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C. Chromosomal nomenclature

1. Relative lengths of chromosome arms

Chromosome arms are defined with respect to the kinetochore. Although the terms "kinetochore" and "centromere" are used interchangeably in chromosome nomenclature, it is probably more correct to refer to kinetochore, since we don't really see the centromere, which is simply a DNA sequence. Rather, we see the proteinaceous kinetochore, and the distinct heterochromatic staining that occurs in the vicinity of the centromere.

Long arm (l) and short arm (s) is expressed as a ratio l/s. These values have also been expressed as long arm (q) and short arm (p = "petite") in the study of human chromosomes and the arm ratio given as q/p.

Note: There is no such thing as a truly telocentric chromosome. If the centromere were at the end of the chromosome, it would be lost in a few cell divisions (See 
lecture 12). The term 'telocentric' simply refers to the fact that the short arm of the chromosome, including its telomere, is so short that it can't be seen under the microscope.


Figure 5.4 Karyotype and idiogram of Geimsa N-banded chromosomes of barley

Table 5.2 Comparison of q/p ratios in chromosome arms in barley.

Table 5.3 Comparison of q/p ratios in barley chromosomes, determined by different experimentors.

Tables 5.2 and 5.3 show the kind of ratios seen between long and short arms in barley. All barley chromosomes appear to be metacentric, with the most extreme q/p ratio being around 2. It's interesting to note that in Table 5.2, 10 chromosomes were measured for each homologue. In any given chromosome spread, chromosomes will be folded at different angles, and may vary in staining as well as in degree of coiling. All of these factors could lead to variation in something as simple as arm length. Table 5.3 also illustrates that arm ratios can vary from lab to lab. This could be due to experimental error, to variation in techniques used, or to variations in chromosome preparation techniques. For example, something like salt concentration or the amount of protease added during pretreatment could affect the arm length.


2. Regions and Bands

In human and other genomes, chromosomes are broken down into arms, p & q, regions, and bands. This is illustrated on human chromosome 15. The following rules apply:

Going outward from the kinetochore along the p arm, then, would be 15p11, 15p12, 15p13....
Going outward from the kinetochore along the q arm would be 15q11, 15q12, 15q13, 15q14 ...

3. Position of nucleolar organiser region (NOR)

The NOR is the site of ribosomal RNA genes. Usually, rRNA genes are tandemly-repeated in a hundred or more copies at a small number of NOR loci on several chromosomes. The NOR forms during chromosome decondensation in telophase. Since it contains rRNA genes it serves as the site of rRNA synthesis by RNA polymerase I. This region appears as a secondary constriction on certain chromosomes in the genome. The NOR is not a true constriction and is actually the same diameter as the rest of the chromosome. It appears as a constriction because it is negatively heteropycnotic ie. it does not pick up stain. The lack of staining at the NOR makes the remaining portion of the chromosome above the NOR appear to be removed from the rest of the chromosome as a chromosome fragment or satellite.

Each species has one or more homologous pairs with an NOR. Often each basic genome has a pair of satellite chromosomes. Satellites can serve as markers of basic genomes and are therefore valuable for taxonomic studies. Satellites are heterochromatic and can vary considerably in size.

Figure 2.1. Idiogram of Agropyron orientale (2n=28). The satellite chromosomes are placed at the beginning of the idiogram and are arranged according to the length of their satellites. The rest of the chromosomes are arranged according to the length of their short arms. One unit of the scale to the left of the idiogram equals 0.72 µm. (From Schulz-Schaeffer and Jurasits, 1962.

Figure 2.4 Scultz-Schaeffer. Satellite chromosomes of Bromus species arranged according to the length of the satellites. One scale unit equals 0.5 µm. (From Schulz-Schaeffer, 1960.


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