title: Genomewide expression analysis in zebrafish mind bomb alleles with pancreas defects of different severity identifies putative Notch responsive genes.
abstract: BACKGROUND
  Notch signaling is an evolutionarily conserved developmental pathway. Zebrafish mind bomb (mib) mutants carry mutations on mib gene, which encodes a RING E3 ligase required for Notch activation via Delta/Jagged ubiquitylation and internalization.
  
  
  RESULTS
  We examined the mib mutants for defects in pancreas development using in situ hybridization and GFP expression analysis of pancreas-specific GFP lines, carried out the global gene expression profile analysis of three different mib mutant alleles and validated the microarray data using real-time PCR and fluorescent double in situ hybridization. Our study showed that the mib mutants have diminished exocrine pancreas and this defect was most severe in mib(ta52b) followed by mib(m132) and then mib(tfi91), which is consistent with the compromised Notch activity found in corresponding mib mutant alleles. Global expression profile analysis of mib mutants showed that there is a significant difference in gene expression profile of wt and three mib mutant alleles. There are 91 differentially expressed genes that are common to all three mib alleles. Through detailed analysis of microarray data, we have identified several previously characterized genes and some putative Notch-responsive genes involved in pancreas development. Moreover, results from real-time PCR and fluorescent double in situ hybridization were largely consistent with microarray data.
  
  
  CONCLUSIONS
  This study provides, for the first time, a global gene expression profile in mib mutants generating useful genomic resources and providing an opportunity to identify the function of novel genes involved in Notch signaling and Notch-regulated developmental processes.
authors.affiliation: Laboratory of Developmental Signalling and Patterning, Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore, Singapore.
authors.forename: Ashok
authors.initials: A
authors.lastname: Hegde
authors.forename: Nick Chuanxin
authors.initials: NC
authors.lastname: Qiu
authors.forename: Xuehui
authors.initials: X
authors.lastname: Qiu
authors.forename: Steven Hao-Kee
authors.initials: SH
authors.lastname: Ho
authors.forename: Kenny Qi-Ye
authors.initials: KQ
authors.lastname: Tay
authors.forename: Joshy
authors.initials: J
authors.lastname: George
authors.forename: Felicia Soo Lee
authors.initials: FS
authors.lastname: Ng
authors.forename: Kunde Ramamoorthy
authors.initials: KR
authors.lastname: Govindarajan
authors.forename: Zhiyuan
authors.initials: Z
authors.lastname: Gong
authors.forename: Sinnakaruppan
authors.initials: S
authors.lastname: Mathavan
authors.forename: Yun-Jin
authors.initials: YJ
authors.lastname: Jiang
mesh_terms: D000483:Alleles; D000818:Animals; D020869:Gene Expression Profiling; D017404:In Situ Hybridization, Fluorescence; D009154:Mutation; D010179:Pancreas / Q000002:abnormalities*; D016133:Polymerase Chain Reaction; D051880:Receptors, Notch / Q000502:physiology*; D044767:Ubiquitin-Protein Ligases / Q000235:genetics*; D015027:Zebrafish / Q000235:genetics*; D029961:Zebrafish Proteins / Q000235:genetics*
chemical_list: D051880:Receptors, Notch; D029961:Zebrafish Proteins; D044767:Ubiquitin-Protein Ligases; C471932:mib1 protein, zebrafish