DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes最新文献

{"title":"Monitoring of methyl jasmonate-responsive genes in Arabidopsis by cDNA macroarray: self-activation of jasmonic acid biosynthesis and crosstalk with other phytohormone signaling pathways.","authors":"Yuko Sasaki, E. Asamizu, D. Shibata, Yasukazu Nakamura, T. Kaneko, K. Awai, Masayuki Amagai, C. Kuwata, T. Tsugane, T. Masuda, H. Shimada, K. Takamiya, H. Ohta, S. Tabata","doi":"10.1093/DNARES/8.4.153","DOIUrl":"https://doi.org/10.1093/DNARES/8.4.153","url":null,"abstract":"Jasmonates mediate various physiological events in plant cells such as defense responses, flowering, and senescence through intracellular and intercellular signaling pathways, and the expression of a large number of genes appears to be regulated by jasmonates. In order to obtain information on the regulatory network of jasmonate-responsive genes (JRGs) in Arabidopsis thaliana (Arabidopsis), we screened 2880 cDNA clones for jasmonate responsiveness by a cDNA macroarray procedure. Since many of the JRGs reported so far have been identified in leaf tissues, the cDNA clones used were chosen from a non-redundant EST library that was prepared from above-ground organs. Hybridization to the filters was achieved using alpha-33P-labeled single-strand DNAs synthesized from mRNAs obtained from methyl jasmonate (MeJA)-treated and untreated Arabidopsis seedlings. Data analysis identified 41 JRGs whose mRNA levels were changed by more than three fold in response to MeJA. This was confirmed by Northern blot analysis by using eight representatives. Among the 41 JRGs identified, 5 genes were JA biosynthesis genes and 3 genes were involved in other signaling pathways (ethylene, auxin, and salicylic acid). These results suggest the existence of a positive feedback regulatory system for JA biosynthesis and the possibility of crosstalk between JA signaling and other signaling pathways.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":"221 1","pages":"153-61"},"PeriodicalIF":0.0,"publicationDate":"2001-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78428682","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of novel transcribed sequences on human chromosome 22 by expressed sequence tag mapping.","authors":"M. Hirosawa, T. Nagase, Y. Murahashi, R. Kikuno, O. Ohara","doi":"10.1093/DNARES/8.1.1","DOIUrl":"https://doi.org/10.1093/DNARES/8.1.1","url":null,"abstract":"To identify sequences on the human genome that are actually transcribed, we mapped expressed sequence tags (ESTs) of long cDNAs ranging from 4 kb to 7 kb along a 33.4-Mb sequence of human chromosome 22, the first human chromosome entirely sequenced. By the EST mapping of 30,683 long cDNAs in silico, 603 cDNA sequences were found to locate on chromosome 22 and classified into 169 clusters. Comparison of the genomic loci of these cDNA sequences with 679 genes already annotated on chromosome 22q revealed that 46 clusters represented newly identified transcribed sequences. To further characterize these sequences, we sequenced 12 cDNAs in their entirety out of 46 clusters. Of these 12 cDNAs, 6 were predicted to include a protein-coding region while the remaining 6 were unlikely to encode proteins. Interestingly, 3 out of the 12 cDNAs had the nucleotide sequences of the opposite strands of the genes previously annotated, which suggested that these genomic regions were transcribed bi-directionally. In addition to these newly identified 12 cDNAs, another 12 cDNAs were entirely sequenced since these cDNAs were likely to contain new information about the predicted protein-coding sequences previously annotated. In the cases of KIAA1670 and KIAA1672, these single cDNA sequences covered two separately annotated transcribed regions. For example, the sequence of a clone for KIAA1670 indicated that the CHKL and CPT1B genes were co-transcribed as a contiguous transcript without making both the protein-coding regions fused. In conclusion, the mapping of ESTs derived from long cDNAs followed by sequencing of the entire cDNAs provided indispensable information for the precise annotation of genes on the genome together with ESTs derived from short cDNAs.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":"8 1 1","pages":"1-9"},"PeriodicalIF":0.0,"publicationDate":"2001-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89335936","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Arabidopsis cDNA clones isolated by transcomplementation of the fission yeast cAMP phosphodiesterase mutant.","authors":"S. Oshitani-Okamoto, T. Kuromori, M. Goto, M. Yamamoto","doi":"10.1093/DNARES/8.4.189","DOIUrl":"https://doi.org/10.1093/DNARES/8.4.189","url":null,"abstract":"We isolated three kinds of Arabidopsis thaliana cDNA clones that could rescue the mating-defective phenotype of the pde1 mutant of fission yeast Schizosaccharomyces pombe, which lacked cAMP phosphodiesterase. One of them, named APS1, encoded a protein similar to Rat Arf1p GTPase-activating protein (Arf1p GAP), which has a Cys2/Cys2-type GATA-1-like zinc-finger motif, suggesting that APS1 is a novel member of this class of zinc-finger protein gene family in Arabidopsis. Disruption of the zinc-finger motif in the gene product APS1, however, did not abolish its ability to suppress pde1. Cyclic AMP (cAMP) plays an important signaling role in initiation of sexual development in fission yeast. cAMP is synthesized by adenylate cyclase encoded by the cyr1 gene, and hydrolyzed by cAMP phosphodiesterase encoded by the pde1/cgs2 gene. When the intracellular cAMP level is high, protein kinase A (PKA) is activated by the binding of cAMP to the regulatory subunit, which in turn represses transcription of the ste11 gene encoding a key transcription factor for mating, meiosis and sporulation. A decrease in the cAMP level under poor nutritional conditions triggers ste11 transcription and induces sexual development. Although cAMP is predicted to serve as a second messenger in higher plants, as in many other organisms, the biological significance of cAMP is still largely unknown. To better understand the role of cAMP in higher plants, especially its possible relation to the regulation of sexual development, we previously set out to isolate Arabidopsis cDNAs that could suppress mating-deficiency of the pde1 mutant using transcomplementation. To extend our previous study, we repeated the same screening here. The S. pombe pde1 strain JZ666 was transformed with an Arabidopsis cDNA","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":"125 1","pages":"189-92"},"PeriodicalIF":0.0,"publicationDate":"2001-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89468664","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A genome-wide analysis of transcriptional effect of Gal11 in Saccharomyces cerevisiae: an application of \"mini-array hybridization technique\".","authors":"Toshio Fukasawa, Mariko Fukuma, Ken Ichi Yano, Hiroshi Sakurai","doi":"10.1093/DNARES/8.1.23","DOIUrl":"https://doi.org/10.1093/DNARES/8.1.23","url":null,"abstract":"The Gal11 protein is a subunit of the Mediator complex. Biochemical as well as genetic studies have strongly suggested that Gal11 is a positive global regulator of transcription. Some reports argue that Gal11 is a negative regulator, however. Here we have adopted the \"Mini-array membrane hybridization\" to analyze the effect of Gal11 in a genome-wide fashion. This technique has been demonstrated to be reliable to identify genes whose expression is controlled by a specific set of genetic and/or physiological signals. Our experiments indicate that this technique is applicable to profile the gene expression in yeast grown in rich medium. Thus mRNAs of 40% of significantly expressed genes are reduced more than two fold in gal11null yeast, in which only 3% of mRNAs are increased more than two fold. These results strongly suggest that Gal11 functions globally as a positive regulator in vivo.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":"109 1","pages":"23-31"},"PeriodicalIF":0.0,"publicationDate":"2001-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79589532","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mapping of quantitative trait locus related to submergence tolerance in rice with aid of chromosome walking.","authors":"W. Kamolsukyunyong, V. Ruanjaichon, M. Siangliw, S. Kawasaki, T. Sasaki, A. Vanavichit, S. Tragoonrung","doi":"10.1093/DNARES/8.4.163","DOIUrl":"https://doi.org/10.1093/DNARES/8.4.163","url":null,"abstract":"The major QTL for submergence tolerance was locate in the 5.9 cM interval between flanking RFLP markers. To narrow down this region, a physical map was constructed using YAC and BAC clones. A 400-kb YAC was identified in this region and later its end fragments were used to screen a rice BAC library. Through chromosome walking, 24 positive BAC clones formed two contigs around linked-RFLP markers, R1164 and RZ698. Using one YAC end, six BAC ends and three RFLP markers, a fine-scale map was constructed of the 6.8-cM interval of S10709-RZ698 on rice chromosome 9. The submergence tolerance and related trait were located in a small, well-defined region around BAC-end marker 180D1R and RFLP marker R1164. The physical-to-map distance ratio in this region is as small as 172.5 kb/cM, showing that this region is a hot spot for recombination in the rice genome.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":"57 1","pages":"163-71"},"PeriodicalIF":0.0,"publicationDate":"2001-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88112387","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A new class of LINEs (ATLN-L) from Arabidopsis thaliana with extraordinary structural features.","authors":"K. Noma, H. Ohtsubo, E. Ohtsubo","doi":"10.1093/DNARES/8.6.291","DOIUrl":"https://doi.org/10.1093/DNARES/8.6.291","url":null,"abstract":"The Arabidopsis thaliana genome has about 250 copies of LINEs (here called ATLNs). Of these, some, called ATLN-Ls, have an extra sequence of about 2 kb in the region downstream of two consecutive open reading frames, orf1 and orf2. Interestingly, the extra sequences in these ATLN-L members have another open reading frame, designated as orf3. Each member is flanked by direct repeats of a target site sequence, showing that ATLN-L members with the three open reading frames have retrotransposed as a unit. The ATLN-L members are also distinct from other ATLN members: orf1 terminates with TAA (or TAG) and is located in the same frame as orf2, and the ATG initiation codon of orf2 is not present in the proximal region. A sequence that may form a pseudoknot structure in ATLN-L mRNA was present in the proximal region of orf2, therefore the TAA (or TAG) termination codon of orf1 is assumed to be suppressed to produce an Orf1-Orf2 transframe protein during the translation of the ATLN-L mRNA. The region between orf2 and orf3 is several hundred bp long, suggesting that orf3 expression is independent of orfl-orf2. The amino acid sequences of the proteins Orf1 and Orf3 are highly homologous in their N-terminal half regions that have a retroviral zinc-finger motif for RNA binding. Orf3, however, has a leucine-zipper motif in addition to the zinc-finger motif. The C-terminal regions of the Orf1 and Orf3 proteins have poor homology, but seem to have nuclear localization signals, suggesting that these proteins are involved in the transfer of ATLN-L mRNA to nuclei. A phylogenetic tree shows that Orf3 proteins form a branch distinct from the branches of the Orf1 proteins encoded by ATLN-L members. This indicates that an ancestor element of ATLN-Ls has incorporated the orf1 frame carried by another ATLN member into its distal region to orf1-orf2 during evolution.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":"19 1","pages":"291-9"},"PeriodicalIF":0.0,"publicationDate":"2001-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87907874","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Prediction of the coding sequences of unidentified human genes. XXI. The complete sequences of 60 new cDNA clones from brain which code for large proteins.","authors":"T. Nagase, R. Kikuno, Osamu Ohara","doi":"10.1093/DNARES/8.4.179","DOIUrl":"https://doi.org/10.1093/DNARES/8.4.179","url":null,"abstract":"As an extension of a sequencing project of human cDNA clones which encode large proteins of unidentified genes, we herein present the entire sequences of 60 cDNA clones for the genes named KIAA1879-KIAA1938. The cDNA clones were isolated from size-fractionated cDNA libraries derived from human fetal brain, adult whole brain and amygdala, and their protein-coding sequences were predicted. Thirty-seven cDNA clones entirely sequenced in this study were selected as cDNAs which have coding potentiality by in vitro transcription/translation experiments, and the remaining 23 cDNA clones were chosen by computer-assisted analysis of terminal sequences of cDNAs. The average sizes of the inserts and corresponding open reading frames of cDNA clones analyzed here were 4.5 kb and 2.2 kb (733 amino acid residues), respectively. Sequence analyses against the public databases enabled us to annotate the functions of the predicted products of the 25 genes; 84% of these predicted gene products (21 gene products) were classified into proteins related to cell signaling/communication, nucleic acid management, and cell structure/motility. In addition to the sequence information about these 60 genes, their expression profiles were also studied in some human tissues including brain regions by reverse transcription-coupled polymerase chain reaction, products of which were quantified by enzyme-linked immunosorbent assay.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":"26 1","pages":"179-87"},"PeriodicalIF":0.0,"publicationDate":"2001-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79010072","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Allele-specific X-linked gene activity in normal human cells assayed by expressed single nucleotide polymorphisms (cSNPs).","authors":"L. Vasques, L. Pereira","doi":"10.1093/DNARES/8.4.173","DOIUrl":"https://doi.org/10.1093/DNARES/8.4.173","url":null,"abstract":"In mammals, dosage compensation at X-linked loci is achieved by the process of X chromosome inactivation in the homogametic sex. While most genes on the inactive X chromosome (Xi) are subjected to transcriptional inactivation, some escape inactivation and present biallelic expression. The expression status of X-linked genes has been extensively studied in somatic cell hybrids containing only the human Xi. Although this approach has recently been used to generate a profile of X-linked gene activity, it may not reflect what happens in a normal human cell. The recent development of a database of single nucleotide polymorphisms (SNPs) throughout the human genome enables investigation of allele-specific gene expression in normal human cells. In this study, we established a panel of X-linked expressed SNPs (cSNPs). These markers were used for monitoring gene expression in primary human fibroblast cell lines with completely skewed XCI, demonstrating the potential of this system for studying X-linked gene expression in normal human cells.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":"38 1","pages":"173-7"},"PeriodicalIF":0.0,"publicationDate":"2001-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85395170","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Complete genome sequence of an aerobic thermoacidophilic crenarchaeon, Sulfolobus tokodaii strain7.","authors":"Y. Kawarabayasi, Y. Kawarabayasi, Y. Hino, H. Horikawa, Koji Jin-no, Mikio Takahashi, M. Sekine, S. Baba, Akiho Ankai, H. Kosugi, A. Hosoyama, Shigehiro Fukui, Y. Nagai, Keiko Nishijima, R. Otsuka, H. Nakazawa, M. Takamiya, Y. Kato, Takio Yoshizawa, Toshihiro Tanaka, Y. Kudoh, J. Yamazaki, N. Kushida, A. Oguchi, Ken-ichi Aoki, S. Masuda, Masao Yanagii, Masami Nishimura, A. Yamagishi, Tairo Oshima, H. Kikuchi","doi":"10.1093/DNARES/8.4.123","DOIUrl":"https://doi.org/10.1093/DNARES/8.4.123","url":null,"abstract":"The complete genomic sequence of an aerobic thermoacidophilic crenarchaeon, Sulfolobus tokodaii strain7 which optimally grows at 80 degrees C, at low pH, and under aerobic conditions, has been determined by the whole genome shotgun method with slight modifications. The genomic size was 2,694,756 bp long and the G + C content was 32.8%. The following RNA-coding genes were identified: a single 16S-23S rRNA cluster, one 5S rRNA gene and 46 tRNA genes (including 24 intron-containing tRNA genes). The repetitive sequences identified were SR-type repetitive sequences, long dispersed-type repetitive sequences and Tn-like repetitive elements. The genome contained 2826 potential protein-coding regions (open reading frames, ORFs). By similarity search against public databases, 911 (32.2%) ORFs were related to functional assigned genes, 921 (32.6%) were related to conserved ORFs of unknown function, 145 (5.1%) contained some motifs, and remaining 849 (30.0%) did not show any significant similarity to the registered sequences. The ORFs with functional assignments included the candidate genes involved in sulfide metabolism, the TCA cycle and the respiratory chain. Sequence comparison provided evidence suggesting the integration of plasmid, rearrangement of genomic structure, and duplication of genomic regions that may be responsible for the larger genomic size of the S. tokodaii strain7 genome. The genome contained eukaryote-type genes which were not identified in other archaea and lacked the CCA sequence in the tRNA genes. The result suggests that this strain is closer to eukaryotes among the archaea strains so far sequenced. The data presented in this paper are also available on the internet homepage (http://www.bio.nite.go.jp/E-home/genome_list-e.html/).","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":"83 1","pages":"123-40"},"PeriodicalIF":0.0,"publicationDate":"2001-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79985527","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterization of genes encoding multi-domain proteins in the genome of the filamentous nitrogen-fixing Cyanobacterium anabaena sp. strain PCC 7120.","authors":"M. Ohmori, M. Ikeuchi, N. Sato, P. Wolk, T. Kaneko, T. Ogawa, M. Kanehisa, S. Goto, S. Kawashima, S. Okamoto, H. Yoshimura, H. Katoh, T. Fujisawa, S. Ehira, A. Kamei, S. Yoshihara, R. Narikawa, S. Tabat","doi":"10.1093/DNARES/8.6.271","DOIUrl":"https://doi.org/10.1093/DNARES/8.6.271","url":null,"abstract":"Computational analysis of gene structures in the genome of Anabaena sp. PCC 7120 revealed the presence of a large number of genes encoding proteins with multiple functional domains. This was most evident in the genes for signal transduction pathway and the related systems. Comparison of the putative amino acid sequences of the gene products with those in the Pfam database indicated that and PAS domains which may be involved in signal recognition were extremely abundant in Anabaena: 87 GAF domains in 62 ORFs and 140 PAS domains in 59 ORFs. As for the two-component signal transduction system, 73, 53, and 77 genes for simple sensory His kinases, hybrid His kinases and simple response regulators, respectively, many of which contained additional domains of diverse functions, were presumptively assigned. A total of 52 ORFs encoding putative Hanks-type Ser/Thr protein kinases with various domains such as WD-repeat, GAF and His kinase domains, as well as genes for presumptive protein phosphatases, were also identified. In addition, genes for putative transcription factors and for proteins in the cAMP signal transduction system harbored complex gene structures with multiple domains.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":"61 1","pages":"271-84"},"PeriodicalIF":0.0,"publicationDate":"2001-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83926532","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}