A transcription factor affinity-based code for mammalian transcription initiation

A transcription factor affinity-based code for mammalian transcription initiation.

The recent arrival of large-scale cap analysis of gene expression (CAGE) data sets in mammals provides a wealth of quantitative information on coding and noncoding RNA polymerase II transcription start sites (TSS). Genome-wide CAGE studies reveal that a large fraction of TSS exhibit peaks where the vast majority of associated tags map to a particular location ( approximately 45%), whereas other...

A code for transcription initiation in mammalian genomes.

Genome-wide detection of transcription start sites (TSSs) has revealed that RNA Polymerase II transcription initiates at millions of positions in mammalian genomes. Most core promoters do not have a single TSS, but an array of closely located TSSs with different rates of initiation. As a rule, genes have more than one such core promoter; however, defining the boundaries between core promoters i...

Supplemental Data Genome-wide Prediction of Mammalian Enhancers Based on Analysis of Transcription-Factor Binding Affinity

Affinity score is from human to mouse alignment (affinity of the weaker species is shown). Affinity score is from human to mouse alignment (affinity in the weaker species is shown). Affinity score is from human to mouse alignment (affinity of the weaker species is shown). Compare to Table S2 (predictions made using EEL). Predicted enhancer modules with two or more GLI sites in a single predicte...

Genome-wide Prediction of Mammalian Enhancers Based on Analysis of Transcription-Factor Binding Affinity

Understanding the regulation of human gene expression requires knowledge of the "second genetic code," which consists of the binding specificities of transcription factors (TFs) and the combinatorial code by which TF binding sites are assembled to form tissue-specific enhancer elements. Using a novel high-throughput method, we determined the DNA binding specificities of GLIs 1-3, Tcf4, and c-Et...

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