Biomedical subjects

Masuko Katoh

Publications and source records attributed to Masuko Katoh.

At least 73 records · Page 4Linked to original sources

PubMed2004

Identification and characterization of human FCHO2 and mouse Fcho2 genes in silico.

FNBP1, FNBP1L, CIP4/TRIP10, FNBP2, SRGAP1/ARHGAP13, SRGAP2/ARHGAP14, ARHGAP4, FCHSD1, and FCHSD2 constitute the FCFBS superfamily characterized by FES-CIP4 homology (FCH) domain, Formin-binding FNBP1-FNBP2 homology (FBH) domain, and SRC homology 3 (SH3) domain. During genome-wide searching for human genes encoding FCH domain molecules, we identified the FCHO2 gene by using bioinformatics. DKFZp451B033 (AL831971.1) was the representative cDNA derived from human FCHO2 gene, while FLJ32208 (AK056770.1) was a chimeric cDNA generated by the recombination between FCHO2 and CSH1 genes. MGC63242 (BC052456.1) rather than 5832424M12 (AK031041.1) was the representative cDNA derived from mouse Fcho2 gene. FCHO2 gene, consisting of 26 exons, was mapped to human chromosome 5q13.2. Human FCHO2 (810 aa) showed 94.6% total-amino-acid identity with mouse Fcho2 (809 aa), and 50.4% total-amino-acid identity with human FCHO1. Drosophila CG8176 (NP_788613.1) and C. elegans 2B609 (NP_493947.1) were homologs of mammalian FCHO2 and FCHO1. FCHO-homologous (FOH) domain (codon 527-810 of human FCHO2) was identified as the novel domain conserved among FCHO homologs. Human FCHO2, FCHO1, Drosophila CG8176 and C. elegans 2B609 were found consisting of N-terminal FCH domain and C-terminal FOH domain. This is the first report on identification and characterization of evolutionarily conserved FCHO homologs as well as the novel FOH domain.

Amino Acid Sequence↗

PubMed2004

Identification and characterization of ARHGAP24 and ARHGAP25 genes in silico.

RhoGAP family proteins, encoded by ARHGAP family genes, are negative regulators of Rho family GTPases, which are implicated in actin remodeling, cell polarity control, and cell migration. Based on the homology with ARHGAP22, we identified and characterized two novel ARHGAP family genes, ARHGAP24 and ARHGAP25. FLJ33877 cDNA (AK091196.1) and aberrant DKFZp564- B1162 cDNA (NM_031305.1) were derived from human ARHGAP24 gene. Two isoforms of KIAA0053 type (D29642.1) and BM927439 type were derived from human ARHGAP25 gene due to alternative splicing (alternative promoter). Mouse 0610025G21 (NM_029270.1) and A130039I20 (AK037710.1) were representative cDNAs derived from mouse Arhgap24 and Arhgap25 genes, respectively. Exon-intron structure of ARHGAP25 gene at human chromosome 2p13 was slightly divergent from that of ARHGAP22 and ARHGAP24 genes. MGC35285, MAPK8 and C10orf64 genes linked to ARHGAP22 gene were paralogs of PTPN13, MAPK10 and WDFY3 genes linked to ARHGAP24 gene, respectively. MGC35285-ARHGAP22-MAPK8-C10orf64 locus at human chromosome 10q11 and the WDFY3-ARHGAP24-MAPK10-PTPN13 locus at human chromosome 4q21 were paralogous regions (paralogons) within the human genome. Human ARHGAP24 showed 91.8% and 48.6% total-amino-acid identity with mouse Arhgap24 and human ARHGAP22, respectively. Human ARHGAP25 showed 86.1% and 40.8% total-amino-acid identity with mouse Arhgap25 and human ARHGAP22, respectively. ARHGAP22, ARHGAP24 and ARHGAP25 were found to constitute the RhoGAP subfamily featured by Pleckstrin homology (PH) domain and C-terminal Coiled-coil domain. This is the first report on identification and characterization of the ARHGAP24 and ARHGAP25 genes.

Alternative Splicing↗

PubMed2004

Identification and characterization of TMEM24 family genes in silico.

MLL gene at human chromosome 11q23.3 is frequently rearranged or amplified in hematological malignancies, while PHLDB1, BCL9L, FOXN5 (FOXR1), RNF26, and MFRP genes linked to MLL gene are deleted in neuroblastoma. Here, we characterized the TMEM24 gene family by using bioinformatics. KIAA0285 gene within the 11q23.3 commonly deleted region of neuroblastoma was designated TMEM24, because KIAA0285 gene product was a 707-aa (or 706-aa) protein with N-terminal short cytoplasmic region, single transmembrane domain, and C-terminal large extracellular region. C21orf25 (NM_199050.1) encoded an N-terminally truncated 541-aa protein homologous to TMEM24. Complete coding sequence of C21orf25 was determined by assembling exons 1 and 2 within human genome sequence AP001745 and NM_199050.1 cDNA. Full-length C21orf25 encoded a 696-aa TMEM24-related protein with similar membrane topology. Exon-intron structure was conserved between TMEM24 and C21orf25 genes. TMEM24-ABCG4 locus at human chromosome 11q23.3 and C21orf25-ABCG1 locus at human chromosome 21q22.3 were paralogous regions (paralogons) with insertions of other genes due to recombination during evolution. Mouse 1300006O23 (BC060156.1) and 5830404H04 (NM_174847.1) cDNAs were derived from orthologs of human TMEM24 and C21orf25 genes, respectively. TMEM24 homologous domains (TM24H1 and TM24H2) were identified as novel domains conserved among TMEM24, C21orf25, 1300006O23, and 5830404H04. Human TMEM24, C21orf25 and their mouse homologs were type II transmembrane proteins with extracellular TM24H1 and TM24H2 domains. This is the first report on identification and characterization of the TMEM24 family.

Amino Acid Sequence↗

PubMed2004

Identification and characterization of human DFNA5L, mouse Dfna5l, and rat Dfna5l genes in silico.

An evolutionary recombination hotspot around the GSDML-GSDM locus at human chromosome 17q21 is closely linked to an oncogenomic recombination hotspot around the PPP1R1B-STARD3-TCAP-PNMT-PERLD1 (MGC9753)-ERBB2-C17orf37 (MGC14832)-GRB7 locus at human chromosome 17q12. Here, we identified DFNA5L (GSDMDC1) gene related to GSDM and GSDML genes by using bioinformatics. Human DFNA5L gene at chromosome 8q24.3 was linked to ZC3HDC3, PP3856, EEF1D, and TIGD5 genes. NM_024736.4 (AK127941.1), AK022212.1, BC008904.2, and BC069000.1 cDNAs were derived from human DFNA5L gene. BC008904.2 was the representative human DFNA5L cDNA, while NM_024736.4 was an aberrant human DFNA5L cDNA with frame shifts due to the retention of introns 1, 3, 4, 5 and 8. Human DFNA5L mRNA was expressed in placenta, pancreatic cancer, prostate cancer, melanoma, salivary gland tumor, Jarkat T cells, and Ramos B cells. Complete coding sequence of rat Dfna5l cDNA was determined by assembling 11 exons of rat Dfna5l gene within AC120830.4 genome sequence, and that of mouse Dfna5l cDNA was derived from 1810036L03 (NM_026960.1). Exon-intron boundaries were conserved among human DFNA5L and rodent Dfna5l genes. Human DFNA5L (484 aa) showed 59.5% total-amino-acid identity with rat Dfna5l (488 aa), and 58.7% total-amino-acid identity with mouse Dfna5l (487 aa). DFNA5L orthologs were DNFA5 (GSDM) domain containing DFNA5 DC or GSDMDC proteins with Coiled-coil and Leucine zipper domains. Human DFNA5L, GSDM, GSDML, MLZE, DFNA5 and their mammalian orthologs were found to constitute the DFNA5 DC (GSDMDC) family. Because DFNA5 and MLZE are cancer-associated genes, DFNA5L, GSDM, and GSDML are predicted cancer associated genes.

Amino Acid Sequence↗

PubMed2004

Germ-line mutation of Foxn5 gene in mouse lineage.

Amplified region (amplicon) around MLL gene is closely linked to the 11q23.3 commonly deleted region of neuroblastoma, which includes cancer-associated genes such as PHLDB1 (LL5A), BCL9L, FOXN5 (FOXR1), CBL, MFRP, and PVRL1 (Nectin) genes. FOXN6 (FOXR2) gene at human chromosome Xp11.21 is generated due to retrotransposition of ancestral Foxn5 gene during evolution. FOXN5 and FOXN6 orthologs share the common domain structure consisting of FN56 and Forhead-box (FOX) domains. Here, we identified and characterized mouse Foxn5 gene by using bioinformatics. Mouse Foxn5, consisting of six exons, was located within mouse genome sequences AC122428.4 and AC125129.5. Foxn5 locus at mouse chromosome 9B was synthenic to rat chromosome 8q22 and human chromosome 11q23.3. Mouse Foxn5 (180 aa) was C-terminally truncated compared with rat Foxn5 and human FOXN5. Mouse 'Foxn5' protein without FOX domain was generated due to a frame shift introduced by germ-line one-base deletion within exon 3. Mouse Foxn5 mRNA was expressed in embryonic germ cells and fertilized eggs. Germ-line mutation of Foxn5 gene in the mouse lineage might lead to divergent scenario of early embryogenesis between mouse and rat through the deregulation of Foxn5 target genes in mouse early embryos, and explain the difficulty in manipulation of rat embryonic stem (ES) cells based on the mouse equivalent system. This is the first report on identification and characterization of mouse Foxn5 gene as well as on species specific germ-line mutation of the Fox family gene.

Amino Acid Sequence↗

PubMed2004

Characterization of FMN2 gene at human chromosome 1q43.

Mouse Formin (Fmn1) is an actin regulator interacting with Profilin, SRC, EMS1, FNBP1, FNBP2, FNBP3, FNBP4, WBP4 and alpha-catenin. FMN1, FHOD1, FHOD3, GRID2IP and FHDC1 are non-FDD-type Formin homology proteins, while FMNL1, FMNL2, FMNL3, DIAPH1, DIAPH2, DIAPH3, DAAM1 and DAAM2 are FDD-type Formin homology proteins. Here, we characterized human FMN2 gene by using bioinformatics. Complete coding sequence of human FMN2 cDNA was determined by assembling AL359918, AL513342, AL590490, AL646016 genome sequences, AF218941 partial cDNA, and AF218942 partial cDNA. FMN2 mRNA was expressed in fetal brain, adult whole brain, hypothalamus, retina, pancreatic islet and germinal-center B cells. Among various human tumors, FMN2 mRNA was expressed in parathyloid tumor, glioblastoma, retinoblastoma and chondrosarcoma. Human FMN2 (1722 aa) showed 74.7% total-amino-acid identity with mouse Fmn2, and 31.9% total-amino-acid identity with human FMN1. Although N-terminal half was divergent between FMN2 orthologs and FMN1 orthologs, FH1 and FH2 domains were conserved among FMN2 and FMN1 orthologs. Exon-intron structure was conserved between FMN2 and FMN1 genes. RYR2-FMN2-CKTSF1B2 (PRDC) locus at human chromosome 1q43 and RYR3-FMN1-CKTSF1B1 (Gremlin) locus at human chromosome 15q13-q14 were paralogous regions (paralogons) within the human genome. This is the first report on comprehensive characterization of the human FMN2 gene.

Amino Acid Sequence↗

PubMed2004

Characterization of RUSC1 and RUSC2 genes in silico.

We have previously cloned (or identified) and characterized novel genes encoding SH3 domain proteins, such as MAP3K10, FNBP1L, FNBP2, FCHSD1, FCHSD2, LASP2 and MPP7. During characterization of SH3 domain molecules, we found the existence of an N-terminally- truncated 433-aa RUSC1 protein (NP_055143.2). Here, we characterized RUSC1 and RUSC2 genes by using bioinformatics. IMAGE 5204626 (BC025680.1) and KIAA0375 (AB002373.2) were representative cDNAs derived from human RUSC1 and RUSC2 genes, respectively. 2210403N08 (AK039664.1) and MGC73483 (BC056360.1) cDNAs were derived from mouse Rusc1 gene, while Kiaa0375 (AK122263.1) cDNA was derived from mouse Rusc2 gene. RUSC1 gene, consisting of 11 exons, was mapped to human chromosome 1q22. RUSC2 gene, consisting of 12 exons was mapped to human chromosome 9p13. Human RUSC1 gene as well as mouse Rusc1 gene were found to encode two isoforms with or without 411-bp exon 3 due to alternative splicing of exon-skipping type. RUSC1 isoform 1 (1039 aa) and RUSC2 (1516 aa) showed 30.5% total amino-acid identity. Human RUSC1, RUSC2, mouse Rusc1 and Rusc2 proteins were found to share the common domain structure, consisting of RUN, Leucine zipper, and SH3 domains. RUSC1, RUSC2, RIPX, RUFY1, RUFY2, RUTBC1, RUTBC2, RUTBC3, RUB6IP1, and PLEKHM1 were RUN domain proteins within the human proteome. This is the first report on comprehensive characterization of RUSC1 and RUSC2 orthologs.

Adaptor Proteins, Signal Transducing↗

PubMed2004

Identification and characterization of human CXXC10 gene in silico.

CXXC4 gene encodes Dishevelled-binding protein, functioning as a negative regulator of WNT - beta-catenin signaling pathway. CXXC5, encoding CXXC finger (PHD domain) protein, is the paralog of CXXC4. CXXC6, MLL, DNMT1, ASXL1, ASXL2, and ASXL3 are cancer-associated genes belonging to the CXXC gene family. Here, we identified and characterized CXXC10 (CXXL4L or CXXC6L) gene by using bioinformatics. Complete coding sequence of human CXXC10 cDNA was determined by assembling AI438961 EST, AC073046.7 genome sequence, BX492895 EST, and MGC22014 5'-truncated cDNA. CXXC10 gene products derived from nucleotide positions 428-739 and 811-3624 were designated CXXC10-1 and CXXC10-2, respectively. CXXC10-1 (103 aa) was homologous to CXXC4 and CXXC6 within the CXXC domain. CXXC10-2 (937 aa) was homologous to CXXC6, and KIAA1546. Complete coding sequence of KIAA1546 cDNA was determined by assembling BF900449 EST, IMAGE3536481 partial cDNA, and KIAA1546 5'-truncated cDNA (AB046766.1). LCXH1 domain (codon 1-273 of CXXC10-2) and LCXH2 domain (codon 778-854 of CXXC10-2) were conserved among CXXC10-2, KIAA1546, and CXXC6. CXXC4 and KIAA1546 genes were closely linked in head to head manner with an interval of about 700 kb. CXXC10 locus at 2p13.1, CXXC4-KIAA1546 locus at 4q24, and CXXC6 locus at 10q21.3 were paralogous regions within the human genome. Because CXXC4 and KIAA1546 genes were located in the opposite direction, intragenetic inversion might be generated within the ancestral CXXC4-KIAA1546 locus during evolution. This is the first report on CXXC10 gene as well as on the CXXC10, CXXC4-KIAA1546, and CXXC6 paralogs.

Amino Acid Sequence↗

PubMed2004

Characterization of human ARHGAP10 gene in silico.

ARHGAP family genes encode Rho/Rac/Cdc42-like GTPase activating proteins with RhoGAP domain. Here, we characterized human ARHGAP10 gene by using bioinformatics. Complete coding sequence of ARHGAP10 isoform A was determined by assembling nucleotide position 1-725 of FLJ41791 cDNA (AK123785.1) and 5'-truncated IMAGE4310652 cDNA (BC011920.2). Nucleotide position 240-2600 of ARHGAP10 isoform A was identical to GRAF2 cDNA (AB050785.1). Complete coding sequence of ARHGAP10 isoform B was derived from FLJ41791 cDNA. ARHGAP10 isoform A, consisting of exons 1-23, encoded full-length protein (786 aa). ARHGAP10 isoform B, consisting of exons 1-5 and intron 5, encoded C-terminally truncated protein (163 aa). ARHGAP10 gene was found encoding two isoforms due to alternative splicing. ARHGAP10 mRNA was expressed in chondrosarcoma, breast cancer, kidney tumors, and brain tumors. ARHGAP10 and ARHGAP26 (GRAF), showing 57.9% total amino-acid identity, shared the common-domain structure with BAR, PH, RhoGAP and SH3 domains. ARHGAP10-NR3C2 locus at human chromosome 4q31.23 and ARHGAP26-NR3C1 locus at human chromosome 5q31 were paralogous regions (paralogons) within the human genome. ARHGAP gene family was found consisting of at least 32 members, including ARHGAP1, ARHGAP2 (CHN1), ARHGAP3, (CHN2), ARHGAP4, ARHGAP5, ARHGAP6 (STARD8), ARHGAP7 (STARD12 or DLC1), ARHGAP8, ARHGAP9, ARHGAP10, ARHGAP12, ARHGAP13 (SRGAP1), ARHGAP14 (SRGAP2), ARHGAP15, ARHGAP17 (RICH1), ARHGAP18, ARHGAP19, ARHGAP20, ARHGAP21, ARHGAP22, ARHGAP23, ARHGAP24, ARHGAP25, ARHGAP26, STRAD13 (DLC2), HA-1, GMIP, PARG1, PIK3R1, PIK3R2, RACGAP1, and FNBP2. Genetic alterations of ARHGAP family genes lead to carcinogenesis through the dysregulation of Rho/Rac/Cdc42-like GTPases.

Amino Acid Sequence↗

PubMed2004

Identification and characterization of human HESL, rat Hesl and rainbow trout hesl genes in silico.

Activation of Notch signaling pathway leads to nuclear translocation of Notch intracellular domain (NIC), and transcriptional activation of target genes through the interaction between CSL proteins (RBPSUH or RBPSUHL) and NIC. HES1, HES5, HEY1 and HEY2 are Notch target genes. Mammalian HES/HEY family proteins as well as Drosophila Hairy and Enhancer of split are implicated in the cell fate determination. We have previously identified and characterized human HES2, HES3 and HES5 genes. Here, we identified and characterized human HES-like (HESL), rat Fesl, and rainbow trout fesl genes by using bioinformatics. Human HESL gene, located within AC093824.3 genome sequence, was mapped to human chromosome 4q35.1 between ACSL1 and SLC25A4 genes. Rat Fesl gene, located within AC111303.4 genome sequence, was mapped to rat chromosome 16q11. EST BX875070.2 was the representative rainbow trout fesl cDNA. HESL-ACSL1 locus was conserved among human, rat, mouse, and zebrafish genomes. Human HESL (241 aa) showed 92.9% total-amino-acid identity with rat Hesl (240 aa), 92.1% total-amino-acid identity with mouse Hesl (240 aa), and 68.0% total-amino-acid identity with rainbow trout hesl (235 aa). HESL orthologs consist of basic Helix-loop-helix (bHLH) domain and ORANGE domain. C-terminal region of HESL orthologs were divergent from that of HES, HEY, and DEC homologs. Phylogenetic analyses revealed that bHLH transcription factors with ORANGE domain were classified into the following three groups: (group I) HES1, HES2, HES4 and HES6 orthologs; (group II) HESL, HES5, HES7, HEY1, HEY2 and HEYL orthologs; (group III) HES3, DEC1/BHLHB2 and DEC2/BHLHB3 orthologs.

Amino Acid Sequence↗

PubMed2004

Characterization of human TMEM16G gene in silico.

TMEM16A, TMEM16B, TMEM16C, TMEM16D, TMEM16E, TMEM16F and TP53I5 are TMEM16 family eight-transmembrane proteins with N- and C-terminal tails facing the cytoplasm. TMEM16A gene at human chromosome 11q13.3 is amplified in head and neck tumors, and TMEM16E gene at human chromosome 11p14.3 is mutated in gnathodiaphyseal dysplasia (GDD). Ngep cDNA (NM_207031.1) is derived from mouse Tmem16g gene. Here, we characterized human TMEM16G gene by using bioinformatics. TMEM16G gene, consisting of 25 exons, was located at human chromosome 2q37.3. Intra-species comparative genomics revealed that the PASK-PPP1R7-TMEM16G-HDLBP-NEDD5 locus was the unique region without paralogous region. TMEM16G mRNA was preferentially expressed in normal prostate and prostate cancer. Complete coding sequence of TMEM16G cDNA was determined by assembling 25 exons of TMEM16G gene. Human TMEM16G gene was found to encode 932-amino-acid TMEM16G protein with TM16H1, TM16H2 and TM16H3 domains. Comparative proteomics revealed that T844N amino-acid substitution occurred in human TMEM16G during evolution. TMHMM2 program predicted that mouse Tmem16g and artificial human TMEM16G (844T) were eight-transmembrane proteins, but that wild-type human TMEM16G (844N) was a seven-transmembrane protein. These facts indicate that amino-acid substitution at codon 844 of human TMEM16G resulted in the mis-folding of the eighth transmembrane helix. Human TMEM16G with altered membrane topology might show functional divergence compared with other members of the TMEM16 family.

Amino Acid Sequence↗

PubMed2004

Human FOX gene family (Review).

Human Forkhead-box (FOX) gene family consists of at least 43 members, including FOXA1, FOXA2, FOXA3, FOXB1, FOXC1, FOXC2, FOXD1, FOXD2, FOXD3, FOXD4, FOXD5 (FOXD4L1), FOXD6 (FOXD4L3), FOXE1, FOXE2, FOXE3, FOXF1, FOXF2, FOXG1 (FOXG1B), FOXH1, FOXI1, FOXJ1, FOXJ2, FOXJ3, FOXK1, FOXK2, FOXL1, FOXL2, FOXM1, FOXN1, FOXN2 (HTLF), FOXN3 (CHES1), FOXN4, FOXN5 (FOXR1), FOXN6 (FOXR2), FOXO1 (FOXO1A), FOXO2 (FOXO6), FOXO3 (FOXO3A), FOXO4 (MLLT7), FOXP1, FOXP2, FOXP3, FOXP4, and FOXQ1. FOXE3-FOXD2 (1p33), FOXQ1-FOXF2-FOXC1 (6p25.3), and FOXF1-FOXC2-FOXL1 (16q24.1) loci are FOX gene clusters within the human genome. Members of FOX subfamilies A-G, I-L and Q were grouped into class 1 FOX proteins, while members of FOX subfamilies H and M-P were grouped into class 2 FOX proteins. C-terminal basic region within the FOX domain was the common feature of class 1 FOX proteins. FOXH1 and FOXO1 mRNAs are expressed in human embryonic stem (ES) cells. FOXC1, FOXC2, FOXE1, FOXE3, FOXL2, FOXN1, FOXP2 and FOXP3 genes are mutated in human congenital disorders. FOXA1 gene is amplified and over-expressed in esophageal and lung cancer. FOXM1 gene is up-regulated in pancreatic cancer and basal cell carcinoma due to the transcriptional regulation by Sonic Hedgehog (SHH) pathway. FOXO1 gene is fused to PAX3 or PAX7 genes in rhabdomyosarcoma. FOXO3 and FOXO4 genes are fused to MLL gene in hematological malignancies. Deregulation of FOX family genes leads to congenital disorders, diabetes mellitus, or carcinogenesis. Expression profiles, genetic alterations and epigenetic changes of FOX family genes as well as binding proteins and target genes of FOX family transcription factors should be comprehensively investigated to develop novel therapeutics and preventives for human diseases.

Amino Acid Sequence↗

PubMed2004

Characterization of human FOXN4 gene in silico.

Forkhead-box (FOX) superfamily genes are implicated in carcinogenesis through gene amplification, retroviral integration and chromosomal translocation. FOX superfamily genes within the human genome are classified into 17 or 18 families, designated FOX# (# is alphabet A-Q or R). FOXN1, FOXN2 (HTLF), FOXN3 (CHES1), FOXN4, FOXN5 (FOXR1) and FOXN6 (FOXR2) genes constitute the FOXN gene family. Here, we characterized human FOXN4 gene by using bioinformatics. FOXN4 gene at human chromosome 12q24.12 was found to encode three isoforms. FOXN4 isoform 1 (representative transcript), encoding a 518-aa protein, consists of exons 1-10. FOXN4 isoform 2 (NM_ 213596.1), encoding a 337-aa protein, consists of exons 1, 2, 7v, 8-10. FOXN4 isoform 3, encoding a 314-aa protein, consists of exons 1-5, 7-10. Codon 205-518 of isoform 1 was conserved in isoforms 2 and 3. FOXN4 mRNA was expressed in testis, embryonic stem (ES) cells, uterus tumors, and leiomyosarcoma. FOXN4 was most homologous to FOXN1 among human FOXN family members. FOXN4 and FOXN1 showed 41.3% total-amino-acid identity. FOX domain (codon 192-305 of FOXN4) was well conserved among mammalian FOXN family members. FN14 domain (codon 367-456 of FOXN4) was identified as the novel domain conserved among FOXN4 and FOXN1 orthologs. FOXN4 and FOXN1 orthologs were found to share the common domain structure, consisting of FOX and FN14 domains. This is the first report on comprehensive characterization of the human FOXN4 gene as well as on identification of the FN14 domain.

Amino Acid Sequence↗

PubMed2004

Identification and characterization of FBXL19 gene in silico.

CXXC1, CXXC2 (FBXL10), CXXC3 (MBD1), CXXC4 (IDAX), CXXC5, CXXC6, CXXC7 (MLL), CXXC8 (FBXL11), CXXC9 (DNMT1) and CXXC10 are CXXC family genes within the human genome. Recently, we identified and characterized CXXC5 and CXXC10 genes as the homologs of CXXC4, which is implicated in the WNT signaling pathway. Here, we identified human FBXL19 (CXXC11) gene by using bioinformatics. Complete coding sequence of FBXL19 cDNA was determined by assembling 10 exons within AC135048.2 genome sequence. NM_019085.1 cDNA was a 5'-truncated partial cDNA corresponding to nucleotide position 138-2025 of FBXL19 complete coding sequence. FBXL19-BCL7C locus at chromosome 16p11.2, FBXL10-RHOF-BCL7A locus at chromosome 12q24.31, and FBXL11-RHOD locus at chromosome 11q13.2 were paralogous regions within the human genome. FBXL19 gene was found to encode a 674-amino-acid FBXL19 protein. Human FBXL19 showed 97.5% total-amino-acid identity with mouse Fbxl19. FBXHA domain (codon 11-128 of FBXL19) and FBXHB domain (codon 404-674 of FBXL19) were identified as novel domains conserved among FBXL19, FBXL10 and FBXL11. CXXC domain was located within the FBXHA domain, and F-box domain was located within the FBXHB domain. FBXL19 consists of FBXHA and FBXHB domains, while FBXL10 and FBXL11 consist of Jumonji C (JmjC), FBXHA and FBXHB domains. This is the first report on human FBXL19 gene as well as FBXHA and FBXHB domains.

Amino Acid Sequence↗

PubMed2003

Identification and characterization of human Inscuteable gene in silico.

Neuroblast undergoes asymmetrical cell division to produce the neuroblast itself and ganglion mother cell along the apical-basal axis. Inscuteable (Insc) and Partner of Inscuteable (Pins) are translocated to the apical cell cortex during asymmetrical cell division of Drosophila neuroblast. Insc is implicated in the apical-basal orientation of mitotic spindle and the basal localization of Prospero (Pros) and Numb. Here, we identified and characterized human Inscuteable (INSC) gene using bioinformatics. Human INSC gene, consisting of at least 13 exons, was located within human genome draft sequence AC090744.5 (around nucleotide position 150581-16936 in reverse orientation). Human INSC gene, closely linked to CALCB gene with an interval of about 30 kb, was assigned to human chromosome 11p15.2-p15.1. Amino-acid sequence of human INSC polypeptide (579 aa) was determined based on exon sequences of human INSC gene. C. elegans hypothetical protein F43E2.3 (NP_495539), homologous to human INSC, was designated C. elegans Insc. Central INSC homologous (ISH) domain and C-terminal PDZ-binding motif were evolutionary conserved among INSC proteins. The former part of ISH domain is implicated in Pros localization, while function of the latter part of ISH domain and C-terminal PDZ-binding motif remain to be elucidated. Human INSC mRNA was expressed in eye, kidney, fetal cochlea, parathyroid tumor, chondrosarcoma, epidermoid carcinoma, and skin tumor. Because LGN/Pins, PARD3/Par-3Bazooka, PARD6A/Par-6 and PRKCZ/aPKC genes implicated in asymmetrical cell division are evolutionarily and functionally conserved, human INSC protein might be implicated in asymmetrical cell division of human neural stem cells and other stem cells.

Amino Acid Sequence↗

PubMed2003

Identification and characterization of human PRICKLE1 and PRICKLE2 genes as well as mouse Prickle1 and Prickle2 genes homologous to Drosophila tissue polarity gene prickle.

Drosophila prickle is implicated in tissue polarity or planar polarity. Here, human PRICKLE1 gene corresponding to FLJ31937 cDNA and human PRICKLE2 gene corresponding to DKFZp686D143 cDNA were identified to be homologous to Drosophila prickle gene by using bioinformatics. PRICKLE1 gene was mapped to human chromosome 12p11-q12, and PRICKLE2 gene was mapped to human chromosome 3p14. Mouse Prickle1 and Prickle2 genes were next identified in mouse genome draft sequences NW_000106.1 and NW_000262.1, respectively. Human PRICKLE1, PRICKLE2, Xenopus Prickle, and Drosophila prickle were homologous in the PET domain, three LIM domains, and the C-terminal Prickle homologous (PKH) domain. LMO6 and TESTIN, containing the PET domain and three LIM domains, were found to lack the PKH domain. Therefore, PRICKLE1 and PRICKLE2 rather than LMO6 and TESTIN were found to be human homologs of Drosophila prickle. PRICKLE1 and PRICKLE2 mRNAs were expressed together in brain, eye and testis. PRICKLE1 mRNA was expressed in fetal heart and hematological malignancies, while PRICKLE2 mRNA in fetal brain, adult cartilage, pancreatic islet, gastric cancer with signet-ring cell features, and uterus tumors. Because tissue polarity genes frizzled, dishevelled, flamingo, and Vang are evolutionary and functionary conserved from Drosophila to human, PRICKLE1 and PRICKLE2 might be implicated in the localization of Frizzled and Dishevelled proteins, just like Drosophila prickle. This is the first report on identification and characterization of human PRICKLE1, PRICKLE2, mouse Prickle1, and Prickle2 genes.

Adaptor Proteins, Signal Transducing↗

PubMed2003

Identification and characterization of human SNAIL3 (SNAI3) gene in silico.

Human SNAIL1 (SNAI1) protein encoded by SNAI1/SNA gene represses transcription of E-cadherin/CDH1 gene. Human SNAIL2 (SNAI2) protein encoded by SNAI2/SLUG gene induces the first phase of epithelial-mesenchymal transition (EMT), including desmosome dissociation, cell spreading, and initiation of cell separation. Here, we have identified human SNAIL3 (SNAI3) gene using bioinformatics. Human SNAI3 gene, consisting of at least three exons, spans around the nucleotide position 320214-328221 of human reference genomic contig NT_010404.8 in the reverse orientation. SNAI3 gene, was located between KIAA0233 gene and CBFA2T3 gene in human chromosome 16q24.3, a region affected in breast cancer, gastric cancer, hepatocellular carcinoma, ovarian cancer, and therapy-related myeloid leukemia with t(16;21)(q24;q22) translocation. Human SNAI3 gene was found to encode 292-amino-acid polypeptide with the N-terminal SNAG domain and five zinc finger domains. N-terminal SNAG domain was identified in zinc finger proteins SNAI1, SNAI2, SNAI3, SCRATCH (SCRT1), GFI1, and GFI1B. ATP/GTP binding site was identified in SCRT1, GFI1 and GFI1B, but not in SNAI1, SNAI2 and SNAI3. Phylogenetic analysis of human zinc finger proteins with SNAG domain revealed that SNAI1, SNAI2 and SNAI3 were more closely related. These results clearly indicate that SNAI1, SNAI2 and SNAI3 constitute a subfamily among SNAG zinc-finger proteins. Human SNAI3 mRNA was expressed in skin melanotic melanoma, lung epidermoid carcinoma, and germ cell tumor. Because SNAG zinc-finger proteins are transcriptional repressors implicated in carcinogenesis and embryogenesis, SNAI3 gene might be a potent target of pharmacogenomics in the field of oncology and regenerative medicine.

Amino Acid Sequence↗

PubMed2003

Identification and characterization of human DAPPER1 and DAPPER2 genes in silico.

WNT signals play key roles in carcinogenesis and embryogenesis through the specification of cell fate and polarity. Dishevelled (DVL) proteins are WNT signaling molecules implicated in beta-catenin pathway and PCP pathway. Xenopus Dapper and Frodo are Dvl-binding proteins, showing 89.8% total-amino-acid identity. Here, we identified and characterized human homologs of Xenopus Dapper and Frodo using bioinformatics. Human DAPPER1 gene was located within human genome draft sequence NT_025892.9 (nucleotide position 39378960-39387891 in the forward orientation), and human DAPPER2 gene within NT_007302.10 (nucleotide position 660279-672480 in the reverse orientation). DAPPER1 (799-amino-acids) and DAPPER2 (774-amino-acids) showed 28.8% total-amino-acid identity. Seven DAPPER homologous (DAPH) domains, including DAPH2 (leucine zipper), DAPH3 (serine rich) and DAPH7 (PDZ binding), were conserved between DAPPER1 and DAPPER2. Phylogenetic analysis of vertebrate Dapper proteins revealed that Xenopus Dapper and Frodo are orthologs of human DAPPER1. DAPPER1 mRNA was expressed in amnion, fetal brain, eye, heart, adult brain medulla, gastric cancer (signet ring cell features), RER+ colon tumor, acute lymphoblastic leukemia, germ cell tumor, chondrosarcoma, and parathyroid tumor. DAPPER2 mRNA was expressed in placenta, genitourinary tract tumor, and endometrial adenocarcinoma. DAPPER1 and DAPPER2 genes were mapped to human chromosome 14q22.3 and 6q27, respectively. Human chromosome 14q22.3 is deleted in astrocytoma, while human chromosome 6q27 is deleted in breast, ovarian, and gastric cancer. Based on evolutionary and functional conservation of WNT signaling molecules as well as human chromosomal localization, DAPPER1 and DAPPER2 genes are predicted to be potent cancer-associated genes.

Adaptor Proteins, Signal Transducing↗