13.2: DNA Packaging

Eukaryotes have large genomes compared to prokaryotes. In order to fit their genomes into a cell, eukaryotes must pack their DNA tightly inside the nucleus. To do so, DNA is wound around proteins called histones to form nucleosomes, the main unit of DNA packaging. Nucleosomes then coil into compact fibers known as chromatin.

You Have Enough DNA to Stretch to the Sun and Back Hundreds of Times

Most cells in the human body contain about 3 billion base pairs of DNA packaged into 23 pairs of chromosomes. It is hard to imagine exactly how much DNA these numbers represent. So how much packing has to happen to fit the genome into a cell?

We can gain some insight by expressing the genome in terms of length. If we were to arrange the DNA of a single human cell, like a skin cell, into a straight line, it would be two meters long–over 6.5 feet. The human body contains around 50 trillion human cells. This means that each person has a total of about 100 trillion meters of DNA. In other words, each person has enough DNA to stretch from the Earth to the Sun 300 times!

And humans do not have particularly large genomes–those of many fish, amphibians, and flowering plants are much larger. For example, the genome of the flowering plant Paris japonica is 25 times larger than the human diploid genome. These figures emphasize the astonishing task that eukaryotes must accomplish to pack their DNA inside cells.

Nucleosomes Are Central Players in DNA Packaging

Each nucleosome consists of DNA wrapped around a core of eight histone proteins. Each core is composed of four different types of histones—H2A, H2B, H3, and H4—that are each present in two copies. Another type of histone—H1—binds to both the nucleosome and the linker DNA, stabilizing the structure.

DNA becomes more compact as nucleosomes and linker DNA coil into chromatin fibers. Uncondensed chromatin fibers, or euchromatin, are approximately 10 nm in diameter. Nucleosomes resemble beads on a string in these fibers. As DNA continues to condense, the 10-nm fibers coil into strands that are approximately 30 nm thick, which in turn form loops that make 300-nm thick fibers. When chromatin is fully compacted it is known as heterochromatin.

The loosely packed structure of euchromatin allows enzymes, such as RNA polymerase, access to the DNA. Transcription, therefore, tends to occur predominantly in euchromatic regions of the genome, which are rich in genes. By contrast, the tightly packed structure of heterochromatin blocks access to the DNA, preventing transcription. Heterochromatin predominates in the centromeres and telomeres of chromosomes, where highly repetitive DNA sequences are much more common than genes. Furthermore, organisms can dynamically adjust the level of DNA packing in response to cellular and external environmental cues, de-condensing DNA when genes need to be turned on, and re-condensing it to turn them off.

In eukaryotes, double-stranded DNA is specially organized within a membrane-bound nucleus to accommodate the cell's limited space.

At the first level of compaction, DNA is wrapped tightly around specific proteins called histones. A histone core and the DNA wrapped around it are together known as a nucleosome, the basic unit of DNA packaging. Nucleosomes are joined together by linker DNA to resemble beads on a string. In the next level of packaging, nucleosomes and linker DNA coil to form chromatin fibers.

Finally, additional fibrous proteins compact the chromatin even further, allowing such long lengths of DNA into such tightly-condensed units recognized as chromosomes, depending on the phase of cell division.