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‘Genome design’ model and multicellular complexity: golden middle

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 pat...

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Autor principal: Vinogradov, Alexander E.
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2006
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1635334/
https://www.ncbi.nlm.nih.gov/pubmed/17062620
http://dx.doi.org/10.1093/nar/gkl773
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author Vinogradov, Alexander E.
author_facet Vinogradov, Alexander E.
author_sort Vinogradov, Alexander E.
collection PubMed
description 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 modules (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 organisms is probably caused by the burden of regulatory complexity acted on the intermediately expressed genes.
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spelling pubmed-16353342006-12-26 ‘Genome design’ model and multicellular complexity: golden middle Vinogradov, Alexander E. Nucleic Acids Res Computational Biology 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 modules (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 organisms is probably caused by the burden of regulatory complexity acted on the intermediately expressed genes. Oxford University Press 2006-11 2006-11-12 /pmc/articles/PMC1635334/ /pubmed/17062620 http://dx.doi.org/10.1093/nar/gkl773 Text en © 2006 The Author(s)
spellingShingle Computational Biology
Vinogradov, Alexander E.
‘Genome design’ model and multicellular complexity: golden middle
title ‘Genome design’ model and multicellular complexity: golden middle
title_full ‘Genome design’ model and multicellular complexity: golden middle
title_fullStr ‘Genome design’ model and multicellular complexity: golden middle
title_full_unstemmed ‘Genome design’ model and multicellular complexity: golden middle
title_short ‘Genome design’ model and multicellular complexity: golden middle
title_sort ‘genome design’ model and multicellular complexity: golden middle
topic Computational Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1635334/
https://www.ncbi.nlm.nih.gov/pubmed/17062620
http://dx.doi.org/10.1093/nar/gkl773
work_keys_str_mv AT vinogradovalexandere genomedesignmodelandmulticellularcomplexitygoldenmiddle