1: Oncol Rep. 2005 Sep;14(3):797-800. 

Comparative genomics on SOX2 orthologs.

Katoh Y, Katoh M.

M&M Medical BioInformatics, Hongo 113-0033, Japan.

SOX2 and POU5F1 (OCT3 or OCT4) transcription factors are implicated in FGF4
expression in embryonic stem (ES) cells. SOX2, POU5F1, and FGF4 are key
molecules for the integrome network in oncology and stem cell biology. SOX2 gene
at human chromosome 3q26.33, SOX1 gene at 13q34, and SOX3 gene at Xq27.1
constitute a subfamily among the SOX gene family. Here, rat Sox2 and Xenopus
sox2 genes were identified and characterized by using bioinformatics for
comparative genomics and comparative proteomics analyses. Rat Sox2 gene,
encoding a 319-aa protein, was located around the nucleotide position
73213-75621 of rat genome sequence AC123231.4. Xenopus tropicalis sox2 complete
coding sequence, encoding a 311-aa protein, was derived from CR760314.1 cDNA.
Rat Sox2 showed 98.4%, 97.8%, 92.2%, 88.1% and 86.8% total amino-acid identity
with mouse Sox2, human SOX2, chicken sox2, Xenopus sox2 and zebrafish sox2,
respectively. SOX123C domain was identified as the novel domain corresponding to
the C-terminal region conserved among SOX1, SOX2 and SOX3 orthologs. Vertebrate
SOX1, SOX2 and SOX3 orthologs were found consisting of HMG box and SOX123C
domain. SOX9, TCF/LEF, POU2F1 and COMP1 binding sites were conserved among human
SOX2 promoter, rat Sox2 promoter, and mouse Sox2 promoter. SOX2 mRNA was
expressed in ES cells, fetal brain, anaplastic oligodendroglioma,
rhabdomyosarcoma, and small cell lung carcinoma. Due to the pivotal role of SOX2
in the early embryogenesis, SOX2 promoter and SOX2 protein were well conserved
during vertebrate evolution. This is the first report on comparative integromics
analyses on the SOX2 orthologs.

PMID: 16077994 [PubMed - indexed for MEDLINE]


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2: Int J Oncol. 2005 May;26(5):1435-40. 

Comparative genomics on Vangl1 and Vangl2 genes.

Katoh Y, Katoh M.

M and M Medical BioInformatics, Hongo 113-0033, Japan.

WNT signals are transduced to the beta-catenin pathway or the planar cell
polarity (PCP) pathway. WNT - beta-catenin pathway is implicated in
carcinogenesis, while WNT-PCP pathway is implicated in cell motility and
metastasis. Drosophila Van Gogh (Vang), Frizzled (Fz), Starry night (Stan),
Prickle (Pk) and Diego (Dgo) are PCP signaling molecules. Vangl1 (Strabismus 2)
and Vangl2 (Strabismus 1 or Ltap) are mammalian homologs of Drosophila Vang
interacting with PRICKLE1, PRICKLE2, ANKRD6, DVL1, DVL2, DVL3, KAI1 and MAGI3.
Here we identified and characterized rat Vangl1 and Vangl2 genes by using
bioinformatics. Rat Vangl1 gene, consisting of eight exons, was located within
AC098913.7 and AC108524.6 genome sequences. Rat Vangl2 gene, consisting of eight
exons, was located within AC118856.3 and AC115243.5 genome sequences.
Exon-intron structure of mammalian Vangl1 and Vangl2 orthologs was well
conserved. E47 and double ELK1-binding sites were conserved among promoters of
mammalian Vangl1 orthologs. PAX4, NFkappaB, HNF4, SOX9, RFX1, and POU2F1
(OCT1)-binding sites were conserved among promoters of mammalian Vangl2
orthologs. Rat Vangl1 (526 aa) and Vangl2 (521 aa) were four-transmembrane
proteins with 71.5% total-amino-acid identity. Ser cluster motif
(SxxSxxSxxSxxSxxS) in the N-terminal cytoplasmic region and PDZ-binding motif in
the C-terminal cytoplasmic tail were evolutionarily conserved among vertebrate
Vangl1 and Vangl2 orthologs. This is the first report on rat Vangl1 and Vangl2
genes as well as on comparative genomics for Vangl1 and Vangl2 orthologs.

PMID: 15809738 [PubMed - indexed for MEDLINE]


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