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Masaki Kajikawa

Publications and source records attributed to Masaki Kajikawa.

12 recordsLinked to original sources
PubMed2006

Novel retrotransposon analysis reveals multiple mobility pathways dictated by hosts.

Autonomous non-long-terminal-repeat retrotransposons (NLRs) proliferate by retrotransposition via coordinated reactions of target DNA cleavage and reverse transcription by a mechanism called target-primed reverse transcription (TPRT). Whereas this mechanism guarantees the covalent attachment of the NLR and its target site at the 3' junction, mechanisms for the joining at the 5' junction have been conjectural. To better understand the retrotransposition pathways, we analyzed target-NLR junctions of zebrafish NLRs with a new method of identifying genomic copies that reside within other transposons, termed "target analysis of nested transposons" (TANT). Application of the TANT method revealed various features of the zebrafish NLR integrants; for example, half of the integrants carry extra nucleotides at the 5' junction, which is in stark contrast to the major human NLR, LINE-1. Interestingly, in a cell culture assay, retrotransposition of the zebrafish NLR in heterologous human cells did not bear extra 5' nucleotides, indicating that the choice of the 5' joining pathway is affected by the host. Our results suggest that several pathways exist for NLR retrotransposition and argue in favor of host protein involvement. With genomic sequence information accumulating exponentially, our data demonstrate the general applicability of the TANT method for the analysis of a wide variety of retrotransposons.

Animals↗
PubMed2006

Functional splice sites in a zebrafish LINE and their influence on zebrafish gene expression.

Long interspersed elements (LINEs) are transposable elements that exist in many kinds of eukaryotic genomes, where they have a large effect on genome evolution. There are several thousands to hundreds of thousands of LINE copies in each eukaryotic genome. LINE elements are amplified by a mechanism called retrotransposition, in which a LINE-encoded protein reverse transcribes (copies) its own RNA. We previously isolated two retrotransposition-competent LINEs, ZfL2-1 and ZfL2-2, from zebrafish. Although it has generally been thought that LINEs do not have 'introns' (because the LINE RNA is used as the template during retrotransposition), we now show that these two LINEs contain multiple putative functional splice sites. We further show that at least one pair of these splice sites is actually functional in zebrafish cells. Moreover, some of these splice sites are coupled with the splicing signal of a host endogenous gene, thereby generating a new chimeric spliced mRNA variant for this gene. Our results suggest the possible role of these LINE splice sites in modulating retrotransposition and host gene expression.

Animals↗
PubMed2006

Solution structure and functional importance of a conserved RNA hairpin of eel LINE UnaL2.

The eel long interspersed element (LINE) UnaL2 and its partner short interspersed element (SINE) share a conserved 3' tail that is critical for their retrotransposition. The predicted secondary structure of the conserved 3' tail of UnaL2 RNA contains a stem region with a putative internal loop. Deletion of the putative internal loop region abolishes UnaL2 mobilization, indicating that this putative internal loop is required for UnaL2 retrotransposition; the exact role of the putative internal loop in retrotransposition, however, has not been elucidated. To establish a structure-based foundation on which to address the issue of the putative internal loop function in retrotransposition, we used NMR to determine the solution structure of a 36 nt RNA derived from the 3' conserved tail of UnaL2. The region forms a compact structure containing a single bulged cytidine and a U-U mismatch. The bulge and mismatch region have conformational flexibility and molecular dynamics simulation indicate that the entire stem of the 3' conserved tail RNA can anisotropically fluctuate at the bulge and mismatch region. Our structural and mutational analyses suggest that stem flexibility contributes to UnaL2 function and that the bulged cytidine and the U-U mismatch are required for efficient retrotransposition.

Animals↗
PubMed2006

[A case of endocrine cell carcinoma (small cell carcinoma) of duodenum].

Extra-ampullary duodenal endocrine cell carcinoma is extremely rare. A 65-year-old woman visited our hospital, complaining of epigastralgia, anorexia and vomiting. She was admitted for suspected duodenal or pancreas head tumor by abdominal CT. Fiberscopic examination revealed a circumferential tumor in the extra-ampullary duodenal second portion. Histopathological findings of biopsy specimen showed a small cell carcinoma, and positive immunohistochemical staining for synaptophysin revealed this tumor to be endocrine cell carcinoma. Pylorus-preserving pancreaticoduodenectomy with partial transversocolectomy was performed, and intraoperative washing cytology detected tumor cells in the peritoneal cavity. Although she discharged from hospital uneventfully, she died 11 months later of multiple liver metastases and peritoneal dissemination. This case showed the high malignant potential of this tumor.

Aged↗
PubMed2005

Probing the secondary structure of salmon SmaI SINE RNA.

SmaI is a short interspersed element (SINE) of the salmon genome, and is derived from tRNA(Lys). We probed the secondary structure of SmaI SINE RNA by enzymatic cleavage and found that the RNA structure comprises three separate domains. The 5'-terminal region (the 5' domain) forms a tRNA-like cloverleaf structure, whereas the 3'-terminal region (the 3' domain) forms an extended stem-loop. The loop region is thought to be recognized by the reverse transcriptase (RT) encoded by the long interspersed element (LINE). The two structural domains are linked by a single-stranded region (the linker domain). Our melting profile analyses indicated the presence of two structural domains having different thermal stabilities, thus supporting the domain composition described above. Based on these results, we discuss the structural generality and evolutionary advantage of the domain composition of SINE RNA.

Animals↗
PubMed2005

Isolation and characterization of retrotransposition-competent LINEs from zebrafish.

Long interspersed elements (LINEs) are a type of retroposon and are widely distributed in most eukaryotic genomes. LINEs are classified into two groups, the stringent type and relaxed type, based on the recognition of the 3' tail of their own RNA by reverse transcriptase (RT) during retrotransposition. Although most LINEs are thought to belong to the stringent type, retrotransposition studies of the stringent type LINEs are relatively limited compared with those of the relaxed type. We have now isolated two retrotransposition-competent LINEs (ZfL2-1 and ZfL2-2) from the zebrafish genome. Both ZfL2-1 and ZfL2-2 are members of the L2 clade; ZfL2-1 encodes two open reading frames (ORFs) and ZfL2-2 encodes one ORF, and each of the ORFs is required for retrotransposition. Using a retrotransposition assay in HeLa cells, we established that both ZfL2-1 and Zfl2-2 belong to the stringent type. We also demonstrated that an esterase (ES) domain encoded by ZfL2-1 ORF1 strongly enhances its own retrotransposition. The ES domain is encoded only in ORF1 of LINEs classified in the CR1 and L2 clades, although its function or significance in retrotransposition has not been elucidated. Thus, this is the first experimental evidence that the ES domain has an enhancing function during retrotransposition. These zebrafish LINEs will be useful for determining the function of ORF1 and the retrotransposition mechanism of stringent-type LINEs.

5' Untranslated Regions↗
PubMed2005

[A phase I study of TS-1 and weekly cisplatin in patients with advanced gastric cancer].

This is a phase I study to determine the maximum tolerated dose (MTD) and toxicity of a combination of TS-1 and weekly cisplatin (CDDP) in advanced gastric cancer patients. TS-1 was administered orally twice daily after meals, at a standard dose of 80 mg/m2. One course consisted of 21 days' consecutive administration followed by 14 days' rest. Cisplatin (CDDP) was injected intravenously on days 8, 15 and 22 using the following dose levels: dose level 1 20 mg/m2, dose level 2 25 mg/m2, and dose level 3 30 mg/m2. Twelve patients were entered in this trial. One of the 6 patients at dose level 3 had neutropenia NCI-CTC grade 3, while another patient at dose level 3 suffered from DLT (liver function grade 3. The maximal tolerable dose (MTD) was not reached using dose level 3. Partial responses were seen in 5 (62.5%) of 8 patients with evaluable lesions. At level 2 (25 mg/m2), the response rate was 100%. We recommended dose level 2 for phase II trials from the standpoint of toxicity and response rate.

Adult↗
PubMed2004

Isolation and characterization of active LINE and SINEs from the eel.

Long interspersed elements (LINEs) and short interspersed elements (SINEs) are retrotransposons. These elements can mobilize by the "copy-and-paste" mechanism, in which their own RNA is reverse-transcribed into complementary DNA (cDNA). LINEs and SINEs not only are components of eukaryotic genomes but also drivers of genomic evolution. Thus, studies of the amplification mechanism of LINEs and SINEs are important for understanding eukaryotic genome evolution. Here we report the characterization of one LINE family (UnaL2) and two SINE families (UnaSINE1 and UnaSINE2) from the eel (Anguilla japonica) genome. UnaL2 is approximately 3.6 kilobases (kb) and encodes only one open reading frame (ORF). UnaL2 belongs to the stringent type--thought to be a major group of LINEs--and can mobilize in HeLa cells. We also show that UnaL2 and the two UnaSINEs have similar 3' tails, and that both UnaSINE1 and UnaSINE2 can be mobilized by UnaL2 in HeLa cells. These elements are thus useful for delineating the amplification mechanism of stringent type LINEs as well as that of SINEs.

Amino Acid Sequence↗
PubMed2004

Solution structure of an RNA stem-loop derived from the 3' conserved region of eel LINE UnaL2.

The eel long interspersed element (LINE) UnaL2 and its partner short interspersed element (SINE) share a conserved 3' tail containing a stem-loop that is critical for their retrotransposition. Presumably, the first step of retrotransposition is the recognition of their 3' tails by UnaL2-encoded reverse transcriptase. The solution structure of a 17-nucleotide RNA derived from the 3' tail of UnaL2 was determined by NMR. The GGAUA loop forms a specific structure in which the uridine is exposed to solvent with the third and fifth adenosines stacked. A sharp turn in the phosphodiester backbone occurs between the second guanosine and third adenosine. When the uridine is mutated (but not deleted), all mutants form the loop structure, indicating that the loop structure requires an exposed fourth residue. The retrotransposition assay in HeLa cells revealed that retrotransposition requires the second guanosine, although any nucleoside functions at the fourth position, suggesting that UnaL2 reverse transcriptase specifically recognizes the 5' side of the GGANA loop.

Animals↗
PubMed2004

[A case of recurrent advanced gastric cancer with lung metastasis effectively treated by combined chemotherapy of TS-1 and weekly CDDP].

We report a case of a patient with recurrent gastric cancer and lung metastasis, who responded remarkably to combination chemotherapy using TS-1 and weekly CDDP. The patient was administered 2 courses of TS-1 (80 mg/m2/day, on day 1-21) and CDDP (25 mg/m2/day, on day 8, 15, 22) every 5 weeks. The regimen was done on an outpatient basis. The treatment resulted in the metastatic tumors in the lung disappearing after 1 course. No severe side effects were observed. This combination therapy proved useful for treating lung metastasis from gastric cancer in this patient.

Adenocarcinoma↗
PubMed2002

LINEs mobilize SINEs in the eel through a shared 3' sequence.

We characterized members of the LINE (UnaL2) and SINE (UnaSINE1) families from the eel genome and found that these LINE/SINE partners share similar 3' tails. A retrotransposition assay in HeLa cells demonstrated that the 3' conserved tail of UnaL2 is necessary for its retrotransposition. This 3' tail is recognized in trans by the UnaL2 reverse transcriptase at a surprisingly high rate, and that of UnaSINE1 can also be recognized, thus providing experimental evidence that a SINE can be mobilized by the retrotransposition machinery of a partner LINE. We also demonstrated that short repeats at the 3' end of UnaL2 are required for retrotransposition suggesting that UnaL2 retrotransposes in a manner reminiscent of the reverse transcriptase activity of telomerases.

Anguilla↗