Unusual sequence characteristics of human chromosome 19 are conserved across 11 nonhuman primates.

TitleUnusual sequence characteristics of human chromosome 19 are conserved across 11 nonhuman primates.
Publication TypeJournal Article
Year of Publication2020
AuthorsHarris, RA, Raveendran, M, Worley, KC, Rogers, J
JournalBMC Evol Biol
Date Published2020 Feb 27
KeywordsAnimals, Base Composition, Base Sequence, Chromosomes, Chromosomes, Human, Pair 19, Conserved Sequence, CpG Islands, Dinucleoside Phosphates, DNA Methylation, Genome, Humans, Lemur, Mice, Multigene Family, Phylogeny, Primates, Promoter Regions, Genetic, Regulatory Sequences, Nucleic Acid

BACKGROUND: Human chromosome 19 has many unique characteristics including gene density more than double the genome-wide average and 20 large tandemly clustered gene families. It also has the highest GC content of any chromosome, especially outside gene clusters. The high GC content and concomitant high content of hypermutable CpG sites raises the possibility chromosome 19 exhibits higher levels of nucleotide diversity both within and between species, and may possess greater variation in DNA methylation that regulates gene expression.

RESULTS: We examined GC and CpG content of chromosome 19 orthologs across representatives of the primate order. In all 12 primate species with suitable genome assemblies, chromosome 19 orthologs have the highest GC content of any chromosome. CpG dinucleotides and CpG islands are also more prevalent in chromosome 19 orthologs than other chromosomes. GC and CpG content are generally higher outside the gene clusters. Intra-species variation based on SNPs in human common dbSNP, rhesus, crab eating macaque, baboon and marmoset datasets is most prevalent on chromosome 19 and its orthologs. Inter-species comparisons based on phyloP conservation show accelerated nucleotide evolution for chromosome 19 promoter flanking and enhancer regions. These same regulatory regions show the highest CpG density of any chromosome suggesting they possess considerable methylome regulatory potential.

CONCLUSIONS: The pattern of high GC and CpG content in chromosome 19 orthologs, particularly outside gene clusters, is present from human to mouse lemur representing 74 million years of primate evolution. Much CpG variation exists both within and between primate species with a portion of this variation occurring in regulatory regions.

Alternate JournalBMC Evol Biol
PubMed ID32106815
PubMed Central IDPMC7045612
Grant ListR24 OD011173 / OD / NIH HHS / United States

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