Systems biology of regulatory motifs and networks – towards understanding gene expression from the DNA sequence
The regulation of gene expression in response to developmental or environmental stimuli is a crucial process in all organisms. Transcription is regulated by trans-acting transcription factors that recognize cis-regulatory DNA elements (CRMs or enhancers) and function in a combinatorial fashion. Enhancers retain their activity even when placed in artificial contexts (e.g. in reporter gene assays), but the exact requirements for enhancer function, i.e. a regulatory code, remains unknown and enhancer activity cannot be predicted from the DNA sequence.
Identification of transcription factor binding sites from ChIP-seq data at high resolution
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