Levels at which eukaryotic gene expression is controlled Initiating or inhibiting Transcription [majority] –Transcriptional activators, coactivators, repressors.

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 (Post-translational modification)

Found in the mature mRNA from all cell types

Not found in all mature mRNAs

Alternatively spliced versions vary in function to meet the needs of the different cell types

Brooker, Figure 17.17

1 654 10987 1413121132

1 654 1098 142

1 654 1098 12113

Intron Exon α-tropomyosin pre-mRNA

5′ 3′

5′ 3′

Constitutive exons

Alternativesplicing

or

Alternative exons

Smooth muscle cells

5′ 3′ Striated muscle cells

Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

Brooker Figure 15.17a

1 432

1 432

1 432

1 43

5′

5′ 3′ 5′ 3′ 5′ 3′

3′

5′ 3′

The spliceosomerecognizes all thesplice junctions.

All 4 exons are containedwithin the mRNA.

Splicing repressors

Splicejunctions

5′

5′ 3′ 5′ 3′ 5′ 3′

3′

5′ 3′

A splicing repressor prevents therecognition of a 3′-splice junction.The next 3′-splice junction thatprecedes exon 3 will be chosen.

Exon 2 is skipped and notincluded in the mRNA.

Splicejunctions

Splicingrepressor

Alternativesplicing

Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

Figure 17.18b

1 432 1 432

1 42 1 432

5′

5′ 3′ 5′ 3′ 5′ 3′

3′

5′ 3′

The spliceosome onlyrecognizes 4 of the6 splice junctions.

Exon 3 is included in the mRNA.

Splicing enhancers

Splicejunctions

5′

5′ 3′ 5′ 3′ 5′ 3′

3′

Splicejunctions

Alternativesplicing

The binding of splicing enhancerspromotes the recognition ofpoorly recognized junctions. All 6junctions are recognized.

5′ 3′

Exon 3 is not included in the mRNA.

These 2 splice junctionsare not readily recognizedby the spliceosome.

Splicingenhancer

Homeotic Transcription

Factors: “Master Genes” turn on

cascade of other genes (which

developmental pathway?)

WT

Homeotic Mutant

(a) Homeotic gene

(b) Homeotic protein bound to DNA

DNA-binding domain(shown in orange),the Homeodomain

DNA

Homeobox (180 bp)

Transcriptionalactivation domain

Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display Brooker, Fig 24 - 14

Homeotic Genes often identify transcription

factor proteins with DNA-binding Homeodomains

Peter J. Russell, iGenetics: Copyright © Pearson Education, Inc., publishing as Benjamin Cummings.

Drosophila development occurs in specific segments

Fig from iGenetics, Russell

Embryo(10 hours)

Flychromosome

Adult

Antennapediacomplex

bithoraxcomplex

lab pb Dfd Scr Antp Ubx abd-A Abd-B

Brooker, Fig 24.12

Co-linearity of Homeotic genes

the order of gene expression, from

anterior to posterior, parallels the order of

genes on the chromosome

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

Mouse homeobox genes

Chromosome 6,

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”)

Expression of Mouse Homeobox Genes (Hox) coincides with region of

tissue specification

Anterior Posterior

CaudalSacralLumbarThoracicOccipital Cervical

Ver

teb

rae

Expression patternHox A1

Hox B1

Hox A3

Hox D4

Hox A4

Hox A5

Hox B4

Hox B5

Hox A6

Hox A7

Hox D8

Hox B7

Hox C9

Hox D8

Hox D9

Hox D10

Hox D11

Hox D13

Hox D12

Hox10 and Hox11 Genes AreRequired 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

Brooker, Fig 24 - 18

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20

Vertebrae:

Vertebrae:

Vertebrae:

Vertebrae: No "neck," no forelimb

Mouse

Chicken

Snake

Goose

Hundreds of vertebrae

44 total vertebrae

36 total vertebrae

36 total vertebrae

Neck vertebrae

HoxC-6

HoxC-6

HoxC-6

HoxC-6

Anterior boundary of HoxC-6 gene expression