Abstract

The identification and characterization of mammalian core promoters and transcription start sites is a prerequisite to understanding how RNA polymerase II transcription is controlled. New experimental technologies have enabled genome-wide discovery and characterization of core promoters, revealing that most mammalian genes do not conform to the simple model in which a TATA box directs transcription from a single defined nucleotide position. In fact, most genes have multiple promoters, within which there are multiple start sites, and alternative promoter usage generates diversity and complexity in the mammalian transcriptome and proteome. Promoters can be described by their start site usage distribution, which is coupled to the occurrence of cis-regulatory elements, gene function and evolutionary constraints. A comprehensive survey of mammalian promoters is a major step towards describing and understanding transcriptional control networks.

Author affiliations

1. ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane QLD, 4072, Australia.
2. The Bioinformatics Centre, Department of Molecular Biology & Biotech Research and Innovation Centre, Ole Maaløes Vej 5, DK-2100 København Ø, Denmark.
3. Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
4. Genome Science Laboratory, Discovery and Research Institute, RIKEN Wako Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
5. Computational Biology Unit, Bergen Center for Computational Science, and Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, N-5008 Bergen, Norway.
6. MRC Functional Genetics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, United Kingdom.

Correspondence to: David A. Hume¹ Email: d.hume@imb.uq.edu.au

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