Eric Davidson's Regulatory Genome for Computer Science: Causality, Logic, and Proof Principles of the Genomic cis-Regulatory Code
نویسندگان
چکیده
منابع مشابه
Logic Functions of the Genomic Cis-regulatory Code
cis-Regulatory modules that control developmental gene expression process the regulatory inputs provided by the transcription factors for which they contain specific target sites. A prominent class of cis-regulatory processing functions can be modeled as logic operations. Many of these are combinatorial because they are mediated by multiple sites, although others are unitary. In this work, we i...
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For cellular fitness and survival, gene expression levels need to be regulated in response to a wealth of cellular and environmental signals. TFs (transcription factors) execute a large part of this regulation by interacting with the basal transcription machinery at promoter regions. Archaea are characterized by a simplified eukaryote-like basal transcription machinery and bacteria-type TFs, wh...
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The definitive feature of the many thousand cis-regulatory control modules in an animal genome is their information processing capability. These modules are "wired" together in large networks that control major processes such as development; they constitute "genomic computers." Each control module receives multiple inputs in the form of the incident transcription factors which bind to them. The...
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Urochordates are the closest relatives of vertebrates and at the larval stage, possess a characteristic bilateral chordate body plan. In vertebrates, the genes that orchestrate embryonic patterning are in part regulated by highly conserved non-coding elements (CNEs), yet these elements have not been identified in urochordate genomes. Consequently the evolution of the cis-regulatory code for uro...
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ژورنال
عنوان ژورنال: Journal of Computational Biology
سال: 2019
ISSN: 1557-8666
DOI: 10.1089/cmb.2019.0144