Construction of a human full-length cDNA bank

Kato, Souichiro; Sekine, Shingo; Oh, Suwan; Nam-Soon, Kim; Umezawa, Yukiko; Abe, Naomi; Yokoyama-Kobayashi, Midori; Aoki, Takashi

doi:10.1016/0378-1119(94)90433-2

Cited by 74 publications

(5 citation statements)

References 21 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Protein functions that potentially change between alternative isoforms were compared with ProtFun [49]. Regulatory RNA elements in UTRs related to transcriptional and translational regulation were predicted by RegRNA [22,50,51]. …”

Section: Methodsmentioning

confidence: 99%

Tumor-specific usage of alternative transcription start sites in colorectal cancer identified by genome-wide exon array analysis

et al. 2011

View full text Add to dashboard Cite

BackgroundApproximately half of all human genes use alternative transcription start sites (TSSs) to control mRNA levels and broaden the transcriptional output in healthy tissues. Aberrant expression patterns promoting carcinogenesis, however, may arise from alternative promoter usage.ResultsBy profiling 108 colorectal samples using exon arrays, we identified nine genes (TCF12, OSBPL1A, TRAK1, ANK3, CHEK1, UGP2, LMO7, ACSL5, and SCIN) showing tumor-specific alternative TSS usage in both adenoma and cancer samples relative to normal mucosa. Analysis of independent exon array data sets corroborated these findings. Additionally, we confirmed the observed patterns for selected mRNAs using quantitative real-time reverse-transcription PCR. Interestingly, for some of the genes, the tumor-specific TSS usage was not restricted to colorectal cancer. A comprehensive survey of the nine genes in lung, bladder, liver, prostate, gastric, and brain cancer revealed significantly altered mRNA isoform ratios for CHEK1, OSBPL1A, and TCF12 in a subset of these cancer types.To identify the mechanism responsible for the shift in alternative TSS usage, we antagonized the Wnt-signaling pathway in DLD1 and Ls174T colorectal cancer cell lines, which remarkably led to a shift in the preferred TSS for both OSBPL1A and TRAK1. This indicated a regulatory role of the Wnt pathway in selecting TSS, possibly also involving TP53 and SOX9, as their transcription binding sites were enriched in the promoters of the tumor preferred isoforms together with their mRNA levels being increased in tumor samples.Finally, to evaluate the prognostic impact of the altered TSS usage, immunohistochemistry was used to show deregulation of the total protein levels of both TCF12 and OSBPL1A, corresponding to the mRNA levels observed. Furthermore, the level of nuclear TCF12 had a significant correlation to progression free survival in a cohort of 248 stage II colorectal cancer samples.ConclusionsAlternative TSS usage in colorectal adenoma and cancer samples has been shown for nine genes, and OSBPL1A and TRAK1 were found to be regulated in vitro by Wnt signaling. TCF12 protein expression was upregulated in cancer samples and correlated with progression free survival.

show abstract

Section: Methodsmentioning

confidence: 99%

Tumor-specific usage of alternative transcription start sites in colorectal cancer identified by genome-wide exon array analysis

et al. 2011

View full text Add to dashboard Cite

show abstract

“…By finding a simple pattern C m T n C (where m = 0,1,2 and n > 0) against 1496 human full-length cDNAs, Kato et al . (12) identified 21 TOP genes besides ribosomal proteins. Based on this, Amaldi and Pierandrei-Amaldi (1) estimated that the total number of TOP genes should be at least 100.…”

Section: Introductionmentioning

confidence: 99%

Comprehensive detection of human terminal oligo-pyrimidine (TOP) genes and analysis of their characteristics

Yamashita

Suzuki

Takeuchi

et al. 2008

Nucleic Acids Research

114

123

View full text Add to dashboard Cite

Although the knowledge accumulated on the transcriptional regulations of eukaryotes is significant, the knowledge on their translational regulations remains limited. Thus, we performed a comprehensive detection of terminal oligo-pyrimidine (TOP), which is one of the well-characterized cis-regulatory motifs for translational controls located immediately downstream of the transcriptional start sites of mRNAs. Utilizing our precise 5′-end information of the full-length cDNAs, we could screen 1645 candidate TOP genes by position specific matrix search. Among them, not only 75 out of 78 ribosomal protein genes but also eight previously identified non-ribosomal-protein TOP genes were included. We further experimentally validated the translational activities of 83 TOP candidate genes. Clear translational regulations exerted on the stimulation of 12-O-tetradecanoyl-1-phorbol-13-acetate for at least 41 of them was observed, indicating that there should be a few hundreds of human genes which are subjected to regulation at translation levels via TOPs. Our result suggests that TOP genes code not only formerly characterized ribosomal proteins and translation-related proteins but also a wider variety of proteins, such as lysosome-related proteins and metabolism-related proteins, playing pivotal roles in gene expression controls in the majority of cellular mRNAs.

show abstract

“…The several protocols for cDNA library constructionwere previously reported that exploit the mRNA cap structure to enrich for full-length sequence [3], the "oligo-capping" method [4,5], CAPture [2], CAP-trapper [1] and SMART TM technology of constructing full-length cDNA library [6]. We also obtained good quality cDNA library using safe size fraction method.…”

Section: Discussionmentioning

confidence: 88%

Effective Procedure for Development of EST-SSR Markers Using cDNA Library

Kim¹,

Park²,

Sohn³

et al. 2012

AJPS

View full text Add to dashboard Cite

The present study was conducted to develop EST-SSR markers using the cDNA library from rice plant. Total RNA extracted from the leaves of brown plant hopper resistance gene originated from a rice cultivar "Cheongcheong" and sensitive rice cultivar "Nakdong" were used to synthesize a cDNA library. As a result of analyzing the cDNA library, the 17 EST-SSR primer sets were developed. This study enables to provide effective marker assisted selection (MAS) methods on the selection of white-backed planthopper resistance gene originated from a rice plant more simply, quickly and precisely. Furthermore, using this marker's advantage of deriving from cDNA, it is possible to identify the white-backed planthopper resistance gene. In addition, this study introduces a technique for construction of a cDNA library safely without using radioactivity.

show abstract

Construction of a human full-length cDNA bank

Cited by 74 publications

References 21 publications

Tumor-specific usage of alternative transcription start sites in colorectal cancer identified by genome-wide exon array analysis

Tumor-specific usage of alternative transcription start sites in colorectal cancer identified by genome-wide exon array analysis

Comprehensive detection of human terminal oligo-pyrimidine (TOP) genes and analysis of their characteristics

Effective Procedure for Development of EST-SSR Markers Using cDNA Library

Contact Info

Product

Resources

About