ArticleBMC genomics2004
Comprehensive analysis of the base composition around the transcription start site in Metazoa.
Article in BMC genomics, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 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
45 citing papers in PubMed, 75 citations in OpenAlex.
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- Genome-Wide Prediction of Transcription Start Sites in Conifers.International journal of molecular sciences · 2022Article
- Why are so many MLL lysine methyltransferases required for normal mammalian development?Cellular and molecular life sciences : CMLS · 2019Review
- Genomic Landscape of Methylation Islands in Hymenopteran Insects.Genome biology and evolution · 2018Article
- Energetic funnel facilitates facilitated diffusion.Nucleic acids research · 2018Article
- A damaged genome's transcriptional landscape through multilayered expression profiling around in situ-mapped DNA double-strand breaks.Nature communications · 2017Article
- Evolutionary Transition of Promoter and Gene Body DNA Methylation across Invertebrate-Vertebrate Boundary.Molecular biology and evolution · 2016Article
- Distribution of CpG Motifs in Upstream Gene Domains in a Reef Coral and Sea Anemone: Implications for Epigenetics in Cnidarians.PloS one · 2016Article
- GC skew is a conserved property of unmethylated CpG island promoters across vertebrates.Nucleic acids research · 2015Article
- Genome-wide analysis of promoters: clustering by alignment and analysis of regular patterns.PloS one · 2014Article
- Drosophila functional elements are embedded in structurally constrained sequences.PLoS genetics · 2013Article
- Genome-wide computational prediction and analysis of core promoter elements across plant monocots and dicots.PloS one · 2013Article
- Position-dependent correlations between DNA methylation and the evolutionary rates of mammalian coding exons.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- R-loop formation is a distinctive characteristic of unmethylated human CpG island promoters.Molecular cell · 2012Article
- Opposite GC skews at the 5' and 3' ends of genes in unicellular fungi.BMC genomics · 2011Article
- Eukaryotic and prokaryotic promoter prediction using hybrid approach.Theory in biosciences = Theorie in den Biowissenschaften · 2011Article
- Amino acid biosynthetic cost and protein conservation.Journal of molecular evolution · 2011Article
- Article
- Structural genomics: correlation blocks, population structure, and genome architecture.Current genomics · 2011Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe transcription start site of a metazoan gene remains poorly understood, mostly because there is no clear signal present in all genes. Now that several sequenced metazoan genomes have been annotated, we have been able to compare the base composition around the transcription start site for all annotated genes across multiple genomes.
resultsThe most prominent feature in the base compositions is a significant local variation in G+C content over a large region around the transcription start site. The change is present in all animal phyla but the extent of variation is different between distinct classes of vertebrates, and the shape of the variation is completely different between vertebrates and arthropods. Furthermore, the height of the variation correlates with CpG frequencies in vertebrates but not in invertebrates and it also correlates with gene expression, especially in mammals. We also detect GC and AT skews in all clades (where %G is not equal to %C or %A is not equal to %T respectively) but these occur in a more confined region around the transcription start site and in the coding region.
conclusionsThe dramatic changes in nucleotide composition in humans are a consequence of CpG nucleotide frequencies and of gene expression, the changes in Fugu could point to primordial CpG islands, and the changes in the fly are of a totally different kind and unrelated to dinucleotide frequencies.
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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.