Selection of neural differentiation-specific genes by comparing profiles of random differentiation.
Differentiation of embryonic stem cells (ESCs) into neurons requires a high level of transcriptional regulation. To further understand the transcriptional regulation of neural differentiation of ESCs, we used oligonucleotide microarray to examine the gene expressions of the guided differentiation (GD) model for dopaminergic (DA) neurons from mouse ESCs. We also determined the gene expression profiles of the random differentiation (RD) model of mouse ESCs into embryoid bodies. From K-means clustering analysis using the expression patterns of the two models, most of the genes (1,282 of 1,884 genes [68.0%]) overlapped in their expression patterns. Six hundred twenty-two differentially expressed genes (DEGs) from the GD model by random variance F-test were classified by their critical molecular functions in neurogenesis and DNA replication (Gene Ontology analysis). However, 400 genes among GD-DEGs (64.3%) showed a high correlation with RD in Spearman's correlation analysis (Spearman's coefficient p(s) >or= .6). The genes showing marginal correlation (-.4 < p(s) < .6) were present in the early stages of differentiation of both GD and RD, which were non-specific to brain development. Finally, we distinguished 66 GD-specific genes based on p(s) <or= -.4, the molecular functions of which were related mainly to vesicle formation, neurogenesis, and transcription factors. From among these GD-specific genes, we confirmed the expression of Serpini1 and Rab33a in P19 differentiation models and adult brains. From these results, we identified the specific genes required for neural differentiation by comparing gene expressions of GD with RD; these would potentially be the highly specific candidate genes necessary for differentiation of DA neurons.
Lee
Min Su
MS
Department of Computer Science and Engineering, Ewha Womans University, Seoul, Korea.
Jun
Dae-Hyun
DH
Hwang
Chang-Il
CI
Park
Seung Soo
SS
Kang
Jason Jongho
JJ
Park
Hyun-Seok
HS
Kim
Jihoon
J
Kim
Ju Han
JH
Seo
Jeong-Sun
JS
Park
Woong-Yang
WY
D000818:Animals; D002454:Cell Differentiation / Q000235:genetics* / Q000502:physiology*; D002460:Cell Line; D016000:Cluster Analysis; D004248:DNA (Cytosine-5-)-Methyltransferases / Q000235:genetics; D015254:DNA Modification Methylases / Q000235:genetics / Q000378:metabolism; D053595:Embryonic Stem Cells / Q000166:cytology / Q000502:physiology; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental / Q000235:genetics*; D018392:Genomic Imprinting; D051379:Mice; D008957:Models, Genetic; D009474:Neurons / Q000166:cytology / Q000502:physiology*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods
D015254:DNA Modification Methylases; C498796:Dnmt3l protein, mouse; D004248:DNA (Cytosine-5-)-Methyltransferases