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Daisuke Nakajima

Publications and source records attributed to Daisuke Nakajima.

23 records · Page 2Linked to original sources
PubMed2003

Prediction of the coding sequences of mouse homologues of KIAA gene: II. The complete nucleotide sequences of 400 mouse KIAA-homologous cDNAs identified by screening of terminal sequences of cDNA clones randomly sampled from size-fractionated libraries.

We have accumulated information of the coding sequences of uncharacterized human genes, which are known as KIAA genes, and the number of these genes exceeds 2000 at present. As an extension of this sequencing project, we recently have begun to accumulate mouse KIAA-homologous cDNAs, because it would be useful to prepare a set of human and mouse homologous cDNA pairs for further functional analysis of the KIAA genes. We herein present the entire sequences of 400 mouse KIAA cDNA clones and 4 novel cDNA clones which were incidentally identified during this project. Most of clones entirely sequenced in this study were selected by computer-assisted analysis of terminal sequences of the cDNAs. The average size of the 404 cDNA sequences reached 5.3 kb and that of the deduced amino acid sequences from these cDNAs was 868 amino acid residues. The results of sequence analyses of these clones showed that single mouse KIAA cDNAs bridged two different human KIAA cDNAs in some cases, which indicated that these two human KIAA cDNAs were derived from single genes although they had been supposed to originate from different genes. Furthermore, we successfully mapped all the mouse KIAA cDNAs along the genome using a recently published mouse genome draft sequence.

Animals↗
PubMed2002

Construction of expression-ready cDNA clones for KIAA genes: manual curation of 330 KIAA cDNA clones.

We have accumulated information on protein-coding sequences of uncharacterized human genes, which are known as KIAA genes, through cDNA sequencing. For comprehensive functional analysis of the KIAA genes, it is necessary to prepare a set of cDNA clones which direct the synthesis of functional KIAA gene products. However, since the KIAA cDNAs were derived from long mRNAs (> 4 kb), it was not expected that all of them were full-length. Thus, as the first step toward preparing these clones, we evaluated the integrity of protein-coding sequences of KIAA cDNA clones through comparison with homologous protein entries in the public database. As a result, 1141 KIAA cDNAs had at least one homologous entry in the database, and 619 of them (54%) were found to be truncated at the 5' and/or 3' ends. In this study, 290 KIAA cDNA clones were tailored to be full-length or have considerably longer sequences than the original clones by isolating additional cDNA clones and/or connected parts of additional cDNAs or PCR products of the missing portion to the original cDNA clone. Consequently, 265, 8, and 17 predicted CDSs of KIAA cDNA clones were increased in the amino-, carboxy-, and both terminal sequences, respectively. In addition, 40 cDNA clones were modified to remove spurious interruption of protein-coding sequences. The total length of the resultant extensions at amino- and carboxy-terminals of KIAA gene products reached 97,000 and 7,216 amino acid residues, respectively, and various protein domains were found in these extended portions.

Cloning, Molecular↗
PubMed2002

Mammalian fat3: a large protein that contains multiple cadherin and EGF-like motifs.

Using computer-based, motif-trap screening, we have identified a third member of the mammalian fat family, fat3. Human and rat fat3 are also similar to the Drosophila tumor suppressor gene fat. The rat fat3 gene encodes a large protein of 4555 amino acids with 34 cadherin domains, 4 epidermal growth factor (EGF)-like motifs, a laminin A-G motif, and a cytoplasmic domain. Each member of the fat family is differentially expressed in the central nervous system during development. While both fat3 mRNA and fat1 mRNA are abundantly expressed in the fetal brain, the expression of MEGF1/fat2 mRNA is restricted to the postnatal cerebellum. fat3 mRNA and protein expression in the brain peaks at E15 during embryonic development. During this time, robust fat3 immunoreactivity is also observed in the spinal cord. These data suggest that the fat3 protein plays an important role in axon fasciculation and modulation of the extracellular space surrounding axons during embryonic development.

Amino Acid Motifs↗
PubMed2002

MEGF1/fat2 proteins containing extraordinarily large extracellular domains are localized to thin parallel fibers of cerebellar granule cells.

The MEGF1 (protein 1 with multiple EGF-like domains) gene, which was identified using motif-trap screening, encodes an extraordinarily large protein containing two EGF-like and 34 cadherin motifs. In situ hybridization analysis revealed that the MEGF1 gene was specifically expressed in granule cells of the cerebellum. Interestingly, in the developing cerebellum, granule cells in the inner external germinal layer and migrating granule cells expressed MEGF1 mRNA, whereas proliferating cells in the outer external germinal layer did not express MEGF1 mRNA. Expression levels in the internal granule cell layer peaked during the third postnatal week and remained considerably high in the adult cerebellum. MEGF1 protein was detected in only the cerebellum as a single 480-kDa band by immunoblot analyses using polyclonal antibodies against either the N-terminal or the C-terminal region of MEGF1 protein. Using light and electron microscopic immunocytochemistry, specific immunostaining of the MEGF1 protein was observed in the molecular layer of the cerebellum, suggesting that MEGF1 protein was localized in the parallel fibers of cerebellar granule cells. This was corroborated by results from experiments using primary dispersed cultures of cerebellar granule cells and cerebellar microexplant cultures. The homophilic interaction of MEGF1 proteins was confirmed with both a cell aggregation assay and an in vitro copurification assay. Based on these results, a novel function of the enormous protocadherins in cerebellar development, namely, the modulation of the extracellular space surrounding parallel fibers during development, was proposed.

Aging↗