BodyMap: A Collection of 3' ESTs for Analysis of Human Gene Expression Information

Kawamoto, Shoko; Yoshii, Junji; Mizuno, Katsuya; Ito, Kouichi; Miyamoto, Yasuhide; Ohnishi, Tadashi; Matoba, Ryo; Hori, Naohiro; Matsumoto, Yuhiko; Okumura, Toshiyuki; Nakao, Yuko; Yoshii, Hisae; Arimoto, Junko; Ōhashi, Hiroko; Nakanishi, Hiroyuki; Ohno, Ikko; Hashimoto, Jun; Shimizu, Kikuo; Maeda, Kazuhisa; Kuriyama, Hiroshi; Nishida, Kohji; Shimizu-Matsumoto, Akiyo; Adachi, Wakako; Ito, Reiko; Kawasaki, Satoshi; Chae, Keon‐Sang; Murakawa, Katsuji; Yokoyama, M.; Fukushima, Atsushi; Hishiki, Teruyoshi; Nakaya, Akihiko; Sese, Jun; Monma, Norikazu; Nikaido, Hitoshi; Morishita, Shinichi; Matsubara, Kazuo; Okubo, Kousaku

doi:10.1101/gr.151500

Cited by 43 publications

(27 citation statements)

References 34 publications

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“…Whereas the selection of a protein from a given tissue-specific library clearly demonstrates its presence in that tissue, failure to select it from another library does not prove its absence. Indeed, a comparison of the tissue of origin data for five of the most frequent clones (Table I) to the tissue distribution reported in the Bodymap data base (20) showed no significant correlation (data not shown).…”

Section: Discussionmentioning

confidence: 99%

In Vitro Selection and Characterization of Bcl-XL-binding Proteins from a Mix of Tissue-specific mRNA Display Libraries

Hammond¹,

Alpin²,

Rise³

et al. 2001

Journal of Biological Chemistry

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The covalent coupling of an mRNA to the protein that it encodes (mRNA display) provides a powerful tool for analysis of protein function in the post-genomic era. This coupling allows the selective enrichment of individual members from libraries of displayed proteins and the subsequent regeneration of an enriched library using the RNA moiety. Tissue-specific libraries from poly(A) ؉ mRNA were prepared by priming first and second strand cDNA synthesis with oligonucleotides containing nine random 3 nucleotides, the fixed regions of which encoded the requisite sequences for formation of mRNA display constructs and a library-specific sequence tag. Starting with a pool of uniquely tagged libraries from different tissues, an iterative selection was performed for binding partners of the anti-apoptotic protein Bcl-X L . After four rounds of selection, the pool was deconvoluted by polymerase chain reaction amplification with library-specific primers. Subsequent clonal sequence analysis revealed the selection of three members of the Bcl-2 family known to bind to Bcl-X L . In addition, several proteins not previously demonstrated to interact with Bcl-X L were identified. The relative binding affinities of individual selected peptides were determined, as was their susceptibility to competition with a BH3 domain peptide. Based on these data, a putative BH3 domain was identified in most peptides.

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Section: Discussionmentioning

confidence: 99%

In Vitro Selection and Characterization of Bcl-XL-binding Proteins from a Mix of Tissue-specific mRNA Display Libraries

Hammond¹,

Alpin²,

Rise³

et al. 2001

Journal of Biological Chemistry

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“…Recent experiments using DNA array technology have shown that expression of RP mRNAs in yeast is strictly regulated in a manner responsive to changes in growth conditions (Brown and Botstein 1999). Systematic analysis of the human transcriptome also suggests that transcriptional regulation plays an essential part in the expression of this class of genes (Kawamoto et al 2000; N. Kenmochi and K. Okubo, unpubl.). Although we found possible binding sites for various transcription factors in the 5Ј-flanking regions, common regulatory factors such as Rap1, which controls most yeast RP gene expression (Lascaris et al 1999), have not yet been identified elsewhere.…”

Section: Promoter Structure and Gene Expressionmentioning

confidence: 99%

The Human Ribosomal Protein Genes: Sequencing and Comparative Analysis of 73 Genes

Yoshihama¹,

Uechi²,

Asakawa³

et al. 2002

Genome Res.

167

154

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The ribosome, as a catalyst for protein synthesis, is universal and essential for all organisms. Here we describe the structure of the genes encoding human ribosomal proteins (RPs) and compare this class of genes among several eukaryotes. Using genomic and full-length cDNA sequences, we characterized 73 RP genes and found that (1) transcription starts at a C residue within a characteristic oligopyrimidine tract; (2) the promoter region is GC rich, but often has a TATA box or similar sequence element; (3) the genes are small (4.4 kb), but have as many as 5.6 exons on average; (4) the initiator ATG is in the first or second exon and is within ± 5 bp of the first intron boundaries in about half of cases; and (5) 5Ј-and 3Ј-UTRs are significantly smaller (42 bp and 56 bp, respectively) than the genome average. Comparison of RP genes from humans, Drosophila melanogaster, Caenorhabditis elegans, and Saccharomyces cerevisiae revealed the coding sequences to be highly conserved (63% homology on average), although gene size and the number of exons vary. The positions of the introns are also conserved among these species as follows: 44% of human introns are present at the same position in either D. melanogaster or C. elegans, suggesting RP genes are highly suitable for studying the evolution of introns.[The sequence data described in this paper have been submitted to the DDBJ/EMBL/GenBank databases under accession nos. AB055762-AB055780, AB056456, AB061820-AB061859, AB062066-AB062071, and AB070559.]The ribosome is the cellular organelle responsible for protein synthesis in all cells. Recent analyses of the ribosome's structure using X-ray crystallography have enhanced our understanding of the structural basis of ribosome function (Ban et al. 2000;Schluenzen et al. 2000;Wimberly et al. 2000;Yusupov et al. 2001). In contrast, comparatively little is known about ribosome biogenesis, especially in higher eukaryotes. In mammalian cells, the biogenesis of cytoplasmic ribosomes requires assembly of 4 RNA molecules and 79 different proteins (Wool 1979). With the exception of two proteins, all of these components are present as single copies within the ribosome. Typically, mammalian cells contain ∼4 ‫ן‬ 10 6 cytoplasmic ribosomes, which account for 80% of all cellular RNA and 5%-10% of cellular proteins.Investigation of the mechanism that controls the coordinated expression of these components is a challenge. Three different RNA polymerases are involved in production of these RNAs and proteins, RNA polymerase I (POL I) is involved in production of the 28S, 18S, and 5.8S rRNAs, POL II in production of ribosomal proteins (RPs), and POL III in production of the 5S rRNA. The amino acid sequences of all rat and human RPs have been deduced (Wool et al. 1996), and the nucleotide sequences of thousands of eukaryotic rRNAs are now known (The Ribosome Database Project; Maidak et al. 2001). On the other hand, only a handful of mammalian RP genes have been studied in terms of their genomic structure. Unlike rRNAs, which are encoded by several ...

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“…Even with their intrinsic shortcomings such as contamination by genomic DNA and limited sequence quality, EST clusters have been a major source of information for many academic laboratories and pharmaceutical companies in the identification of novel genes (Adams et al 1991). Furthermore, qualitative or quantitative patterns of gene expression can be inferred by inspecting the tissue origin of the cDNA libraries comprising an EST cluster, as for example seen in the BodyMap project (Kawamoto et al 2000).…”

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confidence: 99%

ECgene: Genome-based EST clustering and gene modeling for alternative splicing

Kim¹,

Shin²,

Lee³

2005

Genome Res.

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With the availability of the human genome map and fast algorithms for sequence alignment, genome-based EST clustering became a viable method for gene modeling. We developed a novel gene-modeling method, ECgene (Gene modeling by EST Clustering), which combines genome-based EST clustering and the transcript assembly procedure in a coherent and consistent fashion. Specifically, ECgene takes alternative splicing events into consideration. The position of splice sites (i.e., exon-intron boundaries) in the genome map is utilized as the critical information in the whole procedure. Sequences that share any splice sites are grouped together to define an EST cluster in a manner similar to that of the genome-based version of the UniGene algorithm. Transcript assembly is achieved using graph theory that represents the exon connectivity in each cluster as a directed acyclic graph (DAG). Distinct paths along exons correspond to possible gene models encompassing all alternative splicing events. EST sequences in each cluster are subclustered further according to the compatibility with gene structure of each splice variant, and they can be regarded as clone evidence for the corresponding isoform. The reliability of each isoform is assessed from the nature of cluster members and from the minimum number of clones required to reconstruct all exons in the transcript.

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BodyMap: A Collection of 3' ESTs for Analysis of Human Gene Expression Information

Cited by 43 publications

References 34 publications

In Vitro Selection and Characterization of Bcl-XL-binding Proteins from a Mix of Tissue-specific mRNA Display Libraries

In Vitro Selection and Characterization of Bcl-XL-binding Proteins from a Mix of Tissue-specific mRNA Display Libraries

The Human Ribosomal Protein Genes: Sequencing and Comparative Analysis of 73 Genes

ECgene: Genome-based EST clustering and gene modeling for alternative splicing

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