The sequencing of eukaryotic genomes also tells us a lot about how genetic information is organized within chromosomes. We now know that the density of genes varies greatly among and within chromosomes. For example, human chromosome 19 has a high density of genes, with about 26 genes per million base pairs. Chromosome 13, on the other hand, has only about 6.5 genes per million base pairs. Gene density can also vary among different regions of the same chromosome: some parts of the long arm of chromosome 13 have only 3 genes per million base pairs, whereas other parts have almost 30 genes per million base pairs. And the short arm of chromosome 13 contains almost no genes, consisting entirely of heterochromatin.

The functional role of DNA sequences that do not encode proteins, including repetitive DNA, has been addressed by the Encyclopedia of DNA Elements (ENCODE) project (see Chapter 15). The purpose of ENCODE was to identify all nucleotides within the human genome that have some function. The project concluded that much of the genome is transcribed and that at least 80% of the sequences are functional. However, some researchers have challenged the conclusion that the vast majority of DNA sequences are functional.

In addition, some DNA in eukaryotes is found associated with cytoplasmic organelles such as mitochondria and chloroplasts. This organelle DNA encodes traits that exhibit cytoplasmic inheritance (see Chapter 4). In contrast with nuclear DNA, organelle DNA is typically circular and is not complexed with histone proteins.