Gene Expression

Chapter Eleven

What is Gene Expression?• When a gene is expressed – that gene’s

protein product is made:1. DNA is transcribed into RNA2. RNA is translated into Protein3. Protein is folded and transported so it is

functional• When a gene is not expressed – these

steps do not happen• Gene is “silenced” – function is off

What is Gene Expression?• We all have the same genes:

– Different races– Apes and Humans– Fruit Flies and Humans– Different cell types – bone vs. eyeballs

• So what makes us so different?• It’s not what genes we are carrying• It’s how and when those genes are

expressed

Questions to ask…1. How does a bone cell know to express

the proteins that make it a bone, and not an eyeball?

2. How do blood stem cells know when to become red blood cells, white blood cells or platelets?

3. What makes us human and them apes?

What regulates gene expression?

How is expression regulated?• Transcription Factors – bind specifically to

gene’s promoters – turn on and off• Methylation – silencing of huge sections of

DNA• Acelylation – activating huge sections of

DNA• Chromatin and histones – bound will

cause a gene to be silenced

How is expression regulated?• RNAi – small pieces of RNA bind to mRNA

and effectively remove it before it can be translated into protein

• Exon shuffling – one gene encodes for different proteins – depends on which exons translation machinery “keeps”

• Protein folding – one protein can be folded differently to have different functions –depends on enzymes and chaperones

How is expression regulated?All levels of transcription and translation are

involved:1. DNA sequence will encode for specific

regulation – promoters, exons/introns, etc2. RNAs – will affect which genes complete

the process to become proteins 3. Proteins – function as enzymes and

machinery to activate or silence specific genes

Transcription Factors• Proteins that bind:

– Promoters– Enhancers or Repressors

• Initiate transcription by bringing over RNA Polymerase and other proteins to the start site of transcription

• Or repress transcription by blocking proteins from binding at start site

Methylation and Acetylation• Methylation adds -CH3

• Acetylation adds -CO2CH3

• Methylation causes DNA to be silenced:– Heterochromatin (darker stained regions of

chromosomes)– Example = Imprinting

• Acetylation causes DNA to be activated:– Move histones away from transcription start

site

Histones• Histones are proteins that wrap up DNA in

order to condense it into Nucleus• When Histones are binding DNA ?DNA is silenced:

– RNA Polymerase can’t bind• When Histones come off DNA ?DNA is free to be expressed:

– RNA Polymerase can bind – transcription

RNAi• Sometimes small interfering RNAs are

made– siRNA

• They will bind to mRNA– Based on complementary base pairing

• mRNA and siRNA complex will be destroyed

• Therefore mRNA cannot be translated into protein

Exon Shuffling• One gene can choose different exons and

skip past others• Therefore one gene can make many

different proteins• The transcription and translation

machinery will regulate which exons to are used and which are skipped

• Depending on tissue and developmental time point – different proteins made

Exon Shuffling

Alternative Splicing• Many mRNA sequences can be spliced

differently• Thereby producing more than one protein

from same sequence

A B C D EPromoter

A B C E A C D E

Protein Folding• Sometimes protein sequence can fold in

more than one way

Sequence

Structure 1

Function A

Structure 2

Function B

Protein Folding• One protein sequence can be folded in

more than one way• Depends on:

– Enzymes– Chaperone proteins

• Different enzymes will be present in different tissues or at different developmental time points – therefore forming different proteins depending

How is expression regulated?1. Transcription Factors2. Methylation3. Acelylation4. Chromatin and histones5. RNAi6. Exon shuffling7. Alternative Splicing8. Protein folding

Hemoglobin SubunitsExcellent example of gene expression

regulation• Hemoglobin is a protein• Made of four subunits• Each subunit carries a “heme” group

– Transports Oxygen– Bound to Iron

Hemoglobin SubunitsDuring development mammals receive

oxygen from different sources:1. Embryonic – oxygen comes directly from

mother’s tissues2. Fetal – oxygen comes through placenta3. Adult – oxygen comes through lungsHemoglobin subunits change according to

developmental time point to handle this

Hemoglobin SubunitsHemoglobin subunits:1. Embryonic – 2 epsilon and 2 zeta

subunits2. Fetal – 2 alpha and 2 gamma subunits3. Adult – 2 alpha and 2 beta subunits“Locus Control Region” produce proteins

that oversee the assembly of hemoglobin and which subunits are used

Blood Cell Types• In bone marrow – one pluripotent stem cell

– Can make different types of cells• Has to choose between becoming:

– Red Blood CellFilled with hemoglobin– White Blood CellProtecting the body from infection– PlateletsBlood clotting

Blood Cell Types• Actually this is more accurate:

Blood Cell Types• Bone Marrow – pluripotent stem cell• Choice based on gene expression:

– Red Blood CellBone marrow activates pathway 1– White Blood CellPathway 2– PlateletsPathway 3

• Think about disease or sickness

1

2

3

Bone vs. Eyeball?• Developing organs depends on:

– Differential gene expression– At specific developmental time points

Bone vs. Eyeball?1. Transcription

Factors 2. Methylation 3. Acelylation 4. Histones 5. RNAi6. Exon shuffling7. Alternative Splicing8. Protein folding

All of these levels of control are happening

Each controlled by:• Developmental time

points• Differences in tissue

types• Differences in genetic

sequence

Proteomics• Study of the structure and function of

proteins, including the way they work and interact with each other inside cell

• Also - analysis of the protein complement of the genome

• Or in other words, which proteins are expressed

• And at what level?

Example from Proteomics

One Gene – Many Proteins1. Exon Shuffling2. Protein Folding3. Genes in both directions

– Another gene lies hidden in the opposite direction

– When DNA is read 5’ to 3’ (non-coding strand) will form a second protein

4. Genes within introns– A second gene is hidden inside the introns

of first

What else is in the Genome?• Only 1.5 % of genome is actually encoding

genes• What is the other 98.5 % then?

– Regulation sequences: promoters, enhancers, repressors, etc

– Noncoding RNA – tRNA, rRNA, etc– Introns – regulation? other genes?– Repeats – unknown function(Some believe repeats are leftovers from

evolution)

What else is in the Genome?Genes

Regulation

Introns

Non-coding RNA

Repeats

Summary• Gene expression – is when a gene is

transcribed and translated into a functional protein

• Regulation of expression happens at:– DNA, RNA and protein level

• Learn 8 different methods to regulate gene expression and be able to tell them apart

• Know how one gene can lead to many proteins

Next Class:• Read Chapter Twelve

• Homework – Chapter Eleven Problems;– Review: 1,3,4,7,13,15– Applied: 3,4,6,8