Finding Genome

Gene of Interest now has an index!  Complete with links to all eight gene posts.  That’s about 0.04% of the entire human genome.  At this rate, I’ll have discussed the entire human genome by sometime in November 2522…  So enjoy it while it lasts.

My brand-new index includes each gene’s cytogenetic location, so I thought I’d make a quick post to explain what that is.

Before the development of modern genetics, we could still study DNA by staining chromosomes and organizing them into a karyogram.  I made one of these back in high school.  You start with a print-out that looks something like this:

Then you cut out each chromosome, match up all 22 pairs (plus the x’s for girls or x/y for boys), and paste them on a clean sheet of paper like this:

My inner neat freak finds this so satisfying.  And this organization makes it easy to spot chromosomal abnormalities, like trisomy 21 (Down syndrome) which is caused by a third copy of chromosome 21 [1].

The bands on each chromosome are made by staining with Giemsa stain [2].  Chromosomal regions rich with adenine and thymine base pairs (AT-rich) stain darker in Giemsa stain. Regions rich with guanine and cytosine (GC-rich) stain lighter.  However, most genes are found in these lighter-stained, GC-rich regions – very few genes are found in the darker regions.  Which begs the question: if there are almost no genes in these darker regions, what’s that DNA for?  (More on that in a later post.)

These Giemsa-stained bands are useful in pinpointing the physical location of a specific gene inside a chromosome, or its cytogenetic location.  Using STAT4 as an example gene, let’s find its position on a chromosome.   Its cytogenetic location is 2q32.2.

The first number indicates which chromosome (1-22) contains the gene.  If the gene were located on one of the sex chromosomes, it would start with an ‘X’ or a ‘Y’ instead [3].

The letter ‘q’ refers the arm on which the gene can be found. Chromosomes are divided into two sections by a constriction called the centromere.  The ‘p’ refers to the shorter arm while ‘q’ refers to the longer arm [3].

The next set of numbers refers to the region and band position, respectively.  These positions are counted out from the centromere.  The number increases with increasing distance from the centromere.  Numbers after the decimal point refer to sub-band locations [3].  (In the example above, STAT4 is located on the 2nd sub-band of the 2nd band in region 3 of the long arm of chromosome 2).

Source: U.S. National Library of Medicine

These locations are identical for everyone – everybody has the same gene in the same spot.  That may seem obvious, but I think there’s something comforting about that universal organization.  To me it means, despite all our differences, we’re really a lot alike.

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References

[1] Patterson, D.; (2009). “Molecular genetic analysis of Down syndrome.” Human Genetics 126 (1): 195–214. PMID 19526251.
[2] Nussbaum, R.; McInnes, R.; Willard, H. (2015). Thompson & Thompson, Genetics in Medicine (Eighth ed.). Canada: Elsevier Inc. p. 58. ISBN 978-1-4377-0696-3.
[3] “How do geneticists indicate the location of a gene”.  Genetics Home Reference. 25 January 2016