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Levels at which eukaryotic
gene expression is controlled
• Initiating or inhibiting Transcription [majority]
– Transcriptional activators, coactivators, repressors
• Promoters
• DNA response elements, enhancers, silencers
– DNA packaging and chromatin structure
• Histone acetylation, histone variation
• DNA methylation
• Initiating or inhibiting Translation
– mRNA processing, alternative splicing
– RNA stability
– RNA silencing
• Initiating or inhibiting protein activity (Posttranslational modification)
Found in the mature mRNA from all cell types
Constitutive exons
Not found in all mature mRNAs
Intron
5′
1
2
α-tropomyosin pre-mRNA
Exon
3
4
Alternative exons
5
6
7
8
9
10
11
12
13 14
Alternative
splicing
5′
1
2
4
5
6
3′
8
9
10 14
8
9
10 11 12
Smooth muscle cells
or
5′
1
3
4
5
6
3′
Striated muscle cells
Alternatively spliced versions vary in function to meet the
needs of the different cell types
Brooker, Figure
17.17
3′
Splicing repressors
Alternative
splicing
5′ 3′
5′
1
5′ 3′
Splice
junctions
5′ 3′
2
3
4
The spliceosome
recognizes all the
splice junctions.
5′
1
2
3
4
All 4 exons are contained
within the mRNA.
3′
3′
5′ 3′
5′
1
2
Splice
junctions
5′ 3′
3
4
3′
A splicing repressor prevents the
recognition of a 3′-splice junction.
The next 3′-splice junction that
precedes exon 3 will be chosen.
Splicing
repressor
5′
5′ 3′
1
3
4
3′
Exon 2 is skipped and not
included in the mRNA.
Brooker Figure 15.17a
Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display
Splicing enhancers
Alternative
splicing
These 2 splice junctions
are not readily recognized
by the spliceosome.
5′ 3′
5′
1
5′
3′
2
5′
Splice
junctions
3′
3
4
3′
The spliceosome only
recognizes 4 of the
6 splice junctions.
5′
1
2
4
3′
Exon 3 is not included in the mRNA.
5′ 3′
5′
5′
1
3′
2
1
Splice
junctions
3′
3
Splicing
enhancer
5′
5′
4
3′
The binding of splicing enhancers
promotes the recognition of
poorly recognized junctions. All 6
junctions are recognized.
2
3
4
3′
Exon 3 is included in the mRNA.
Figure 17.18b
Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display
WT
Homeotic
Mutant
Homeotic
Transcription
Factors: “Master
Genes” turn on
cascade of other
genes (which
developmental
pathway?)
Homeobox (180 bp)
DNA
(a) Homeotic gene
Transcriptional
activation domain
Homeotic Genes often
identify transcription
factor proteins with DNAbinding Homeodomains
DNA-binding domain
(shown in orange),
the Homeodomain
(b) Homeotic protein bound to DNA
Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display
Brooker, Fig 24 - 14
Drosophila development occurs in
specific segments
Peter J. Russell, iGenetics: Copyright © Pearson Education, Inc., publishing as Benjamin Cummings.
Fig from iGenetics, Russell
Antennapedia
complex
bithorax
complex
Fly
chromosome
lab pb Dfd Scr Antp Ubx abd-A Abd-B
Embryo
(10 hours)
Co-linearity of
Homeotic genes
the order of gene
expression, from
anterior to posterior,
parallels the order of
genes on the
chromosome
Adult
Brooker, Fig 24.12
Did Drosophila evolution include a
homeotic mutation in T3?
Dragonflies and butterflies are evolutionarily older than
Drosophila
WT dragonflies and butterflies have four sets of wings
Specific development
of each region and
segment of body
determined by a
homeotic gene
Chromosome 6,
Mouse
homeobox
genes
Chromosome 11,
Chromosome 15,
Chromosome 2,
•Drosophila have one set
of Homeobox genes
(“HOM-C genes”)
•Mammals have four sets
of Homeobox genes
(Mammalian homeobox
genes = “Hox genes”)
Anterior
Cervical
Thoracic
Lumbar
Sacral
Caudal
Vertebrae
Occipital
Posterior
Expression pattern
Hox A1
Hox B1
Hox A3
Hox D4
Hox A4
Hox B4
Hox A5
Hox B5
Hox A6
Hox A7
Hox D8
Hox B7
Hox C9
Hox D8
Hox D9
Hox D10
Expression of Mouse Homeobox
Genes (Hox) coincides with region of
tissue specification
Hox D11
Hox D12
Hox D13
Hox10 and Hox11 Genes Are
Required to Globally Pattern the
Mammalian Skeleton
Deneen M. Wellik and Mario R. Capecchi*
Science, Vol 301, p 363. July 2003
(An example of “reverse genetics”, where a known gene
sequence is knocked out in order to determine the
phenotype.)
Axial Skeleton Pattern in Mouse (WT)
Triple mutant in three Hox 10 genes:
Loss of Hox-A10, Hox-C10 and Hox-D10 shows extra ribs (thoracic vertebrae) and
no lumbar or sacral
Triple mutant in three Hox 11 genes:
Loss of Hox-A11, Hox-C11 and Hox-D11 shows extra lumbar vertebrae, no
sacral
Anterior boundary of HoxC-6 gene expression
Neck vertebrae
Mouse
Vertebrae:
1
2
3
4
5
6
7
8
9 10 11 12 13 14 15 16 17 18 19 20
36 total vertebrae
9 10 11 12 13 14 15 16 17 18 19 20
36 total vertebrae
HoxC-6
Chicken
Vertebrae:
1
2
3
4
5
6
7
8
HoxC-6
Goose
Vertebrae:
1
2
3
4
5
6
7
8
9 10 11 12 13 14 15 16 17 18 19 20
44 total vertebrae
HoxC-6
Snake
Vertebrae:
1
2
3
No "neck," no forelimb
4
5
6
7
8
9 10 11 12 13 14 15 16 17 18 19 20
Hundreds of vertebrae
HoxC-6
Brooker,
Fig 24 - 18