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• W2014317080 endingPage "485" @default.
• W2014317080 startingPage "475" @default.
• W2014317080 abstract "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. 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. the DNA region around TSSs, with the regulatory signals to bind the PIC. a technique based on extracting specific DNA-protein complexes by means of antibodies specific to the protein in question. Can be combined with sequencing (ChIP-seq) or hybridization techniques (ChIP-chip) to investigate the bound DNA. an enzyme or protein complex capable of changing the chromatin landscape e.g. through eviction or displacement of nucleosomes a cytosine followed by a guanine (the ‘p’ refers to the phosphate linker between the nucleotides), often discussed in terms of CpG islands (CGIs). a region where CpGs are over-represented. Because this is a statistical property, many definitions exist, often based on normalized CpG content. a ubiquitous TF that is often a part of the PIC. a promoter region where the CpG content is higher than expected based on the number of individual C and G nucleotides. a promoter region where the CpG content is lower or similar to that of genomic background based on the number of individual C and G nucleotides. the CpG content of a region normalized to that expected given the fraction of Cs and Gs in the DNA sequence, typically used in the definition of CGIs. the region immediately upstream of the TSS that is, on average, depleted of canonical nucleosomes. a protein complex that is assembled on TSSs to initiate transcription, consisting of RNAPII, general TFs, TAFs as well as many other proteins. the enzyme that reads DNA to produce mRNAs. protein that binds to DNA and regulates transcription a short (typically 5–15 nt) DNA sequence that is bound by a TF. the first genomic nucleotide that is transcribed in an mRNA." @default.
• W2014317080 created "2016-06-24" @default.
• W2014317080 creator A5026910430 @default.
• W2014317080 creator A5067360861 @default.
• W2014317080 date "2011-11-01" @default.
• W2014317080 modified "2023-09-25" @default.
• W2014317080 title "Genomic and chromatin signals underlying transcription start-site selection" @default.
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