On the length, weight and GC content of the human genome

Abstract

Objective Basic parameters commonly used to describe genomes including length, weight and relative guanine-cytosine (GC) content are widely cited in absence of a primary source. By using updated data and original software we determined these values to the best of our knowledge as standard reference for the whole human nuclear genome, for each chromosome and for mitochondrial DNA. We also devised a method to calculate the relative GC content in the whole messenger RNA sequence set and in transcriptomes by multiplying the GC content of each gene by its mean expression level. Results The male nuclear diploid genome extends for 6.27 Gigabase pairs (Gbp), is 205.00 cm (cm) long and weighs 6.41 picograms (pg). Female values are 6.37 Gbp, 208.23 cm, 6.51 pg. The individual variability and the implication for the DNA informational density in terms of bits/volume were discussed. The genomic GC content is 40.9%. Following analysis in different transcriptomes and species, we showed that the greatest deviation was observed in the pathological condition analysed (trisomy 21 leukaemic cells) and in Caenorhabditis elegans . Our results may represent a solid basis for further investigation on human structural and functional genomics while also providing a framework for other genome comparative analysis. Electronic supplementary material The online version of this article (10.1186/s13104-019-4137-z) contains supplementary material, which is available to authorized users.

Validation of preimplantation genetic tests for aneuploidy (PGT-A) with DNA from spent culture media (SCM): concordance assessment and implication

“…This difference is why DNA with low GC-content is less stable than DNA with high GC-content. Among all 22 autosomes, the average of GC-content is 41.62% [19,20]. 27.27%, 6/22 of autosomes have GC contents below 40%.…”

“…Due to small sample size, we cannot robustly ascertain whether a low GC-content sequence would be more vulnerable to DNA breakpoints than a high GC-content sequence. However, utilizing GC content and reciprocal sub-chromosomal arm gain-loss complementary as a reference may prove a more e cient tool in distinguishing real DNA segments from NGS data noise generated from a sample of DNA in SCM [19,32] .…”

Investigation of cell nucleus heterogeneity

“…This pronounced difference in stiffness may be explained in terms of molecular structures of chromosomal DNA and mRNA molecules within the nucleus, given that Henderson et al (26) observed that regions of low DNA have a high RNA concentration. DNA molecules in eukaryotic cells are thin polymers of length 3-6 cm (36), that must be compacted to fit in the finite volume of a cell nucleus (typically of diameter is 5-10 μm). Thus, the DNA molecule is envisioned as an extremely long thin string of moderate elasticity that is bent into the configurations required for packaging, and, when associated with histones, this compacted complex forms chromatin (37).…”

Applications of Genome Editing Technology in Research on Chromosome Aneuploidy Disorders

“…Monosomies (possessing only one chromosome of a pair) are basically deleterious due to the level of gene expression being insufficient for cell survival; most such cases, except for monosomy X, are thus embryonically lethal [13]. In contrast, live births occur for trisomies of chromosomes 13, 18, 21, X, and Y, owing to the smaller number of genes encoding proteins located on these chromosomes in comparison to the other autosomal chromosomes [14][15][16][17][18]. However, trisomy 13 and trisomy 18 have severe phenotypic consequences, which are rarely compatible with long-term survival [19][20][21][22].…”