Gene Expression - University of Vermontbiology/Classes/past-classes/295C/pdf/11_GeneExpr… · What...
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Transcript of Gene Expression - University of Vermontbiology/Classes/past-classes/295C/pdf/11_GeneExpr… · What...
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
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• 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?
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)
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