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Literature DB >> 2027755

Non-methylated islands in fish genomes are GC-poor.

S Cross¹, P Kovarik, J Schmidtke, A Bird.

Abstract

In the vertebrate genomes studied to date the 5' end of many genes are associated with distinctive sequences known as CpG islands. CpG islands have three properties: they are non-methylated; the dinucleotide CpG occurs at the frequency predicted by base composition; and they are GC-rich. Unexpectedly we have found that CpG islands in certain fish only have the first two properties; that is, their GC-content is not elevated compared to bulk genomic DNA. Based on this finding, we speculate that the GC-richness of CpG islands in vertebrates other than fish is a passive consequence of a higher mutation rate in regions of open chromatin under conditions where the nucleotide precursor pools are biased.

Entities: Chemical

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Year: 1991 PMID： 2027755 PMCID： PMC333903 DOI： 10.1093/nar/19.7.1469

Source DB: PubMed Journal: Nucleic Acids Res ISSN： 0305-1048 Impact factor: 16.971

22 in total

10. Comparative genomic study reveals a transition from TA richness in invertebrates to GC richness in vertebrates at CpG flanking sites: an indication for context-dependent mutagenicity of methylated CpG sites.

Authors: Yong Wang; Frederick C C Leung
Journal: Genomics Proteomics Bioinformatics Date: 2008-12 Impact factor: 7.691

Non-methylated islands in fish genomes are GC-poor.

1. Compositional transitions in the nuclear genomes of cold-blooded vertebrates.

2. Nucleotide sequence of the trout metallothionein A gene 5' regulatory region.

3. High levels of de novo methylation and altered chromatin structure at CpG islands in cell lines.

4. Alternative chromatin structure at CpG islands.

5. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase.

6. The beta-actin gene of carp (Ctenopharyngodon idella).

7. CpG islands in vertebrate genomes.

8. Molecular basis of base substitution hotspots in Escherichia coli.

9. Mutation rates differ among regions of the mammalian genome.

10. Compositional patterns in the nuclear genome of cold-blooded vertebrates.

1. Methylation of genomes and genes at the invertebrate-vertebrate boundary.

2. The major compositional transitions in the vertebrate genome.

3. The fission yeast gene pmt1+ encodes a DNA methyltransferase homologue.

Review 4. The distribution of genes on chromosomes: a cytological approach.

5. Synthetic CpG islands reveal DNA sequence determinants of chromatin structure.

6. Improved Prediction of Non-methylated Islands in Vertebrates Highlights Different Characteristic Sequence Patterns.

Review 7. Chromatin dynamics at the maternal to zygotic transition: recent advances from the zebrafish model.

8. Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates.

9. CpG island density and its correlations with genomic features in mammalian genomes.

10. Comparative genomic study reveals a transition from TA richness in invertebrates to GC richness in vertebrates at CpG flanking sites: an indication for context-dependent mutagenicity of methylated CpG sites.