding RNAs in the mammalian central nervous system.
    Annu Rev Neurosci. 2006;29:77-103 PMID: 16776580
  21. Single-cell microarray analysis in hippocampus CA1: demonstration and validation of cellular heterogeneity.
    J Neurosci. 2003 May 1;23(9):3607-15 PMID: 12736331
  22. Transcriptional profiling reveals strict boundaries between hippocampal subregions.
    J Comp Neurol. 2001 Dec 17;441(3):187-96 PMID: 11745644
  23. Imaging physiologic dysfunction of individual hippocampal subregions in humans and genetically modified mice.
    Neuron. 2000 Dec;28(3):653-64 PMID: 11163257
  24. Laser capture microdissection.
    Science. 1996 Nov 8;274(5289):998-1001 PMID: 8875945
  25. Clusters of internally primed transcripts reveal novel long noncoding RNAs.
    PLoS Genet. 2006 Apr;2(4):e37 PMID: 16683026
  26. Technology Insight: querying the genome with microarrays--progress and hope for neurological disease.
    Nat Clin Pract Neurol. 2006 Mar;2(3):147-58 PMID: 16932541
  27. A gene expression fingerprint of C. elegans embryonic motor neurons.
    BMC Genomics. 2005;6:42 PMID: 15780142
  28. Analysis of mammalian central nervous system gene expression and function using bacterial artificial chromosome-mediated transgenesis.
    Hum Mol Genet. 2000 Apr 12;9(6):937-43 PMID: 10767317
  29. Microarray analysis of fluoro-gold labeled rat dopamine neurons harvested by laser capture microdissection.
    J Neurosci Methods. 2005 Apr 30;143(2):95-106 PMID: 15814141
  30. Dendritic mRNAs encode diversified functionalities in hippocampal pyramidal neurons.
    BMC Neurosci. 2006;7:17 PMID: 16503994
  31. Expression profiling of GABAergic motor neurons in Caenorhabditis elegans.
    Curr Biol. 2005 Feb 22;15(4):340-6 PMID: 15723795
  32. Brain microarray: finding needles in molecular haystacks.
    J Neurosci. 2005 Nov 9;25(45):10341-6 PMID: 16280569
  33. Amygdala-enriched genes identified by microarray technology are restricted to specific amygdaloid subnuclei.
    Proc Natl Acad Sci U S A. 2001 Apr 24;98(9):5270-5 PMID: 11320257
  34. Molecular characterization of schizophrenia viewed by microarray analysis of gene expression in prefrontal cortex.
    Neuron. 2000 Oct;28(1):53-67 PMID: 11086983
  35. FACS-array profiling of striatal projection neuron subtypes in juvenile and adult mouse brains.
    Nat Neurosci. 2006 Mar;9(3):443-52 PMID: 16491081
  36. The proteomes of neurotransmitter receptor complexes form modular networks with distributed functionality underlying plasticity and behaviour.
    Mol Syst Biol. 2006;2:2006.0023 PMID: 16738568
  37. Single-cell transcriptional analysis of neuronal progenitors.
    Neuron. 2003 Apr 24;38(2):161-75 PMID: 12718852
  38. Gene expression profile of spinal motor neurons in sporadic amyotrophic lateral sclerosis.
    Ann Neurol. 2005 Feb;57(2):236-51 PMID: 15668976
  39. Progress in the use of microarray technology to study the neurobiology of disease.
    Nat Neurosci. 2004 May;7(5):434-9 PMID: 15114354
  40. High-throughput imaging of brain gene expression.
    Genome Res. 2002 Feb;12(2):244-54 PMID: 11827944
  41. Molecular dissection of the amygdala and its relevance to autism.
    Genes Brain Behav. 2003 Oct;2(5):282-94 PMID: 14606693
  42. Molecular taxonomy of major neuronal classes in the adult mouse forebrain.
    Nat Neurosci. 2006 Jan;9(1):99-107 PMID: 16369481
  43. Replaceable neurons and neurodegenerative disease share depressed UCHL1 levels.
    Proc Natl Acad Sci U S A. 2005 May 31;102(22):8036-41 PMID: 15911766
  44. Gene expression analysis of the late embryonic mouse cerebral cortex using DNA microarray: identification of several region- and layer-specific genes.
    Cereb Cortex. 2004 Sep;14(9):1031-44 PMID: 15142957
  45. Regional and strain-specific gene expression mapping in the adult mouse brain.
    Proc Natl Acad Sci U S A. 2000 Sep 26;97(20):11038-43 PMID: 11005875
  46. Gene expression profiles of cholinergic nucleus basalis neurons in Alzheimer's disease.
    Neurochem Res. 2002 Oct;27(10):1035-48 PMID: 12462403
  47. Fezl is required for the birth and specification of corticospinal motor neurons.
    Neuron. 2005 Sep 15;47(6):817-31 PMID: 16157277
  48. Amplification of mRNAs from single, fixed, TUNEL-positive cells.
    Biotechniques. 1998 Oct;25(4):566-8, 570 PMID: 9793634
  49. Molecular analysis of gene expression in the developing pontocerebellar projection system.
    Neuron. 2002 Oct 24;36(3):417-34 PMID: 12408845
  50. Progress in realizing the promise of microarrays in systems neurobiology.
    Neuron. 2005 Jan 20;45(2):183-5 PMID: 15664168
  51. Regional patterns of gene expression in human and chimpanzee brains.
    Genome Res. 2004 Aug;14(8):1462-73 PMID: 15289471
  52. Adult mouse brain gene expression patterns bear an embryologic imprint.
    Proc Natl Acad Sci U S A. 2005 Jul 19;102(29):10357-62 PMID: 16002470
  53. Nuclei and subnuclei gene expression profiling in mammalian brain.
    Brain Res. 2002 Jul 5;943(1):38-47 PMID: 12088837
  54. A general framework for weighted gene co-expression network analysis.
    Stat Appl Genet Mol Biol. 2005;4:Article17 PMID: 16646834
  55. Expression profile of transcripts in Alzheimer's disease tangle-bearing CA1 neurons.
    Ann Neurol. 2000 Jul;48(1):77-87 PMID: 10894219
  56. A functional genomics guide to the galaxy of neuronal cell types.
    Nat Neurosci. 2006 Jan;9(1):10-2 PMID: 16378087
  57. Multiplex three-dimensional brain gene expression mapping in a mouse model of Parkinson's disease.
    Genome Res. 2002 Jun;12(6):868-84 PMID: 12045141
  58. A gene-coexpression network for global discovery of conserved genetic modules.
    Science. 2003 Oct 10;302(5643):249-55 PMID: 12934013
  59. Isolation of mRNA from specific tissues of Drosophila by mRNA tagging.
    Nucleic Acids Res. 2005;33(17):e148 PMID: 16204451
  60. Model-guided microarray implicates the retromer complex in Alzheimer's disease.
    Ann Neurol. 2005 Dec;58(6):909-19 PMID: 16315276
  61. Identification of genes expressed in C. elegans touch receptor neurons.
    Nature. 2002 Jul 18;418(6895):331-5 PMID: 12124626
  62. Laser microdissection in CNS research.
    Drug Discov Today. 2005 Sep 1;10(17):1167-74 PMID: 16182209
  63. Mice, microarrays, and the genetic diversity of the brain.
    Proc Natl Acad Sci U S A. 2000 Sep 26;97(20):10676-8 PMID: 11005850
  64. Genome scale mapping of brain gene expression.
    Biol Psychiatry. 2003 Jun 15;53(12):1069-74 PMID: 12814858
  65. Gene expression profiles in microdissected neurons from human hippocampal subregions.
    Brain Res Mol Brain Res. 2004 Aug 23;127(1-2):105-14 PMID: 15306126
  66. Microarray technology: a review of new strategies to discover candidate vulnerability genes in psychiatric disorders.
    Am J Psychiatry. 2003 Apr;160(4):657-66 PMID: 12668351
Article Info
Journal
The Journal of physiology
Abbr.
J Physiol
ISSN
0022-3751
DOI
10.1113/jphysiol.2006.112623
Published
2006-09-01
Epub
2006-00-29
Pages
353-9
Language
English
Region
England
NLM ID
0266262
PMCID
PMC1819448
Subset
IM
External Links
PubMed source DOI: 10.1113/jphysiol.2006.112623 PMC Full Text View journal details
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