An Expressed-Sequence-Tag Database of the Human Prostate: Sequence Analysis of 1168 cDNA Clones

doi:10.1006/geno.1997.5035

Genomics

Volume 47, Issue 1, 1 January 1998, Pages 12-25

https://doi.org/10.1006/geno.1997.5035 Get rights and content

Abstract

The human prostate is a complex glandular organ with functional development under hormonal regulation. Diseases of the prostate result in significant morbidity and mortality in the form of benign prostatic hypertrophy and prostate adenocarcinoma. The characterization of the molecular framework of the human prostate at the level of expressed genes will facilitate the understanding of normal and pathological prostate biology. The purposes of this study were to acquire an initial assessment of the qualitative and quantitative diversity of gene expression in the normal human prostate and to determine the extent that genes with prostate-restricted expression can be assessed using an expressed sequence tag approach. We have constructed a directional cDNA library from normal adult human prostate tissue and partially sequenced the 5′ end of 1168 randomly selected cDNA clones, resulting in more than 400 kb of DNA sequence. Homology searches of the sequenced cDNAs against the GenBank and dbEST databases revealed that 43% of the sequences are identical to human genes whose functions are known, 5% are similar but not identical to known genes in humans or lower organisms, 5% match the mitochondrial genome, 9% are composed of interspersed DNA repeats, 30% are homologous to sequences in the dbEST database without a described function, and 6% are novel sequences. A total of 780 distinct species were identified. In addition to the 74 novel transcripts, 4 genes, prostate-specific antigen (PSA), prostate secretory protein (PSP), prostate acid phosphatase (PAP), and human glandular kallekrein 2 (HK2), have no homologous sequences in the databases that originate from sources other than prostate and thus may represent genes with prostate-restricted expression. Sequences matching PSA, PSP, and PAP each accounted for >1% of the total ESTs and represent highly abundant transcripts, correlating with the abundance of these proteins in the prostate gland. No novel transcripts were represented by more than one EST and thus are expressed at levels much lower than the known prostate-specific genes.

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^☆: Sequence data from this article have been deposited with the EMBL/GenBank Data Libraries under Accession Nos. AA447269–AA447338.

^☆☆: EST, expressed sequence tag; PSA, prostate-specific antigen; PSP, prostate secretory protein; PAP, prostate acid phosphatase; HK2, human glandular kallekrein 2; PSMA, prostate-specific membrane antigen; RACE, rapid amplification of cDNA ends

¹: To whom correspondence should be addressed at Department of Molecular Biotechnology, Box 357730 HSB, Room K360, University of Washington, Seattle, WA 98195. Telephone: (206) 685-7336. Fax: (206) 685-7301. E-mail: [email protected].

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Regular ArticleAn Expressed-Sequence-Tag Database of the Human Prostate: Sequence Analysis of 1168 cDNA Clones☆,☆☆

Abstract

J. Mol. Biol.

FEBS Lett.

Biochem. Biophys. Res. Commun.

Gene

Genomics

J. Mol. Biol.

Urology

Methods Enzymol.

Anal. Biochem.

Cell

Complementary DNA sequencing: Expressed sequence tags and the Human Genome Project

Science

Initial assessment of human gene diversity and expression patterns based upon 83 million nucleotides of cDNA sequence

Nature

Three abundance classes in HeLa cell messenger RNA

Nature

ESTablishing a human transcript map

Nat. Genet.

dbEST-database for “expressed sequence tags.”

Nat. Genet.

One-tube double-stranded cDNA synthesis using cloned M-MLV reverse transcriptase

Focus

Neuroendocrine differentiation in human prostatic carcinoma

Hum. Pathol.

Prostate specific antigen—New applications in breast and other cancers

Anticancer Res.

Analysis of gene expression in single live neurons

Proc. Natl. Acad. Sci. USA

How many genes in the human genome?

Nat. Genet.

Identification of protein coding regions by database similarity search

Nat. Genet.

Evaluation of PAP and PSA gene expression in prostatic hyperplasia and prostatic carcinoma using Northern-blot analysis, in situ hybridization and immunohistochemical stainings with monoclonal and bispecific antibodies

Int. J. Cancer

Two prostate-specific antigens, gamma-seminoprotein and beta-microseminoprotein

J. Lab. Clin. Med.

Expression of the gene coding for human prostate-specific antigen and related hGK-1 in benign and malignant tumors of the human prostate

Int. J. Cancer

Generation and analysis of 280,000 human expressed sequence tags

Genome Res.

Regular Article
An Expressed-Sequence-Tag Database of the Human Prostate: Sequence Analysis of 1168 cDNA Clones☆,☆☆