title: MicroRNA gene expression signatures in the developing neural tube.
abstract: BACKGROUND
  Neurulation requires precise, spatio-temporal expression of numerous genes and coordinated interaction of signal transduction and gene regulatory networks, disruption of which may contribute to the etiology of neural tube defects (NTDs). MicroRNAs (miRNAs) are key modulators of cell and tissue differentiation. To define potential roles of miRNAs in development of the murine neural tube (NT), miRNA microarray analysis was conducted to establish expression profiles, and identify miRNA target genes and functional gene networks.
  
  
  METHODS
  The miRNA expression profiles in murine embryonic NTs derived from gestational days 8.5, 9.0, and 9.5 were defined and compared utilizing miRXplore microarrays from Miltenyi Biotec GmbH, Bergisch Gladbach, Germany. Gene expression changes were verified by TaqMan quantitative Real-Time PCR. The clValid R package and the UPGMA (hierarchical) clustering method were utilized for cluster analysis of the microarray data. Functional associations among selected miRNAs were examined via Ingenuity Pathway Analysis.
  
  
  RESULTS
  The miRXplore chips enabled examination of 609 murine miRNAs. Expression of approximately 12% of these was detected in murine embryonic NTs. Clustering analysis revealed several developmentally regulated expression clusters among these expressed genes. Target analysis of differentially expressed miRNAs enabled identification of numerous target genes associated with cellular processes essential for normal NT development. Utilization of Ingenuity Pathway Analysis revealed interactive biologic networks which connected differentially expressed miRNAs with their target genes, and highlighted functional relationships.
  
  
  CONCLUSIONS
  The present study defined unique gene expression signatures of a range of miRNAs in the developing NT during the critical period of NT morphogenesis. Analysis of miRNA target genes and gene interaction pathways revealed that specific miRNAs might direct expression of numerous genes encoding proteins, which have been shown to be indispensable for normal neurulation. This study is the first to identify miRNA expression profiles and their potential regulatory networks in the developing mammalian NT.
authors.affiliation: Department of Molecular, Cellular and Craniofacial Biology, University of Louisville Birth Defects Center, 501 South Preston Street, Louisville, KY 40292, USA.
authors.forename: Partha
authors.initials: P
authors.lastname: Mukhopadhyay
authors.forename: Guy
authors.initials: G
authors.lastname: Brock
authors.forename: Savitri
authors.initials: S
authors.lastname: Appana
authors.forename: Cynthia
authors.initials: C
authors.lastname: Webb
authors.forename: Robert M
authors.initials: RM
authors.lastname: Greene
authors.forename: M Michele
authors.initials: MM
authors.lastname: Pisano
mesh_terms: D000818:Animals; D002454:Cell Differentiation / Q000235:genetics; D016000:Cluster Analysis; D005260:Female; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D053263:Gene Regulatory Networks; D008297:Male; D051379:Mice; D008813:Mice, Inbred ICR; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D054259:Neural Tube / Q000196:embryology*; D009436:Neural Tube Defects / Q000196:embryology / Q000235:genetics; D054261:Neurulation / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D038081:Organogenesis / Q000235:genetics; D016133:Polymerase Chain Reaction; D011247:Pregnancy; D015398:Signal Transduction
chemical_list: D035683:MicroRNAs