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BL414 Genetics Spring 2006
Lecture 11 Outline
March 1, 2006
7.6 -7.7 Repetitive DNA sequences
Eukaryotic genomes vary from species to species in their % GC (or AT)
composition – due to the inherent sequence usage and also depends on the
amount and composition of repetitive sequences: sequences repeated tandemly,
found in various places in eukaryotic genomes
Areas of repetitive sequence often have unusually high or low %GC, they are not
typically found in genes coding for genes, which tend to have unique sequence
compositions
Prokaryotic genomes do not have repetitive sequences, most of their genome is
unique.
Satellite DNA: consists of short sequences tandemly repeated up to ~ 1 million
times
The composition of genomes can be determined without sequencing them
directly, by looking at DNA renaturation kinetics and determining a Cot curve,
which reflects how unique or repetitive a sequence is.
Looking at the overall composition of eukaryotics genomes, the three classes of
sequences are the following – the relative percentages depend on the species:
Unique, single-copy sequences – form the major component, about 30-75% of
chromosomal DNA – these sequences are mostly gene-coding.
Highly repetitive sequences – 5-45% of the genome, they are 5-300 nucleotides
per repeat, may be repeated in up to 105 copies. Satellite DNA belongs in this
category and it is also found to be associated with heterochromatin, the more
darkly staining area of chromosomes. Some retrotransposable elements are in
this category.
Middle-repetitive sequences – about 1-30% of a genome – these sequences are
repeated about 10-1000 copies. Some genes are actually in this type of DNA- for
example the genes for ribosomal RNA, tRNA’s, histone proteins. Some of the
dispersed middle-repetitive DNA consists of transposable elements in
Drosophila. Transposable elements are DNA sequences which can jump around
in the genome.
7.8 The centromere – the region of chromosomal DNA that becomes a visible
constriction and becomes a component of the kinetochore to which the spindles
attach during mitosis and meiosis.
We are used to looking at localized centromeres, which have a single specific
site.
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Point centromeres are very short in terms of DNA e.g. the yeast centromere
Specific DNA sequences are present in the centromeres of all the yeast
chromosomes. They are in a centromeric core particle that is bigger than the
nucleosome “beads.” Spindles attach to the centromeric core particle.
Regional centromeres, found in higher eukaryotes, include a longer stretch of
DNA – up to 100’s of kb’s. The DNA sequences in the regional centromeres tend
to be heterochromatin, consisting of a tandem repeat of 170 bps called alpha
satellite – repeated up to 5000-15,000 copies. Spindle fibers attach to the alpha
satellite DNA. Presumably histone-like proteins may be involved in the structure
and organization of these centromeric alpha satellite DNA. Proteins are
definitely are involved in the kinetochore during mitosis and meiosis.
7.9 The telomere – a special DNA-protein structure that holds together the ends
of chromosomes.
The DNA at the ends of the chromosome is repetitive DNA – tandem repeats of
e.g. 5’-TTAGGG-3’ in vertebrates
Consider DNA replication at the very ends of the chromosomes: the part of DNA
complementary to the primer will not be replicated – instead it will be a 3’
overhang and it gets degraded – with each subsequent cell division, the
chromosome will be increasingly degraded
The riboprotein telomerase is responsible for adding more DNA onto the very
ends of the chromosome. This enzyme complex contains a guide RNA
complementary to the tandem repeat of telomeric DNA. The guide RNA
hybridizes to DNA at the 3’ overhang and the end of chromosomal DNA. It
primes DNA synthesis by DNA polymerase at the 3’ hanging end. The
complementary strand also gets elongated like the lagging strand in normal
DNA replication. On both strands DNA elongation takes place in the 5’ 3’
direction. (cf. Fig. 7.23)
A model for telomere structure proposes that a G quartet structure is present,
involving a 4 way base-quartet among G nucleotides. This structure would be
very stable. A protein has been isolated in the protozoan Oxytricha which binds
to telomeres and promotes formation of G quartets.