‘Genome design’ model and multicellular complexity: golden middle

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‘Genome design’ model and multicellular complexity: golden middle

Publisher
Oxford University Press
Publication Date
Nov 01, 2006
Source
PMC
Keywords
Disciplines
  • Biology
  • Communication
  • Design
License
Unknown

Abstract

gkl773 5906..5914 ‘Genome design’ model and multicellular complexity: golden middle Alexander E. Vinogradov* Institute of Cytology, Russian Academy of Sciences, St Petersburg 194064, Russia Received August 1, 2006; Revised September 13, 2006; Accepted September 28, 2006 ABSTRACT Human tissue-specific genes were reported to be longer than housekeeping genes (both in coding and intronic parts). The competing neutralist and adaptationist models were proposed to explain this observation. Here I show that in human genome the longest are genes with the intermediate expression pattern. From the standpoint of information theory, the regulation of such genes should be most complex. In the genomewide context, they are found here to have the higher informational load on all available levels: from participation in protein interaction networks, pathways and modules reflected in Gene Ontology categories through transcription factor regulatory sets and protein functional domains to amino acid tuples (words) in encoded proteins and nucleotide tuples in introns and promoter regions. Thus, the intermediately expressed genes have the higher functional and regulatory complexity that is reflected in their greater length (which is consistent with the ‘genome design’ model). The dichotomy of housekeeping versus tissue-specific entities is more pronounced on the modular level than on the molecular level. There are much lesser intermediate-specific mod- ules (modules overrepresented in the intermediately expressed genes) than housekeeping or tissue- specific modules (normalized to gene number). The dichotomy of housekeeping versus tissue- specific genes and modules in multicellular organ- isms is probably caused by the burden of regulatory complexity acted on the intermediately expressed genes. INTRODUCTION Human tissue-specific genes were reported to be longer than housekeeping genes, both in coding and intronic parts. The competing models were proposed to explain this observation: selection for economy (i

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