ArticleMolecular biology and evolution2023
Low Complexity Regions in Proteins and DNA are Poorly Correlated.
Article in Molecular biology and evolution, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Genomic indicators of gene function: a systematic assessment of the human genome.G3 (Bethesda, Md.) · 2026Article
- A deep learning-based score to evaluate multiple sequence alignments.Molecular biology and evolution · 2026Article
- A benchmarking framework for comparative evaluation of low-complexity region detection tools in the human proteome.Scientific reports · 2026Article
- Low-complexity regions in fungi display functional groups and are depleted in positively charged amino acids.NAR genomics and bioinformatics · 2025Article
- Characterizing features affecting local ancestry inference performance in admixed populations.American journal of human genetics · 2025Article
- Divergent evolution of low-complexity regions in the vertebrate CPEB protein family.Frontiers in bioinformatics · 2025Article
- Characterizing features affecting local ancestry inference performance in admixed populations.bioRxiv : the preprint server for biology · 2024Article
- Terminal regions of a protein are a hotspot for low complexity regions and selection.Open biology · 2024Article
- Evolution of Transcript Abundance is Influenced by Indels in Protein Low Complexity Regions.Journal of molecular evolution · 2024Article
- AlcoR: alignment-free simulation, mapping, and visualization of low-complexity regions in biological data.GigaScience · 2022Article
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Authors and funding
3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Low complexity sequences (LCRs) are well known within coding as well as non-coding sequences. A low complexity region within a protein must be encoded by the underlying DNA sequence. Here, we examine the relationship between the entropy of the protein sequence and that of the DNA sequence which encodes it. We show that they are poorly correlated whether starting with a low complexity region within the protein and comparing it to the corresponding sequence in the DNA or by finding a low complexity region within coding DNA and comparing it to the corresponding sequence in the protein. We show this is the case within the proteomes of five model organisms: Homo sapiens, Saccharomyces cerevisiae, Drosophila melanogaster, Caenorhabditis elegans, and Arabidopsis thaliana. We also report a significant bias against mononucleic codons in LCR encoding sequences. By comparison with simulated proteomes, we show that highly repetitive LCRs may be explained by neutral, slippage-based evolution, but compositionally biased LCRs with cryptic repeats are not. We demonstrate that other biological biases and forces must be acting to create and maintain these LCRs. Uncovering these forces will improve our understanding of protein LCR evolution.
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