The document discusses DNA methylation, repetitive DNA sequences, the C-value paradox, and their relationships. It provides background on DNA methylation, how it regulates gene expression and is involved in diseases. It describes highly repetitive and satellite DNA sequences. It explains that the C-value paradox stemmed from the observation that genome size did not correlate with complexity, but this was later resolved by discovering non-coding DNA. The paradox questioned how genome size related to gene number.

1. DNA methylation &
C value paradox
DR. M. SONIA ANGELINE
KJC

2. DNA methylation in repetitive and non-
repetitive DNA sequence
 The term “repetitive sequences” (repeats, DNA repeats, repetitive DNA) refers to DNA
fragments that are present in multiple copies in the genome.
 These sequences exhibit a high degree of polymorphism due to variation in the number of their
repeat units caused by mutations involving several mechanisms .
 This hyper variability among related and unrelated organisms makes them excellent markers for
mapping, characterization of the genomes, genotype phenotype correlation, marker assisted
selection of the crop plants, molecular ecology and diversity related studies.
 The nature of repeats provides ample working flexibilities over the other marker systems.
 This is because: (i) short tandem repetitive (STR) sequences are evenly distributed all over the
genome (ii), are often conserved between closely related species (iii) and are co-dominant.

3. Highly repetitive sequences
 These are short sequences (5 to10 bp) amounting 10% of the genome and repeated a number of
times, usually occurring as tandem repeats (present in approximately 106 copies per haploid
genome).
 However, they are not interspersed with different non-repetitive sequences.
 Usually, the sequence of each repeating unit is conserved.
 Most of the sequences in this class are located in the heterochromatin regions of the centromeres
or telomeres of the chromosomes.
 Highly repetitive sequences interacting with specific proteins are involved in organizing
chromosome pairing during meiosis and recombination.
 Satellite DNA
 These are represented by monomer sequences, usually less than 2000-bp long, tandemly
reiterated up to 105 copies per haploid animals and located in the pericentromeric and or
telomeric heterochromatic region.

5. DNA Methylation
 There are many ways that gene expression is controlled in eukaryotes, but methylation of DNA (not
to be confused with histone methylation) is a common epigenetic signaling tool that cells use to
lock genes in the "off" position.
 In recent decades, researchers have learned a great deal about DNA methylation, including how it
occurs and where it occurs, and they have also discovered that methylation is an important
component in numerous cellular processes, including embryonic development, genomic
imprinting, X-chromosome inactivation, and preservation of chromosome stability.
 Given the many processes in which methylation plays a part, it is perhaps not surprising that
researchers have also linked errors in methylation to a variety of devastating consequences, including
several human diseases.
 DNA methylation occurs at the cytosine bases of eukaryotic DNA, which are converted to 5-
methylcytosine by DNA methyltransferase (DNMT) enzymes.
 The altered cytosine residues are usually immediately adjacent to a guanine nucleotide, resulting in
two methylated cytosine residues sitting diagonally to each other on opposing DNA strands.

6. DNA Methylation
 Epigenetic modifications are heritable changes in gene expression not encoded by the
DNA sequence.
 In the past decade, great strides have been made in characterizing epigenetic changes
during normal development and in disease states like cancer.
 However, the epigenetic landscape has grown increasingly complicated,
encompassing DNA methylation, the histone code, noncoding RNA, and nucleosome
positioning, along with DNA sequence.
 As a stable repressive mark, DNA methylation, catalyzed by the DNA methyltransferases
(DNMTs), is regarded as a key player in epigenetic silencing of transcription.
 DNA methylation may coordinately regulate the chromatin status via the interaction of
DNMTs with other modifications and with components of the machinery mediating those
marks.

7. The Role of Methylation in Gene
Expression
 Methylation was believed to play a crucial role in repressing gene expression, perhaps by blocking
the promoters at which activating transcription factors should bind.
 Presently, the exact role of methylation in gene expression is unknown, but it appears that
proper DNA methylation is essential for cell differentiation and embryonic development.
 Moreover, in some cases, methylation has observed to play a role in mediating gene expression.
 DNA methylation in gene expression and cell differentiation, it seems obvious that errors in
methylation could give rise to a number of devastating consequences, including various diseases.
 Indeed, medical scientists are currently studying the connections between methylation abnormalities
and diseases such as cancer, lupus, muscular dystrophy, and a range of birth defects that appear to be
caused by defective imprinting mechanisms

8. DNA Methylation and Diseases
 Given the critical role of DNA methylation in gene expression and cell differentiation,
it seems obvious that errors in methylation could give rise to a number of devastating
consequences, including various diseases.
 Indeed, medical scientists are currently studying the connections between methylation
abnormalities and diseases such as cancer, lupus, muscular dystrophy, and a range
of birth defects that appear to be caused by defective imprinting mechanisms

9. The law of DNA constancy and C-
value paradox
 Law of DNA constancy implies that all cells in a lineage
contain genetic information which in both qualitatively
and quantitatively identical.
 Quantity of DNA in an organism per cell, in all cells, is
always constant, for a given species.

10. C-value paradox
 In 1948, Roger and Colette Vendrely reported a "remarkable constancy in the nuclear DNA
content of all the cells in all the individuals within a given animal species", which they took as
evidence that DNA, rather than protein, was the substance of which genes are composed.
 The term C-value reflects this observed constancy. However, it was soon found that C-values
(genome sizes) vary enormously among species and that this bears no relationship to
the presumed number of genes (as reflected by the complexity of the organism).
 For example, the cells of some salamanders may contain 40 times more DNA than those of
humans.
 Given that C-values were assumed to be constant because genetic information is encoded by
DNA, and yet bore no relationship to presumed gene number, this was understandably
considered paradoxical; the term "C-value paradox" was used to describe this situation by C.A.
Thomas, Jr. in 1971.

11. C-value paradox
 The discovery of non-coding DNA in the early 1970s resolved the main question
of the C-value paradox: genome size does not reflect gene number
in eukaryotes since most of their DNA is non-coding and therefore does not
consist of genes.
 The human genome, for example, comprises less than 2% protein-coding
regions, with the remainder being various types of non-coding DNA
(especially transposable elements).

12. C-value
 C-value is the amount, in picograms, of DNA contained within
a haploid nucleus (e.g. a gamete) or one half the amount in
a diploid somatic cell of a eukaryotic organism.
 In some cases (notably among diploid organisms), the terms C-value
and genome size are used interchangeably; however, in polyploids the C-
value may represent two or more genomes contained within the same
nucleus.

13. C Value:
 The amount DNA found in haploid genome, measured in million base pairs or in pg; the C
may mean constancy of the genome in the species.
 The C-value is the amount of DNA in the haploid genome of an organism.
 It varies over a very wide range, with a general increase in C-value with complexity of
organism from prokaryotes to invertebrates, vertebrates, plants.
 The C-value paradox is basically this: how can we account for the amount of DNA in terms
of known function? Very similar organisms can show a large difference in C-values (e.g.
amphibians). The amount of genomic DNA in complex eukaryotes is much greater than the
amount needed to encode proteins. For example: Mammals have 30,000 to 50,000 genes,
but their genome size (or C-value) is 3 x 109 bp.
 (3 x 109 bp)/3000 bp (average gene size) = 1 x 106 (“gene capacity”).
 Drosophila melanogaster has about 5000 mutable loci (~genes). If the average size of an
insect gene is 2000 bp, then >1 x 108 bp/2 x 103 bp = > 50,000 “gene capacity”.

14.  Our current understanding of complex genomes reveals several factors that help explain the classic C-
value paradox:
 Introns in genes
 Regulatory elements of genes
 Pseudogenes
 Multiple copies of genes
 Intergenic sequences
 Repetitive DNA
 The facts that some of the genomic DNA from complex organisms is highly repetitive, and that some
proteins are encoded by families of genes whereas others are encoded by single genes, mean that the
genome can be considered to have several distinctive components.
 Analysis of the kinetics of DNA reassociation, largely in the 1970's, showed that such genomes have
components that can be distinguished by their repetition frequency.