Control of Gene Expression

Variation in cell morphology with the same genome

A neuron and a lymphocyte share the same genome

An Overview of Gene Expression

The different cell types of a multicellular organism contain the same DNA (experiments to prove) Different cell types produce different sets of proteins A cell can change the expression of its genes in response to external signals Gene expression can be regulated at many of the steps in the pathway from DNA to RNA to protein

All cells contain all the genetic instructions necessary for a complete organism formation

All cells contain all the genetic instructions necessary for a complete organism formation

Different cell types produce different sets of proteins

All protein expressed in a specific cell type can be characterized by proteomic analysis

Different cell types produce different sets of proteins

All protein expressed in a specific cell type can be characterized by proteomic analysis

Slide 14 of 23

Gene expressed in cells

Housekeeping proteins

To maintain basic living of a cell Protein for cytoskeleton, cell replication, protein synthesis machinery, energy production and other basic metabolism P r o t e i n s f o r c e l l s d i s t i n c t i v ep r o p e r t i e s Ex., hemoglobin for reticulocytes, myosin for muscle cell, pigment for skin and eyes,

Specialized proteins

The expression of a different collection of genes in each cell type causes the large variations in size, shape, behavior and function of differentiated cells.

Cells change the expression of their genes in response to external signals

Most

of the specialized cells are capable of altering their patterns of gene expression in response to extracellular cues Hormones, temperature, chemicals, small mo l e c u l e s , p H ,

Gene expression can be controlled at several different steps

Main site of regulation

10

How Transcriptional Switches Work?

Transcription is controlled by proteins binding to regulatory DNA sequences

11

Transcriptional regulation
Usually at initiation step at promoter region and regulatory DNA sequences The size of regulatory sequence can range from 5 to 10000 base pairs which will be recognized and bound by one or more proteins. Protein (factor) binds to DNA by interacting with base pairs in major groove through hydrogen bond, ionic bonds and hydrophobic interaction.

12

Protein bind to the major groove of a DNA

13

DNA binding motifs on DNA binding protein

activator vs repressor

Gene regulatory proteins contain a variety of DNAbinding motifs (A) (B); Homeodomain (C) Zinc finger (D) Leucine zipper

14

Transcription regulation in prokaryotes

15

Concept of Operon in prokaryotes

Operon

a set of genes that is

transcribed

into a single mRNA worked and regulated coordinately

Only

observed in prokaryotes Famous example:

Lac

operon Guanine operon Trp operon

16

Riboswitch

A riboswitch controls purine biosynthesis genes in bacteria

Figure 8-24 Essential Cell Biology ( Garland Science 2010)

Tryptophan operon

18

The constitutively expressed Trp operon can be switched off with repressor proteins in the presence of free Trp molecules (feedback regulation)

19

Trp operon also regulated by attenuation at mRNA level

20

Trp operon regulated by attenuation

lac operon is controlled by two signals

presence of lactose vs. absence of glucose

lac operon is controlled by two signals

presence of lactose vs. absence of glucose

Activator CAP binds cyclic AMP before it can bind to DNA and initiate transcription in response to low glucose environment

23

Transcription regulation in eukaryotes

24

Differences of transcription in eukaryotes from prokaryotes

Three

types of RNA polymerases Require general transcription factors to initiate transcription Regulatory sequences could be far away from promoter sequence Affected by chromosome structural complexity
25

I. RNA polymerases in eukaryotes

26

II. Transcription initiation in eukaryotes requires many factors

Factors assembling and RNA polymerase phosphorylation by TFIIH (protein kinase) to begin its task of making RNA)

27

Binding of TBP and distortion of DNA

28

Phosphorylation of RNA polymerase

Phosphorylation of RNA polymerase II also allows RNA-processing proteins to assemble on its tail.

29

III. Gene activation can occur at a distance in eukaryotes through enhancer (DNA) and mediator (protein)

30

IV. Activator or repressor direct local alterations in chromatin structure

31

The molecular mechanisms that create specialized cell types

32

The molecular mechanisms for cells differentiation

Eukaryotic genes are regulated by combinations of proteins Expression of different genes can be coordinated by a single protein Combinatorial control can create different cell types Stable patterns of gene expression can be transmitted to daughter cells Formation of an entire organ can be triggered by a single gene regulatory protein

33

I. Factors work as a committee to control gene expression

Regulatory proteins work together as a c o mmi t t e e to control the expression of an eukaryotic gene

34

II. A single protein can coordinate expression of many genes by completing the combination of committee
Several genes can be turn on/off simultaneously by completing the complexes with the same single protein

35

A single gene regulatory protein is capable of cell type conversion

Fibroblasts from the skin have been converted to muscle cells by experimentally induced expression of the myoD gene.
36

III. Cell differentiation during development

Combinations of a few gene regulatory proteins can generate many different cell types during development.

37

IV. Cell memory results from a positive feedback loop to maintain the same phenotype for all its progenitor cells

A key gene regulatory protein activates its own transcription in addition to other cell-type specific genes.

38

IV. Cell memory results from maintaining states of chromatin structure

39

DNA methylation patterns can be faithfully inherited

Figure 8-22 Essential Cell Biology ( Garland Science 2010)

Expression of the Drosophila ey gene in the precursor cells of the leg triggers the development of an eye on the leg

41

Post-transcriptional control
Riboswitches Provide An Economical Solution to Gene Regulation The Untranslated Regions (UTR) of mRNAs Can Control Their Translation Small Regulatory RNAs (miRNA) Control the Expression of Thousands of Animal and Plant Genes RNA Interference (RNAi) Destroys DoubleStranded Foreign RNAs Scientists Can Use RNA Interference to Turn Off Genes

Controlled by regulating translation initiation

Figure 8-25 Essential Cell Biology ( Garland Science 2010)

miRNA
(microRNA)

Figure 8-26 Essential Cell Biology ( Garland Science 2010)

RNAi vs. siRNAs

(RNA interference)
vs

(small interference RNAs)

Figure 8-27 Essential Cell Biology ( Garland Science 2010)

How we know about gene regulation

The story of eve

46

Molecules localized at the ends of the Drosophila egg control its anterior-posterior polarity
The first demonstration of asymmetric distribution in cell (embryo)

47

The early Drosophila embryo shows a nonuniform distribution of four gene regulatory proteins

48

A reporter gene reveals the modular construction of the eve gene regulatory region

49

The regulatory module for eve stripe 2 contains binding sites for four different gene regulatory proteins

50

The end

51