Dna content,c value paradox, euchromatin heterochromatin, banding pattern

class notes prepared for UG and PG students on DNA

1. DNA Content
DNA content is defined as the amount of DNA in one copy or in the haploid chomosomes of an
organism. Haploid DNA content is referred to as the "C-value".
The DNA content of an organism can be measured by weight or number of base pairs in a single
copy of the entire sequence of DNA found within cells of that organism.
DNA content varies greatly among organisms. In general, eukaryotes have more DNA content
than prokaryotes.
Among prokaryotes the variation of DNA content or genome size is small ranging only an order
of magnitude, from 0.5 to 5 Mb. The genome sizes of eukaryotes, on the other hand, vary
>80,000-fold. Even among animals there is a nearly 3000-fold variation, and in plants basal
genomes sizes vary by a factor of >6000.
C- Value Complexity and C- Value paradox
Earlier it was believed that DNA-content is correlated with the complexity of an organism. The
idea was that the more complex the species the more genes it needed and hence has more C-
value.
How ever the total amount of chromosomal DNA in different animals and plants does not vary in
a consistent manner with the apparent complexity of the organisms. As compared to human (C-
value 3.3 pg DNA), Amphibians like salamanders (C-value 120 pg DNA), plants like wheat,
broad beans, and garden onions ( C-value 7.0, 14.6, and 16.8 picograms, respectively) are less
complex in their structure and behavior.Even in closely related species like the broad bean and
kidney bean c-value varies about three to four times .
The failure of C values to correspond to phylogenetic complexity is called the C-value paradox.
This perplexing variation in genome size occurs mainly because eukaryotic chromosomes
contain variable amounts of DNA with no demonstrable function, both between genes and within
genes in introns. This apparently nonfunctional DNA is composed of repetitious DNA
sequences, some of which are never transcribed and most all of which are likely dispensable.
These Repetitious DNA include
·Simple DNA repeats
·Moderately repeated DNA
·Transposons
·Viral retro-transposones
·Long interspersed elements
Short interspersed elements
·Unclassified spacer DNA
In addition to the non coding DNA sequences several protein coding genes are present as
multiple copies.These include
·Soiltary genes
·Duplicated and diverged genes(functional gene families and non-functional
pseudogenes)
·Tandem repeated genes encoding rRNA, tRNA and histones

2. Thus there is no direct corelation between total DNA content (C-Value) and the number of
functional genes, which in turn determines the complexity of an organism’s structure and
functions.
Euchromatin and Heterochromatin
Light-microscope studies in the 1930s distinguished between two types of chromatin in the
interphase nuclei of many higher eukaryotic cells: a highly condensed form, called
heterochromatin, and all the rest, which is less condensed, called euchromatin.
It is now established that euchromatin represent the organization level of 30-nm fiber and looped
domains. The loops are between 40 and 100 kbp in length.
Heterochromatin represents more compact levels of organization. Based on compactness feature
heterochromatin can be constitutive if it exist in the compact form permanently or it can be
facultative if compact packing is not permanent.
In a typical mammalian cell, approximately 10% of the genome is packaged into
heterochromatin which is concentrated in specific regions in the chromosome, including the
centromeres and telomeres.
Genes that become packaged into heterochromatin are usually resistant to being expressed,
because heterochromatin is unusually compact, but some genes require location in
heterochromatin regions if they are to be expressed.
When a gene that is normally expressed in euchromatin is experimentally relocated into a region
of heterochromatin, it ceases to be expressed, and the gene is said to be silenced. These
differences in gene expression are examples of position effects, in which the activity of a gene
depend on its position along a chromosome.
The Ends of Chromosomes Have a Special Form of Heterochromatin
In Yeast cells the chromatin extending inward roughly 5000 nucleotide base pairs from each
chromosome end is resistant to gene expression or in other words genes located in this region are
silenced. This corresponds to the heterochromatin.
Extensive genetic analysis has led to the identification of many of the yeast proteins required for
this type of gene silencing.
These include Silent information regulator (Sir) proteins. Sir proteins recognizes underacetylated
N-terminal tails of selected histones .One of the proteins in this complex is a highly conserved

3. histone deacetylase known as Sir2, which has homologs in diverse organisms, including humans,
and presumably has a major role in creating a pattern of histone underacetylation unique to
heterochromatin. Deacetylation of the histone tails is thought to allow nucleosomes to pack
together into tighter arrays and may also render them less susceptible to some chromatin
remodeling complexes. In addition, heterochromatin-specific patterns of histone tail modification
are likely to attract additional proteins involved in forming and maintaining heterochromatin.
These properties of heterochromatin also resemble properties of higher eukaryotic organisms.
Figure : Model for the heterochromatin at the ends of yeast chromosomes
Covalent modifications of the nucleosome core histones have an important role in the
process of heterochromatin formation.
Of special importance in many organisms are the histone methyl transferases, enzymes that
methylate specific lysines on histones including lysine 9 of histone H3 (see Figure 4-35). This
modification is “read” by heterochromatin components (including HP1 in Drosophila) that
specifically bind this modified form of histone H3 to induce the assembly of heterochromatin. It
is likely that a spectrum of different histone modifications is used by the cell to distinguish
heterochromatin from euchromatin .
Having the ends of chromosomes packaged into heterochromatin provides several advantages to
the cell: it helps to protect the ends of chromosomes from being recognized as broken
chromosomes by the cellular repair machinery, it may help to regulate telomere length, and it
may assist in the accurate pairing and segregation of chromosomes during mitosis.

4. Centromeres Are Also Packaged into Heterochromatin
In many complex organisms, including humans, each centromere seems to be embedded in a
very large stretch of heterochromatin that persists throughout interphase, even though the
centromere-directed movement of DNA occurs only during mitosis.
In addition to the modified histones several other protiens are present that compact the
nucleosomes into particularly dense arrangements. For example in yeast a special histone
H3 variant along with the other core histones, is believed to form a centromere-specific
nucleosome. In humans repeated DNA sequences, known as alpha satellite DNA are
charecteristic of centromere heterochromatin.
Figure : Organization of Alpha satellite DNA at the centromere
Heterochromatin May Provide a Defense Mechanism Against Mobile DNA Elements
DNA packaged in heterochromatin often consists of large tandem arrays of short, repeated
sequences that do not code for protein, as we saw above for the heterochromatin of mammalian
centromeres. In contrast, euchromatic DNA is rich in genes and other single-copy DNA
sequences. Although this correlation is not absolute (some arrays of repeated sequences exist in
euchromatin and some genes are present in heterochromatin), this trend suggests that some types
of repeated DNA may be a signal for heterochromatin formation. Repeated tandem copies of
genes results in silencing of these genes.This feature, called repeat-induced gene silencing, may
be a mechanism that cells have for protecting their genomes from being overtaken by mobile

5. genetic elements. These elements can multiply and insert themselves throughout the genome.
According to this idea, once a cluster of such mobile elements has formed, the DNA that
contains them would be packaged into heterochromatin to prevent their further proliferation. The
same mechanism could be responsible for forming the large regions of heterochromatin that
contain large numbers of tandem repeats of a simple sequence, as occurs around centromeres.
DNA Banding Pattern in Eukaryotic chromosomes
When stained with dyes such as Giemsa, mitotic chromosomes show a striking and reproducible
banding pattern along each chromosome.
By examining human chromosomes very early in mitosis, when they are less condensed than at
metaphase, it has been possible to estimate that the total haploid genome contains about 2000
distinguishable bands. These coalesce progressively as condensation proceeds during mitosis,
producing fewer and thicker bands.
Mitotic chromosome bands are detected in chromosomes from species as diverse as humans and
flies. Moreover, the pattern of bands in a chromosome has remained unchanged over long
periods of evolutionary time. Each human chromosome, for example, has a clearly recognizable
counterpart with a nearly identical banding pattern in the chromosomes of the chimpanzee,
gorilla, and orangutan—although there are also clear differences, such as chromosome fusion,
that give the human 46 chromosomes instead of the ape's 48 . This conservation suggests that
chromosomes are organized into large domains that may be important for chromosomal
function.Each band represent more than a million base-pairs.
Chromosomes have regions of variable GC content, which correponds roughly to the banding
pattern in metaphase stage.Bands that stain darkly with Geimsa stain have low GC Content and
are called G-Bands.Bands that stain lightly with Geimsa stain have high GC Content and are
called R-Bands.The GC-rich R-bands have a higher density of genes, especially of “house-
keeping” genes and these are enriched in components that necessary for regulation of gene
expression.

6. Comparison of the Giemsa pattern of the largest human chromosome (chromosome 1) with
that of chimpanzee, gorilla, and orangutan
Comparisons among the staining patterns of all the chromosomes indicate that human
chromosomes are more closely related to those of chimpanzee than to those of gorilla and that
they are more distantly related to those of orangutan

7. Comparison of the Giemsa pattern of the largest human chromosome (chromosome 1) with
that of chimpanzee, gorilla, and orangutan
Comparisons among the staining patterns of all the chromosomes indicate that human
chromosomes are more closely related to those of chimpanzee than to those of gorilla and that
they are more distantly related to those of orangutan