ArticleNucleic acids research2006
'Genome design' model and multicellular complexity: golden middle.
Article in Nucleic acids research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers, 1 of them a synthesis that pooled it.
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Who cites it
21 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Cellular Biogenetic Law and Its Distortion by Protein Interactions: A Possible Unified Framework for Cancer Biology and Regenerative Medicine.International journal of molecular sciences · 2022Pooled it
- An information content principle explains regulatory patterns of gene expression across human tissues.Nature communications · 2026Article
- Polyploidy as a Fundamental Phenomenon in Evolution, Development, Adaptation and Diseases.International journal of molecular sciences · 2022Review
- Growth of Biological Complexity from Prokaryotes to Hominids Reflected in the Human Genome.International journal of molecular sciences · 2021Article
- Phylostratic Shift of Whole-Genome Duplications in Normal Mammalian Tissues towards Unicellularity Is Driven by Developmental Bivalent Genes and Reveals a Link to Cancer.International journal of molecular sciences · 2020Article
- CTCF-mediated chromatin loops enclose inducible gene regulatory domains.BMC genomics · 2016Article
- Deep transcriptome sequencing provides new insights into the structural and functional organization of the wheat genome.Genome biology · 2015Article
- Conservation in first introns is positively associated with the number of exons within genes and the presence of regulatory epigenetic signals.BMC genomics · 2014Article
- What are the determinants of gene expression levels and breadths in the human genome?Human molecular genetics · 2012Article
- Article
- Introns form compositional clusters in parallel with the compositional clusters of the coding sequences to which they pertain.Journal of molecular evolution · 2011Article
- Expression breadth and expression abundance behave differently in correlations with evolutionary rates.BMC evolutionary biology · 2010Article
- Selection for the compactness of highly expressed genes in Gallus gallus.Biology direct · 2010Article
- Genome-wide functional analysis of human 5' untranslated region introns.Genome biology · 2010Article
- DNA methylation and genome evolution in honeybee: gene length, expression, functional enrichment covary with the evolutionary signature of DNA methylation.Genome biology and evolution · 2010Article
- Composition and regulation of maternal and zygotic transcriptomes reflects species-specific reproductive mode.Genome biology · 2010Article
- Adaptive Evolution Hotspots at the GC-Extremes of the Human Genome: Evidence for Two Functionally Distinct Pathways of Positive Selection.Advances in bioinformatics · 2010Article
- In plants, expression breadth and expression level distinctly and non-linearly correlate with gene structure.Biology direct · 2009Article
- Intergenic and genic sequence lengths have opposite relationships with respect to gene expression.PloS one · 2008Article
- A structural split in the human genome.PloS one · 2007Article
Corrections and comments
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1 author.
Funding
No grant is acknowledged in the PubMed record.
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 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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