The Human Genomic Melting Map

Abstract

In a living cell, the antiparallel double-stranded helix of DNA is a dynamically changing structure. The structure relates to interactions between and within the DNA strands, and the array of other macromolecules that constitutes functional chromatin. It is only through its changing conformations that DNA can organize and structure a large number of cellular functions. In particular, DNA must locally uncoil, or melt, and become single-stranded for DNA replication, repair, recombination, and transcription to occur. It has previously been shown that this melting occurs cooperatively, whereby several base pairs act in concert to generate melting bubbles, and in this way constitute a domain that behaves as a unit with respect to local DNA single-strandedness. We have applied a melting map calculation to the complete human genome, which provides information about the propensities of forming local bubbles determined from the whole sequence, and present a first report on its basic features, the extent of cooperativity, and correlations to various physical and biological features of the human genome. Globally, the melting map covaries very strongly with GC content. Most importantly, however, cooperativity of DNA denaturation causes this correlation to be weaker at resolutions fewer than 500 bps. This is also the resolution level at which most structural and biological processes occur, signifying the importance of the informational content inherent in the genomic melting map. The human DNA melting map may be further explored at http://meltmap.uio.no.

Analysis of mutational spectra by denaturing capillary electrophoresis

“…To this end we have worked with our collaborators to have the melting map of the known human genome calculated and made publicly available 25 Soon, the reagent set for the panexonic human genome should be defined. Most recently we have illustrated how the Ekstrøm's laboratory development of cycling denaturing capillary electrophoresis (CyDCE) eliminated the labor-intensive optimization steps attendant on constant denaturing systems.…”

“…The sensitivity of DCE, including CyDCE, permits pooling of 100 persons' DNA to scan and enumerate mutant sequences for any and all human exonic sequences. Assuming ~250,000 scannable exonic segments 25 and the need to scan case cohorts of 10,000 persons for each of 100 common diseases 80 , the task of testing each gene for statistical association with risk for any of these common diseases seems prodigious. However, with 100 person DNA pools, the task is represented by "only" 250,000 x 10,000 = 2.5 x 10 9 CyDCE capillary runs.…”

“…An isomelting domain is a DNA sequence in which calculation of the equilibrium melting temperature reveals all base pairs to have the same melting temperature, T m. As may be seen for the human mitochondrial genome in figure 1 isomelting domains are as short as 50 bp or greater than 1000 bp in length. In 2007, the melting map of the known nuclear sequences of the human genome was calculated and made publicly available 25 . Though limited by the incompleteness of the Human Genome Project (Critical non-repetitive sequences such as in the subtelomeric regions of many chromosomes remain undefined.…”

“…Though limited by the incompleteness of the Human Genome Project (Critical non-repetitive sequences such as in the subtelomeric regions of many chromosomes remain undefined. ), the sequences comprising all known human exons and their splice sites were included in the melting map 25 . The calculations to use this information to define suitable reagents (restriction enzymes, DNA extension primers) for all exons are in progress (E. Hovig, PubGene, Inc., personal communication).…”

“…Solutions of chemicals, which stabilize single stranded DNA, may also be used to define a condition of melting/annealing equilibrium. In physiological saline the range of melting temperatures of the isomelting domains of the human genome is 48°-96°C 25 . In practice it is desirable to work at lower temperatures to avoid DNA degradation and this may be achieved by the use of chemical denaturants such as urea.…”