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Ribosomal
RNA
Gene
Families -
Probably
the
best
known
multigene
families
are
those
encoding
ribosomal
RNA.
The "major" ribosomal
RNA
genes
are
organized
in
long
tandem
arrays
containing
both
gene
and
spacer
sequences.
In
most
animal
cells
there
are
some
100-200
rRNA
genes
and
in
plants
the
numbers
may
be
much
higher.
It
is
not
uncommon
to
find
5,000
rRNA
genes
per
'genome
in
plant
species
with
DNA
contents
typical
of
crop
plants,
and
much
higher
numbers
have
been
reported.
The
genes
exist
in
large
tandem
arrays
at
one
or
a
few
loci
in
the
genome.
The
repeating
unit
in
these
arrays
consists
of
one
large
transcription
unit
containing
genes
for
the
18S,
5.8S
and
25S
rRNAs
as
well
as
for
$pacer
sequences
that
are
removed
during
processing
of
the
large
primary
transcript.
Also
included
in
the
basic
repeat
are
spacer
sequences
which
are
not
part
of
the
primary
transcript
and
often
called
non
transcribed
spacer
or
intergenic
spacer
sequences.
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The
major
rRNA
genes
are
transcribed
by
RNA
polymerase
I,
a
specialized
form
of
RNA
polymerase,
which
transcribes
only
these
genes.
Active
rRNA
genes
are
found
in
the
nucleolus
where
their
transcripts
are
processed
and
assembled
with
ribosomal
proteins.
Genes
for
5S
ribosomal
RNAs
are
also
organized
in
tandem
arrays
although
they
are
located
elsewhere
in
the
genome
away
from
the
major
rRNA
gene
arrays.
They
are
transcribed
by
RNA
polymerase
III
rather
than
polymerase
I.
As
in
the
case
of
the
major
rRNA
genes,
the
arrays
consist
of
alternating
gene
and
spacer
sequences.
In
wheat
two
main
variants
exist
in
which
the
repeating
units
are
410
and
500
bp
long.
Similar
heterogeneity
is
seen
in
flax,
in
which
the
major
length
classes
are
340
and
360
bp.
Within
these
repeats
the
gene
itself
occupies
only
118
bp.
Most
spacer
sequences
are
highly
variable,
even
between
the
different
length
classes
in
a
single
genome,
but
there
is
a
region
of
about
70
bp
5'
to
the
start
of
transcription
that
is
conserved.
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Studies
of
58
genes
in
Xenopus,
however,
have
shown
that
this
region
is
not
required
for
an
accurate
transcriptional
initiation.
Interestingly,
the
promoter
sequences
required
for
proper
initiation
by
polymerase
III
in
extracts
of
Xenopus
oocytes
seem
to
be
located
well
within
the
coding
sequence
of
the
gene.
The
number
of
copies
of
both
the
major
rRNA
genes
and
the
58
rRNA
genes
can
vary
widely
among
closely
related
species
of
plants,
and
even
among
different
races
or
varieties
within
a
species.
For
example,
different
lines
of
flax
have
been
reported
to
contain
between
about
50,000
and
120,000
58
RNA
genes.
The
number
of
major
ribosomal
RNA
genes
varied
between
about
1,400
and
2,700
in
the
same
lines,
although
there
was
no
correlation
between
the
numbers
of
58
genes
and
major
rRNA
genes.
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Extensive
variation
in
the
number
of
major
rRNA
genes
also
occurs
independently
at
each
of
the
several
loci
that
contain
rRNA
genes
in
hexaploid
wheat.
Such
extensive
variation
between
vigorously
growing,
closely
related
genotypes
makes
it
very
difficult
to
argue
that
the
larger
gene
numbers
are
required
for
normal
plant
growth
and
development.
Instead,
it
would
appear
that
plants
simply
tolerate
a
great
deal
more
variation
than
animals
do.
Even
in
plants
with
lower
gene
numbers
there
may
be
a
substantial "excess" over
the
number
of
genes
actually
expressed
in
any
given
cell.
In
addition
to
variation
in
rRNA
gene
number,
many
plants
have
substantial
polymorphism
in
the
length
of
their
tandem
repeat
units.
Both
types
of
variation
are
thought
to
result
from
unequal
crossover
events.
Why
both
copy
number
and
length
variation
can
result
from
unequal
crossover
in
ribosomal
RNA
gene
arrays
can
be
understood
by
considering
the
structure
of
a
typical
repeat
in
such
an
array.
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In
each
repeat
there
is
the
large
transcription
unit
containing
genes
for
the
188,
588,
and
258
RNAs
and
the
spacer
sequences
between
them.
There
is
also
the "nontranscribed
spacer".Within
the
nontranscribed
spacer
there
are
a
number
of
short
(about
130-180
bp) "subrepeat" sequences.
These
subrepeats
provide
another
set
of
tandemly
repeated
sequences
at
which
unequal
crossovers
might
occur.
Unequal
crossover
in
this
region
would
generate
spacer
length
variants
with
different
numbers
of
subrepeat
sequences.
This
model
predicts
that
most
of
the
rRNA
gene
length
variants
seen
in
nature
should
differ
from
each
other
by
lengths
corresponding
to
integral
multiples
of
the
subrepeats
sequence,
and
this
is
exactly
what
is
observed.
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The
evolution
of
ribosomal
RNA
gene
families
is
also
characterized
by
a
rapid
accumulation
of
point
mutations
and
other
sequence
changes
in
the
nontranscribed
spacer
region.
Clearly,
the
sequence
of
this
region
is
not
conserved
in
the
same
way
as
that
in
the
coding
region,
which
shows
strong
homology
over
very
large
evolutionary
distances.
In
spite
of
the
rapid
evolution
of
spacer
sequences,
however,
a
degree
of
sequence
homogeneity
is
somehow
maintained
within
the
arrays
of
a
particular
genome.
This
paradox
provided
the
first
recognized
example
of "concerted
evolution",
in
which
repeated
sequences
of
multicopy
genes
sometimes
show
a
tendency
to
evolve
together
rather
than
diverge
by
accumulating
different
mutations.
Concerted
evolution
is
thought
to
reflect
the
operation
of
homogenizing
processes
such
as
gene
conversion
and
unequal
crossing
over.
Gene
conversion
is
the
direct
conversion
of
one
sequence
to
another
while
the
sequences
are
paired
during
mitosis
or
meiosis.
Unequal
crossovers
within
large
tandem
arrays,
such
as
those
containing
the
ribosomal
RNA
genes,
can
lead
to
the
spread
of
random
sequence
variants
through
the
population
of
genes
by
a
process
that
is
analogous
to
genetic
drift
in
a
population
of
organisms.
Although
it
is
often
thought
(and
in
many
cases
is
undoubtedly
true)
that
sequences
that
diverge
very
rapidly
in
evolution
must
be
phenotypically
neutral
or
unimportant,
the
nontranscribed
spacer
sequences
in
the
major
ribosomal
RNA
genes
contain
transcriptional
promoters
and
enhancers
which
are
essential
to
gene
function.
In
contrast
to
control
sequences
of
protein-coding
genes,
which
can
sometimes
be
recognized
by
their
evolutionary
conservatism,
promoter
and
enhancer
functions
in
ribosomal
RNA
genes
show
a
very
high
degree
of
species
specificity.
This
can
be
demonstrated
by
the
failure
of
heterologous
genes
to
be
transcribed
in
extracts
that
faithfully
transcribe
homologous
ribosomal
RNA
genes.
In
such
a
situation,
genes
from
species
A
work
in
A
extracts
but
not
8
extracts
while
genes
from
species
8
work
in
8
extracts
but
not
those
from
species
A.
Thus
a
kind
of
molecular
co-evolution
must
occur
with
genes
that
encode
transacting
transcription
factors
evolving
in
parallel
with
the
DNA
sequences
these
factors
recognize.
Chromosomal
regions
containing
arrays
of
rRNA
genes
are
potential
sites
of
nucleolus
formation
and
are
thus
referred
to
as "nucleolar
organizers".
Although
there
may
be
more
than
one
nucleolar
organizer
region,
the
number
is
rarely
more
than
two
or
three
per
genome.
It
can
be
shown
by
in
situ
hybridization
that
most
of
the
DNA
that
hybridizes
to
ribosomal
gene
probes
is
located
in
these
regions;
however,
not
all
the
rRNA
genes
are
contained
within
the
nucleolus
itself.
Many
of
the
genes
exist
in
an
apparently
inactive
form
just
outside
the
nucleolus.
Using
genetic
stocks
of
maize
containing
chromosomal
translocations
involving
DNA
near
the
nucleolus,
R.
Philips
and
his
associates
at
the
University
of
Minnesota
were
able
to
show
that
DNA
from
this
region
could
organize
a
nucleolus
when
it
was
transferred
to
another
part
of
the
genome,
even
though
it
had
not
done
so
at
the
original
location.
Thus
the
inactive
genes
are
capable
of
functioning
when
given
the
chance
and
their
inactivity
must
reflect
the
operation
or
a
system
for
regulating
the
number
of
genes
that
can
be
active
in
anyone
nucleus.
A
similar
conclusion
can
be
drawn
from
experiments
in
wheat.
Since
bread
wheat
is
a
hexaploid
species
it
is
possible
to
make
various
aneuploid
derivatives
in
which
the
number
of
nucleolar
organizers,
and
the
total
number
of
rRNA
genes,
varies
considerably.
R.
Flavell
and
his
colleagues
at
the
Plant
Breeding
Institute
in
Cambridge,
England
have
shown
that
the
total
nucleolar
volume,
which
is
an
index
of
rRNA
gene
activity,
remains
relatively
constant
as
the
number
of
genes
is
varied
over
a
wide
range.
This
dosage
compensation
effect
is
evidence
that
the
activity
of
rRNA
genes
is
regulated
by
some
mechanism
independent
of
their
copy
number.
Additional
experiments
with
aneuploid
wheat
lines
and
wheat
lines
that
contain
chromosomes
from
related
species
have
shown
that
different
nucleoli
exhibit
a "dominance
hierarchy".
For
example,
the
nucleolus
on
chromosome
18
is
always
larger
than
that
on
chromosome
68
in
the
euploid
cultivar "Chinese
Spring".
Since
the
nucleolar
organizer
on
68
has
about
twice
as
many
rRNA
genes
as
that
on
1
B,
it
is
not
possible
to
explain
dominance
simply
on
the
basis
of
gene
number.
Instead,
it
seems
more
likely
that
something
about
the
genes
on
1B
makes
them
more
able
to
compete
for
some
limiting
factor
or
factors
required
for
activity.
In
this
connection
it
in
striking
that
the
dominant
genes
generally
contain
larger
numbers
of
the
spacer
sub
repeats
mentioned
previously
in
connection
with
size
polymorphism.
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