ArticleGenome biology2009
Tandem and cryptic amino acid repeats accumulate in disordered regions of proteins.
Article in Genome biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.
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Who cites it
56 citing papers in PubMed.
- Longer internal exons tend to have more tandem repeats and more frequently experience insertions and deletions.Life science alliance · 2025Article
- Chromosome-level genome assembly for Sichuan taimen (Hucho bleekeri) reveals the extraordinary tandem repeat proportions and its persistent population shrinkage.BMC genomics · 2025Article
- Kingdom-wide CRISPR guide design with ALLEGRO.Nucleic acids research · 2025Article
- Article
- Adaptive protein evolution through length variation of short tandem repeats inScience advances · 2023Article
- Expansion and functional analysis of the SR-related protein family across the domains of life.RNA (New York, N.Y.) · 2022Article
- LCD-Composer: an intuitive, composition-centric method enabling the identification and detailed functional mapping of low-complexity domains.NAR genomics and bioinformatics · 2021Article
- Homopeptide and homocodon levels across fungi are coupled to GC/AT-bias and intrinsic disorder, with unique behaviours for some amino acids.Scientific reports · 2021Article
- Article
- Disentangling the complexity of low complexity proteins.Briefings in bioinformatics · 2020Review
- Article
- Atypical structural tendencies among low-complexity domains in the Protein Data Bank proteome.PLoS computational biology · 2020Article
- Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases.Nucleic acids research · 2019Review
- Compound Dynamics and Combinatorial Patterns of Amino Acid Repeats Encode a System of Evolutionary and Developmental Markers.Genome biology and evolution · 2019Article
- Allelic Diversity of Acetyl Coenzyme A CarboxylaseInternational journal of molecular sciences · 2019Article
- Proteome-scale relationships between local amino acid composition and protein fates and functions.PLoS computational biology · 2018Article
- Biological Roles of Protein-Coding Tandem Repeats in the YeastJournal of fungi (Basel, Switzerland) · 2018Article
- POTENCI: prediction of temperature, neighbor and pH-corrected chemical shifts for intrinsically disordered proteins.Journal of biomolecular NMR · 2018Article
- Comparative analysis of low complexity regions in Plasmodia.Scientific reports · 2018Article
- The Repeat Sequences and Elevated Substitution Rates of the ChloroplastFrontiers in plant science · 2018Article
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2 authors.
Funding
Abstract
backgroundAmino acid repeats (AARs) are common features of protein sequences. They often evolve rapidly and are involved in a number of human diseases. They also show significant associations with particular Gene Ontology (GO) functional categories, particularly transcription, suggesting they play some role in protein function. It has been suggested recently that AARs play a significant role in the evolution of intrinsically unstructured regions (IURs) of proteins. We investigate the relationship between AAR frequency and evolution and their localization within proteins based on a set of 5,815 orthologous proteins from four mammalian (human, chimpanzee, mouse and rat) and a bird (chicken) genome. We consider two classes of AAR (tandem repeats and cryptic repeats: regions of proteins containing overrepresentations of short amino acid repeats).
resultsMammals show very similar repeat frequencies but chicken shows lower frequencies of many of the cryptic repeats common in mammals. Regions flanking tandem AARs evolve more rapidly than the rest of the protein containing the repeat and this phenomenon is more pronounced for non-conserved repeats than for conserved ones. GO associations are similar to those previously described for the mammals, but chicken cryptic repeats show fewer significant associations. Comparing the overlaps of AARs with IURs and protein domains showed that up to 96% of some AAR types are associated preferentially with IURs. However, no more than 15% of IURs contained an AAR.
conclusionsTheir location within IURs explains many of the evolutionary properties of AARs. Further study is needed on the types of IURs containing AARs.
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