Telomeres are sequences at the ends of linear chromosomes that protect the essential part of the chromosome from damage following repeated rounds of DNA replication.
Because of the way DNA replication works, it is impossible to replicate both stands of parental DNA right to the very end. Consequently, after each round of DNA replication the chromosome loses a little bit of DNA and the ends get shorter and shorter.
The telomere consists of multiple copies of repetitive DNA. In the case of humans, the repeat is (TTAGGG)n where "n" is usually between 1500-2000 in germ line cells. Thus, the average telomere is about 10 kb (10,000 base pairs) in length (Riethman 2008).
Genomes & Junk DNA
Total Junk so far
After every cell division the telomere gets a little shorter so that in old individuals the average length is reduced to about 2-3 kb in most somatic cells. The original length is preserved in germ line cells.
There are 23 chromosomes in humans. If the average telomere length is about 10 kb then the total amount of TTAGGG repeats is 230 kb, or far less than 1% of the genome. Even if the total amount of essential sequence at chromosome ends is increased to include adjacent regions, it won't even come close to a significant percentage. Thus, while telomeric DNA is essential non-coding DNA—and not junk— it doesn't change our calculation.
[Image Credit: The image shows human chromosomes labelled with a telomere probe (yellow), from Christoher Counter at Duke University.]
Riethman, H. (2008) Human Telomere Structure and Biology. Annual Review of Genomics and Human Genetics 9: epub ahead of print [doi:10.1146/annurev.genom.8.021506.172017]