Prevalence of the initiator over the TATA box in human and yeast genes and identification of DNA motifs enriched in human TATA-less core promoters

Prevalence of the initiator over the TATA box in human and yeast genes and identification of DNA... The core promoter of eukaryotic genes is the minimal DNA region that recruits the basal transcription machinery to direct efficient and accurate transcription initiation. The fraction of human and yeast genes that contain specific core promoter elements such as the TATA box and the initiator (INR) remains unclear and core promoter motifs specific for TATA-less genes remain to be identified. Here, we present genome-scale computational analyses indicating that ∼ 76% of human core promoters lack TATA-like elements, have a high GC content, and are enriched in Sp1-binding sites. We further identify two motifs – M3 (SCGGAAGY) and M22 (TGCGCANK) – that occur preferentially in human TATA-less core promoters. About 24% of human genes have a TATA-like element and their promoters are generally AT-rich; however, only ∼ 10% of these TATA-containing promoters have the canonical TATA box (TATAWAWR). In contrast, ∼ 46% of human core promoters contain the consensus INR (YYANWYY) and ∼ 30% are INR-containing TATA-less genes. Significantly, ∼ 46% of human promoters lack both TATA-like and consensus INR elements. Surprisingly, mammalian-type INR sequences are present – and tend to cluster – in the transcription start site (TSS) region of ∼ 40% of yeast core promoters and the frequency of specific core promoter types appears to be conserved in yeast and human genomes. Gene Ontology analyses reveal that TATA-less genes in humans, as in yeast, are frequently involved in basic “housekeeping” processes, while TATA-containing genes are more often highly regulated, such as by biotic or stress stimuli. These results reveal unexpected similarities in the occurrence of specific core promoter types and in their associated biological processes in yeast and humans and point to novel vertebrate-specific DNA motifs that might play a selective role in TATA-independent transcription. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Gene Elsevier

Prevalence of the initiator over the TATA box in human and yeast genes and identification of DNA motifs enriched in human TATA-less core promoters

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Publisher
Elsevier
Copyright
Copyright © 2006 Elsevier B.V.
ISSN
0378-1119
eISSN
1879-0038
D.O.I.
10.1016/j.gene.2006.09.029
Publisher site
See Article on Publisher Site

Abstract

The core promoter of eukaryotic genes is the minimal DNA region that recruits the basal transcription machinery to direct efficient and accurate transcription initiation. The fraction of human and yeast genes that contain specific core promoter elements such as the TATA box and the initiator (INR) remains unclear and core promoter motifs specific for TATA-less genes remain to be identified. Here, we present genome-scale computational analyses indicating that ∼ 76% of human core promoters lack TATA-like elements, have a high GC content, and are enriched in Sp1-binding sites. We further identify two motifs – M3 (SCGGAAGY) and M22 (TGCGCANK) – that occur preferentially in human TATA-less core promoters. About 24% of human genes have a TATA-like element and their promoters are generally AT-rich; however, only ∼ 10% of these TATA-containing promoters have the canonical TATA box (TATAWAWR). In contrast, ∼ 46% of human core promoters contain the consensus INR (YYANWYY) and ∼ 30% are INR-containing TATA-less genes. Significantly, ∼ 46% of human promoters lack both TATA-like and consensus INR elements. Surprisingly, mammalian-type INR sequences are present – and tend to cluster – in the transcription start site (TSS) region of ∼ 40% of yeast core promoters and the frequency of specific core promoter types appears to be conserved in yeast and human genomes. Gene Ontology analyses reveal that TATA-less genes in humans, as in yeast, are frequently involved in basic “housekeeping” processes, while TATA-containing genes are more often highly regulated, such as by biotic or stress stimuli. These results reveal unexpected similarities in the occurrence of specific core promoter types and in their associated biological processes in yeast and humans and point to novel vertebrate-specific DNA motifs that might play a selective role in TATA-independent transcription.

Journal

GeneElsevier

Published: Mar 1, 2007

References

  • Content analysis of the core promoter region of human genes
    Bajic, V.B.; Choudhary, V.; Hock, C.K.
  • Synergy of human Pol II core promoter elements revealed by statistical sequence analysis
    Gershenzon, N.I.; Ioshikhes, I.P.
  • Composition-sensitive analysis of the human genome for regulatory signals
    Kel-Margoulis, O.V.
  • Destabilization of nucleosomes by an unusual DNA conformation adopted by poly(dA).poly(dT) tracts in vivo
    Shimizu, M.; Mori, T.; Sakurai, T.; Shindo, H.
  • Diverse transcriptional initiation revealed by fine, large-scale mapping of mRNA start sites
    Suzuki, Y.
  • Genome-wide analysis reveals strong correlation between CpG islands with nearby transcription start sites of genes and their tissue specificity
    Yamashita, R.; Suzuki, Y.; Sugano, S.; Nakai, K.

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