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Chapter 3
The Interrupted Gene
3.1
Introduction
 In eukaryotes, a gene may include additional
sequences that lie within the coding region and
interrupt the sequence that codes for the protein.
Figure 3.01: Introns are removed to make mRNA from an interrupted gene.
3.2
An Interrupted Gene Consists of Exons
and Introns
• Introns are removed by the process of RNA
splicing.
• Only mutations in exons can affect polypeptide
sequence.
– Mutations in introns can affect processing of the RNA
and prevent production of polypeptide.
3.2
An Interrupted Gene Consists of Exons
and Introns
Figure 3.02: The order of exons does not change between DNA and RNA.
3.3
Organization of Interrupted Genes May
Be Conserved
• Introns can be detected by the presence of
additional regions.
– Genes are compared with their RNA products
by restriction mapping or electron microscopy.
– The ultimate determination is based on
comparison of sequences.
Figure 3.03: RNA hybridizes with the template strand of the gene.
3.3
Organization of Interrupted Genes May
Be Conserved
Figure 3.04: An intron does not hybridize with mRNA.
Figure 3.05A: Multiple introns form loops in hybridization.
Photo reproduced from Berget, S. M., Moore, C., and Sharp, P.A., Proc. Natl.
Acad. Sci. USA 74 (1977): 3171-3175. Used with permission of Philip Sharp, Koch
Institute for Integrative Cancer Research, Massachusetts Institute of Technology.
Figure 3.05B: Multiple introns form loops in hybridization.
Figure 3.06: Restriction sites in introns are missing from the cDNA.
3.3
Organization of Interrupted Genes May
Be Conserved
• The positions of introns are usually
conserved when homologous genes are
compared between different organisms.
– The lengths of the corresponding introns may
vary greatly.
• Introns usually do not code for
polypeptides.
3.3
Organization of Interrupted Genes May
Be Conserved
Figure 3.07: Continuous open reading frames are created when introns are
removed from RNA.
Figure 3.08: Globin genes vary in intron lengths but have the same
structure.
3.4
Exon Sequences Are Conserved but
Introns Vary
• Comparisons of related genes in different
species show that the sequences of the
corresponding exons are usually conserved
– The sequences of the introns are much less well
related.
• Introns evolve much more rapidly than exons.
– This is due to the lack of selective pressure to
produce a protein with a useful sequence.
3.4
Exon Sequences Are Conserved but
Introns Vary
Figure 3.09: Related genes diverge in the introns.
3.5 Genes Show a Wide Distribution of Sizes
Primarily Due to Intron Size and Number
Variation
• Most genes are uninterrupted in yeasts, but are
interrupted in higher eukaryotes.
Figure 3.10: Interrupted genes predominate in higher eukaryotes.
Figure 3.11: Genes have a wide range of sizes.
3.5 Genes Show a Wide Distribution of Sizes
Primarily Due to Intron Size and Number
Variation
• Introns are short in lower eukaryotes, but range
up to several 10s of kb in length in higher
eukaryotes.
• The overall length of a gene is determined
largely by its introns.
3.5 Genes Show a Wide
Distribution of Sizes
Primarily Due to Intron
Size and Number
Variation
• Exons are usually short,
typically coding for ~100
amino acids.
Figure 3.12: Exons are typically 100-200 bp.
3.5 Genes Show a Wide Distribution of Sizes
Primarily Due to Intron Size and Number
Variation
Figure 3.13: Introns have wide length variation.
3.6
Some DNA Sequences Code for More
Than One Polypeptide
• The use of alternative initiation or termination
codons allows two proteins to be generated
where one is equivalent to a fragment of the
other.
Figure 3.14: Alternative starts (or stops) generate related proteins.
3.6 Some DNA Sequences Code for
More Than One Polypeptide
• Nonhomologous protein sequences can be
produced from the same sequence of DNA when
it is read in different reading frames by two
(overlapping) genes.
Figure 3.15: Overlapping triplets may be used in different reading frames.
3.6
Some DNA Sequences Code for More
Than One Polypeptide
• Homologous proteins that differ by the presence
or absence of certain regions can be generated
by differential (alternative) splicing when certain
exons are included or excluded.
• This may take the form of including or excluding
individual exons or of choosing between
alternative exons.
Figure 3.16: Alternative splicing can subsititute exons.
3.6
Some DNA Sequences Code for More
Than One Polypeptide
Figure 3.17: Different combinations of exons are used in alternative
splicing.
3.7
How Did Interrupted Genes Evolve?
• A major evolutionary question is whether genes
originated as sequences interrupted by introns or
whether they were originally uninterrupted.
– More evidence supports the first (“introns early”)
hypothesis, though it appears that introns can be inserted
into genes.
• Most protein-coding genes probably originated in an
interrupted form, but interrupted genes that code for
RNA may have originally been uninterrupted.
• A special class of introns are mobile and can insert
themselves into genes.
Figure 3.18: Random translocations may produce functional genes.
3.8
Some Exons Can Be Equated with
Protein Functions
• Many exons can be equated with coding for
polypeptide sequences that have particular
functions.
• Related exons are found in different genes.
3.8
Some Exons Can Be Equated with
Protein Functions
Figure 3.19: Immunoglobulin exons code for protein domains
Figure 3.20: Exons in two proteins can be related.
3.9
The Members of a Gene Family Have a
Common Organization
• A common feature in a set of genes is assumed
to identify a property that preceded their
separation in evolution.
• All globin genes have a common form of
organization with three exons and two introns.
– This suggests that they are descended from a single
ancestral gene.
3.9
The Members of a Gene Family Have a
Common Organization
Figure 3.21: Leghemoglobin has an extra intron.
Figure 3.22: One rat insulin gene has lost an intron.
Figure 3.23: Many changes in introns have occured in actin gene evolution.