Anthology of Human Repetitive DNA
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Human repetitive DNA includes tandemly arrayed and interspersed repeats.
Tandemly arrayed microsatellites, minisatellites, telomeric repeats, and centromeric
satellites constitute a signifcant portion oF the genomic DNA, particularly oF hete-
rochromatin. ±urthermore, around 45% oF the genome is represented by so-called
interspersed repeats that are mostly remnants oF retrovirus-like LTR retrotrans-
posons, non-LTR retrotransposons, and DNA transposons inserted in the genomic
DNA over millions oF years. Currently, the most active are L1 and Alu Families oF
non-LTR retrotransposons, and they are known to cause genetic diseases through
insertion into genes. ±urthermore, repetitive sequences, particularly Alu elements,
can stimulate illegitimate recombinations producing chromosomal instabilities lead-
ing to genetic disorders. Analysis oF repetitive DNA is an important part oF genome
studies, and it is based on specialized databases and computer programs.
1
Introduction
The generally synonymous terms
repetitive
elements
,
repetitive
(
reiterated
)
sequences
,and
repeats
describe a broad variety oF DNA
sequences with copies present in multiple
locations throughout the genome. They
can be divided into Families oF similar
or sometimes identical elements. This
defnition also covers Families oF genes
with known Functions, such as RNA genes
and other multigene Families. However,
the subject oF this chapter is limited to
repetitive elements that do not have a
clearly assigned biological Function.
Historically, the frst categorization oF
repetitive DNA into ‘‘highly repetitive’’
and ‘‘middle repetitive’’ was based on
DNA denaturation/renaturation kinetics.
This categorization reFers to the physical
properties oF DNA that cannot be trans-
lated satisFactorily into a classifcation oF
repeats based on cloning and detailed
sequence studies. In general, highly repet-
itive DNA primarily includes the tandemly
repeated sequences described in Sect. 2,
whereas the middle-repetitive DNA in-
cludes repetitive elements interspersed
with single-copy DNA (Sect. 3). However,
the middle-repetitive DNA may contain
sequences with a very high copy num-
ber such as the Alu Family described in
Sect. 3.1.2.2.
On the basis oF chromosomal distribu-
tion, repetitive elements are divided into
tandem repeats
, consisting oF direct repeti-
tions oF the same motiF, and
interspersed
repeats
. Interspersed repeats are mostly
inactive copies oF transposable elements
(TEs). Together, these elements represent
around 50% oF the sequenced human
genome. Some abundant interspersed re-
peats are relatively old and diverse and can-
not be clearly distinguished From ‘‘unique’’
DNA. This is due to the acquisition oF
random mutations and sequence Fragmen-
tation over time. ThereFore, it is believed
that the real contribution oF repetitive DNA
to the human genome is underestimated,
and that the cited proportion oF 50% only
reflects the current limits oF detectability.
2
Tandemly Arrayed Repeats
Tandemly arrayed repeats are composed oF
multiple head-to-tail repetitions oF simple
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