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.

中文翻译：

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人类 19 号染色体的异常序列特征在 11 种非人类灵长类动物中是保守的。

背景技术人类19号染色体具有许多独特的特征，包括基因密度是全基因组平均值的两倍以上以及20个大型串联聚类基因家族。它还具有所有染色体中最高​​的 GC 含量，尤其是在基因簇之外。高GC含量和随之而来的高可变CpG位点含量增加了19号染色体在物种内部和物种之间表现出更高水平的核苷酸多样性的可能性，并且可能在调节基因表达的DNA甲基化方面具有更大的变异。结果 我们检查了灵长类动物代表的 19 号染色体直系同源物的 GC 和 CpG 含量。在所有 12 种具有合适基因组组装的灵长类动物中，19 号染色体直系同源染色体的 GC 含量最高。CpG 二核苷酸和 CpG 岛在 19 号染色体直向同源物中也比其他染色体更普遍。基因簇之外的GC和CpG含量通常较高。基于人类常见 dbSNP、恒河猴、食蟹猕猴、狒狒和狨猴数据集中的 SNP 的种内变异在 19 号染色体及其直系同源物上最为普遍。基于 phyloP 保守性的种间比较显示 19 号染色体启动子侧翼和增强子区域的核苷酸进化加速。这些相同的调控区域显示出所有染色体中最高​​的 CpG 密度，表明它们具有相当大的甲基化调控潜力。结论 19 号染色体直向同源物（特别是基因簇外）中存在高 GC 和 CpG 含量的模式，从人类狐猴到小鼠狐猴，代表了 7400 万年的灵长类动物进化。许多 CpG 变异存在于灵长类动物物种内部和之间，其中一部分变异发生在调节区域。