title: The grammar of transcriptional regulation.
abstract: Eukaryotes employ combinatorial strategies to generate a variety of expression patterns from a relatively small set of regulatory DNA elements. As in any other language, deciphering the mapping between DNA and expression requires an understanding of the set of rules that govern basic principles in transcriptional regulation, the functional elements involved, and the ways in which they combine to orchestrate a transcriptional output. Here, we review the current understanding of various grammatical rules, including the effect on expression of the number of transcription factor binding sites, their location, orientation, affinity and activity; co-association with different factors; and intrinsic nucleosome organization. We review different methods that are used to study the grammar of transcription regulation, highlight gaps in current understanding, and discuss how recent technological advances may be utilized to bridge them.
authors.affiliation: Department of Computer Science, Applied Mathematics and Department of Molecular Cell Biology, Weizmann Institute of Science, 76100, Rehovot, Israel, shira.gabbay@weizmann.ac.il.
authors.forename: Shira
authors.initials: S
authors.lastname: Weingarten-Gabbay
authors.forename: Eran
authors.initials: E
authors.lastname: Segal
mesh_terms: D001665:Binding Sites; D004247:DNA / Q000235:genetics* / Q000378:metabolism; D005786:Gene Expression Regulation; D006801:Humans; D011485:Protein Binding; D012333:RNA, Messenger / Q000235:genetics* / Q000378:metabolism; D050436:Regulatory Elements, Transcriptional; D017422:Sequence Analysis, DNA; D017423:Sequence Analysis, RNA; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D012333:RNA, Messenger; D014157:Transcription Factors; D004247:DNA