Telomeres form caps on the ends of chromosomes that prevent fusion of chromosomal ends and provide genomic stability.
During gametogenesis, reprogramming of the germ cells leads to elongation of telomeres up to their species-specific maximum.
In normal somatic cells, telomeres are progressively shortened with every cell division. This shortening in normal human cells limits the number of cell divisions. For human cells to proliferate beyond the senescence checkpoint, they need to stabilize telomere length. This is accomplished mainly by reactivation of the telomerase enzyme. Telomerase expression is under the control of many factors. Expression of telomerase can lead to cell immortalization and is activated during tumorigenesis, i.e. cancer.
Male Xq-telomeres are 1100 bp shorter than female Xq-telomeres.
The telomeric repeat found on all human chromosomes is “TTAGGG”.
The centromeres and telomeres of the human chromosomes are not defined as region attributes in the Ensembl perl API explicitely, so for checking these regions, one option is to pull them out of the UCSC table browser. For this, select the assembly and use the “Mapping and Sequencing tracks” group and the “Gap” table. The extracted locations of the human telomere regions is provided below for the genome assemblies GRCh37 (hg19) and GRCh38 (hg38). The coordinates are given in the 0-based UCSC coordinated system.
Telomere locations
Telomeres of chromosome 17 have not been defined for assembly GRCh37. They are short, but do exists nonetheless. An assembly patch will address this.
[table id=7 /]
Centromer locations
The centromers for assembly hg38 are defined in different ways in the UCSC system. According to an explanation by Brian Lee and Christopher Lee of UCSC there now is a specific browser track that “shows the location of Karen Miga’s centromere model sequences. However, these annotations can be smaller than the centromeres shown in the chromosome ideogram and Chromosome Bands track. (…) Depending on your purpose you could use the centromere model regions (red), or the broader Chromosome Bands Ideogram definition of centromere which overlap some annotations (cytoBandIdeo table), or the regions of the assembly that are just NNNNN’s (Gap track).” (link, link)
You can see this location in the screenshot below (from the browser):
As the gap extend is slightly larger than the defined regions, we will have to use the definition of “acen” ideogram regions from the gaps table in most cases where we actually need to use the underlying sequence. The combined centromer regions for hg38 are shown below:
[table id=11 /]
Sources:
- UCSC browser
- Rashid-Kolvear et al. 2007
- Moyzis et al. 1988
- Perner et al. 2003
- My original blog post in 2011