ArticleGenome research2003
Nucleotide frequency variation across human genes.
Article in Genome research, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
51 citing papers in PubMed, 109 citations in OpenAlex.
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- The GC-content at the 5' ends of human protein-coding genes is undergoing mutational decay.Genome biology · 2024Article
- CSB-independent, XPC-dependent transcription-coupled repair inProceedings of the National Academy of Sciences of the United States of America · 2022Article
- The two faces of DNA oxidation in genomic and functional mosaicism during aging in human neurons.Frontiers in aging · 2022Review
- Nucleotide spacing distribution analysis for human genome.Mammalian genome : official journal of the International Mammalian Genome Society · 2021Article
- The Role of H3K4 Trimethylation in CpG Islands Hypermethylation in Cancer.Biomolecules · 2021Review
- An intron-derived motif strongly increases gene expression from transcribed sequences through a splicing independent mechanism in Arabidopsis thaliana.Scientific reports · 2019Article
- GC content of vertebrate exome landscapes reveal areas of accelerated protein evolution.BMC evolutionary biology · 2019Article
- Conserved Critical Evolutionary Gene Structures in Orthologs.Journal of molecular evolution · 2019Article
- Tail Wags the Dog? Functional Gene Classes Driving Genome-Wide GC Content in Plasmodium spp.Genome biology and evolution · 2019Article
- DNA methylation and DNA methyltransferases.Epigenetics & chromatin · 2017Review
- Rfx2 Stabilizes Foxj1 Binding at Chromatin Loops to Enable Multiciliated Cell Gene Expression.PLoS genetics · 2017Article
- Article
- Do Intron and Coding Sequences of Some Human-Mouse Orthologs Evolve as a Single Unit?Journal of molecular evolution · 2016Article
- Notes on the role of dynamic DNA methylation in mammalian development.Proceedings of the National Academy of Sciences of the United States of America · 2015Review
- The effects of chromatin organization on variation in mutation rates in the genome.Nature reviews. Genetics · 2015Review
- Unexpected selection to retain high GC content and splicing enhancers within exons of multiexonic lncRNA loci.RNA (New York, N.Y.) · 2015Article
- Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
The frequencies of individual nucleotides exhibit significant fluctuations across eukaryotic genes. In this paper, we investigate nucleotide variation across an averaged representation of all known human genes. Such a representation allows us to average out random fluctuations that constitute noise and uncover remarkable systematic trends in nucleotide distributions, particularly near boundaries between genetic elements--the promoter, exons, and introns. We propose that such variations result from differential mutational pressures and from the presence of specific regulatory motifs, such as transcription and splicing factor binding sites. Specifically, we observe significant GC and TA biases (excess of G over C and T over A) in noncoding regions of genes. Such biases are most probably caused by transcription-coupled mismatch repair, an effect that has recently been detected in mammalian genes. Subsequently, we examine the distribution of all hexanucleotides and identify motifs that are overrepresented within regulatory regions. By clustering and aligning such sequences, we recognize families of putative regulatory elements involved in exonic and intronic splicing control, and 3' mRNA processing. Some of our motifs have been identified in prior theoretical and experimental studies, thus validating our approach, but we detect several novel sequences that we propose as candidates for future functional assays and mutation screens for genetic disorders.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.