Genomic and chromatin signals underlying transcription start-site selection

• Published in: Trends in genetics Vol. 27; no. 11; pp. 475 - 485
• Main Authors: Valen, Eivind, Sandelin, Albin
• Format: Journal Article
• Language: English
• Published: Amsterdam Elsevier Ltd 01.11.2011; Elsevier
• Subjects: Animals; Base Sequence - physiology; Biological and medical sciences; Chromatin - physiology; Chromatin. Chromosome; Diverse techniques; Fundamental and applied biological sciences. Psychology; Gene Expression Regulation; Genetics of eukaryotes. Biological and molecular evolution; Genome - physiology; Humans; Medical Education; Models, Biological; Molecular and cellular biology; Molecular genetics; Regulatory Sequences, Nucleic Acid - physiology; Signal Transduction; Transcription Initiation Site - physiology; Transcription, Genetic; Chromosome; Genetics; Chromatin; Transcription; Genomics; Selection
• ISSN: 0168-9525
• DOI: 10.1016/j.tig.2011.08.001

A central question in cellular biology is how the cell regulates transcription and discerns when and where to initiate it. Locating transcription start sites (TSSs), the signals that specify them, and ultimately elucidating the mechanisms of regulated initiation has therefore been a recurrent theme. In recent years substantial progress has been made towards this goal, spurred by the possibility of applying genome-wide, sequencing-based analysis. We now have a large collection of high-resolution datasets identifying locations of TSSs, protein–DNA interactions, and chromatin features over whole genomes; the field is now faced with the daunting challenge of translating these descriptive maps into quantitative and predictive models describing the underlying biology. We review here the genomic and chromatin features that underlie TSS selection and usage, focusing on the differences between the major classes of core promoters.