Identification and Characterization of the Potential Promoter Regions of 1031 Kinds of Human Genes

Overview

Journal Genome Res

Specialty Genetics

Date 2001 May 5

PMID 11337467

Citations 88

Authors

Y Suzuki

T Tsunoda

J Sese

H Taira

H Hata

T Ota

T Isogai

T Tanaka

Y Nakamura

A Suyama

Y Sakaki

S Morishita

K Okubo

S Sugano

Affiliations

Soon will be listed here.

Abstract

To understand the mechanism of transcriptional regulation, it is essential to identify and characterize the promoter, which is located proximal to the mRNA start site. To identify the promoters from the large volumes of genomic sequences, we used mRNA start sites determined by a large-scale sequencing of the cDNA libraries constructed by the "oligo-capping" method. We aligned the mRNA start sites with the genomic sequences and retrieved adjacent sequences as potential promoter regions (PPRs) for 1031 genes. The PPR sequences were searched to determine the frequencies of major promoter elements. Among 1031 PPRs, 329 (32%) contained TATA boxes, 872 (85%) contained initiators, 999 (97%) contained GC box, and 663 (64%) contained CAAT box. Furthermore, 493 (48%) PPRs were located in CpG islands. This frequency of CpG islands was reduced in TATA(+)/Inr(+) PPRs and in the PPRs of ubiquitously expressed genes. In the PPRs of the CGM2 gene, the DRA gene, and the TM30pl genes, which showed highly colon specific expression patterns, the consensus sequences of E boxes were commonly observed. The PPRs were also useful for exploring promoter SNPs.

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References

Knight J, Udalova I, Hill A, Greenwood B, Peshu N, Marsh K . A polymorphism that affects OCT-1 binding to the TNF promoter region is associated with severe malaria. Nat Genet. 1999; 22(2):145-50. DOI: 10.1038/9649. View

Heinemeyer T, Chen X, Karas H, Kel A, Kel O, Liebich I . Expanding the TRANSFAC database towards an expert system of regulatory molecular mechanisms. Nucleic Acids Res. 1998; 27(1):318-22. PMC: 148171. DOI: 10.1093/nar/27.1.318. View

Tsunoda T, Takagi T . Estimating transcription factor bindability on DNA. Bioinformatics. 1999; 15(7-8):622-30. DOI: 10.1093/bioinformatics/15.7.622. View

Suzuki Y, Maruyama K, Suyama A, Sugano S . Construction and characterization of a full length-enriched and a 5'-end-enriched cDNA library. Gene. 1997; 200(1-2):149-56. DOI: 10.1016/s0378-1119(97)00411-3. View

Perier R, Praz V, Junier T, Bonnard C, Bucher P . The eukaryotic promoter database (EPD). Nucleic Acids Res. 1999; 28(1):302-3. PMC: 102462. DOI: 10.1093/nar/28.1.302. View

Kawamoto S, Ohnishi T, Kita H, Chisaka O, Okubo K . Expression profiling by iAFLP: A PCR-based method for genome-wide gene expression profiling. Genome Res. 1999; 9(12):1305-12. PMC: 311005. DOI: 10.1101/gr.9.12.1305. View

Costello J, Fruhwald M, Smiraglia D, Rush L, Robertson G, Gao X . Aberrant CpG-island methylation has non-random and tumour-type-specific patterns. Nat Genet. 2000; 24(2):132-8. DOI: 10.1038/72785. View

Suzuki Y, Ishihara D, Sasaki M, Nakagawa H, Hata H, Tsunoda T . Statistical analysis of the 5' untranslated region of human mRNA using "Oligo-Capped" cDNA libraries. Genomics. 2000; 64(3):286-97. DOI: 10.1006/geno.2000.6076. View

Berk A, Sharp P . Sizing and mapping of early adenovirus mRNAs by gel electrophoresis of S1 endonuclease-digested hybrids. Cell. 1977; 12(3):721-32. DOI: 10.1016/0092-8674(77)90272-0. View

10.

McKnight S, Kingsbury R . Transcriptional control signals of a eukaryotic protein-coding gene. Science. 1982; 217(4557):316-24. DOI: 10.1126/science.6283634. View

11.

Gardiner-Garden M, Frommer M . CpG islands in vertebrate genomes. J Mol Biol. 1987; 196(2):261-82. DOI: 10.1016/0022-2836(87)90689-9. View

12.

Mitchell P, Tjian R . Transcriptional regulation in mammalian cells by sequence-specific DNA binding proteins. Science. 1989; 245(4916):371-8. DOI: 10.1126/science.2667136. View

13.

Bucher P . Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences. J Mol Biol. 1990; 212(4):563-78. DOI: 10.1016/0022-2836(90)90223-9. View

14.

Altschul S, Gish W, Miller W, Myers E, Lipman D . Basic local alignment search tool. J Mol Biol. 1990; 215(3):403-10. DOI: 10.1016/S0022-2836(05)80360-2. View

15.

Thompson J, Grunert F, Zimmermann W . Carcinoembryonic antigen gene family: molecular biology and clinical perspectives. J Clin Lab Anal. 1991; 5(5):344-66. DOI: 10.1002/jcla.1860050510. View

16.

Larsen F, Gundersen G, Lopez R, Prydz H . CpG islands as gene markers in the human genome. Genomics. 1992; 13(4):1095-107. DOI: 10.1016/0888-7543(92)90024-m. View

17.

Maruyama K, Sugano S . Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides. Gene. 1994; 138(1-2):171-4. DOI: 10.1016/0378-1119(94)90802-8. View

18.

Hauck W, Nedellec P, Turbide C, Stanners C, Barnett T, Beauchemin N . Transcriptional control of the human biliary glycoprotein gene, a CEA gene family member down-regulated in colorectal carcinomas. Eur J Biochem. 1994; 223(2):529-41. DOI: 10.1111/j.1432-1033.1994.tb19022.x. View

19.

Thompson J, Higgins D, Gibson T . CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994; 22(22):4673-80. PMC: 308517. DOI: 10.1093/nar/22.22.4673. View

20.

Hauck W, Stanners C . Transcriptional regulation of the carcinoembryonic antigen gene. Identification of regulatory elements and multiple nuclear factors. J Biol Chem. 1995; 270(8):3602-10. DOI: 10.1074/jbc.270.8.3602. View