Topic 2.2 - Gene regulation

levels of gene regulation (3)

transcriptional regulation → initiation and elongation

post transcriptional regulation → initiation and mRNA stability

post translational regulation → activity, stability and localisation

types of gene expression (2)

constitutive gene expression → gene is transcribed at a relatively constant level under all conditions

regulated gene expression → gene is transcribed under certain cellular or environmental conditions or in certain cell types

gene regulation in single-celled organism

responds to changes in environment

purpose for gene regulation in multicellular organisms

cells in tissue can have varying requirements to other cells and cells in other tissue types

gene regulation in single-celled organisms - example (1)

if glucose becomes available, needs to inhibit transcription of lac operon

gene regulation in multicellular organisms - examples (3)

absorptive cells will need to make lots of membrane for microvilli and enzymes for digestion

goblet cells need to make lots of mucus

stem cels will need proteins involved in cell division

differential gene expression (def)

mechanism where cells activate or suppress specific genes to control protein production

defines distinct cell types and functions from the same genome

essential genes (def)

housekeeping genes needed by all cells → constitutive expression

regulated genes (def)

non-essential genes only needed in certain cell types but are important for their function/ behaviour

differential gene expression - example (neuron v liver)

both have beta tubulin

liver have tyrosine aminotransferase

neurons will have NMDA receptor

prokaryotic transcription factors bind…

near promoter and help recruit RNA pol

eukaryotic specific transcription factors bind…

to enhancer sites a long way from the promoter → DNA can loop over and bring them in contact with the initiation complex

transcription factor types (2)

cis-acting → DNA sequences in the vicinity of the structural portion of a gene (required for gene expression)

trans-acting → usually proteins that bind to the cis-acting sequences to control gene expression

methods of transcription inhibition used by repressors (3)

1. competitive DNA binding → repressor prevents activator form binding

2. masking activation surface → repressor binds to activator and inhibits its function

3. direct interaction with general transcription factors → repressor directly binds and interferes with transcriptional machinery

eukaryotic transcription activators and repressors

can recruit protein complexes that modify histones and remodel the chromatin structure

ligand-regulated DNA (general method)

ligands can regulate DNA binding of transcriptional activators and repressors by changing conformation which affects transcription factor binding to DNA

ligand-regualted DNA - methods (4)

1. ligand needed for activator to bind → positive

2. ligand stops activator binding → negative

3. ligand needed for repressor to bind → negative

4. ligand stops repressor binding → positive

negative v positive ligand-regulated DNA

negative: bound repressor protein prevents transcription

positive: bound activator protein promotes transcription

prokaryotic gene regulation - consensus sequence

region is binding site for sigma factor → binds to both regions of DNA and recruits core enzymes to start transcription initiation

operons (def)

group of contiguous genes that are transcribed as a single mRNA molecule → encodes several different polypeptides

operator region (def)

DNA region within promotor region between consensus sequences in prokaryotes that controls the transcription of an adjacent gene

binding site for a repressor → prevents RNA pol from binding

cistron (def)

section of DNA encoding a single polypeptide which functions as a hereditary unit

commonly used to describe the individual gene units in a prokaryotic operon

polycistronic (def)

mRNA that encodes several different polypeptides

common in proakryotes but very rare in eukaryotes

usually encode proteins whose functions are linked

polycistronic gene example

one polycistronic gene encodes several enzymes that work together to make tryptophan

prokaryote’s preferred carbon source

glucose

will use amino acids, fatty acids, lactose and glycerol if glucose not available

types of eukaryotic gene regulation (3)

spatial → control of where a gene is expressed

temporal → control of when a gene is expressed

spatiotemporal → control of when and where a gene is expressed

combinatorial regulation of expression meaning

expression of a gene depends on expression of its activators and repressors in multicellular organisms

twist - summary (3)

1. transcriptional activator → binds to enhancer site

2. expressed in presumptive mesodermal cells of early fly embryo > causes cells to undergo fundamental changes in cell type

3. expressed in ventral part of embryo

impacts of inappropriate expression of Twist

can cause cancer

turning on of human twist can activate genetic network that causes benign epithelial tumour cells to become migratory and invasive

relation between snail, rhomboid and twist

twist activates snail and rhomboid

snail is repressor of rhomboid

enhancer region of rhomboid

2 binding sites for twist

3 binding sites for snail

bidning sites overlap in one areae

expression of snail vs rhomboid

snail expressed in a ventral band but in more restricted region within Twist

rhomboid expressed where snail is not but twist is

what are twist, snail, rhomboid examples of

spatial gene regulation and combinatorial regulation of expression

haemoglobin structure

tetramer of 2 alpha and 2 beta globins

each globin has iron-containing heme group which binds oxygen

locations of alpha and beta globins (chromosomes)

alpha globins on chromosome 16

beta globins on chromosome 11

evolution of globin genes (3)

1. singular globin gene

2. single alpha globin gene precursor

3. potential duplication event to result in foetal and adult beta-globin

how does foetal and adult haemoglobin composition change throughout development

foetal: high in alpha and gamma

adult: high in alpha and beta

when is foetal haemoglobin more efficient (partial pressures)

at low to medium partial pressures

in placenta, mother’s blood come sinto close proximity to the blood vessels of foetus → oxygen attached to mother’s haemoglobin will be outcompeted by foetal haemoglobin as it has a higher affinity

enhancer region (def)

regulatory DNA sequence to which regulatory proteins bind, increasing rate of transcription of a gene

globin genes - locus control region (def)

enhances expression by interacting with regulatory factors present at the promoters of the globin genes → enhances whichever genes are being expressed

how are enhancers limited in effect

insulator elements create loops in chromosomes

how is spread of heterochromatin prevented

barrier sequences block

anaemia (def)

decrease in number of RBC or less than normal quantity of haemaglobin in the blood

thalassaemia (def)

inherited form of anaemia caused by faulty synthesis of haemoglobin

sickle cell anaemia (def)

autosomal recessive form of anaemia characterised by low RBC count, reduced life of RBC and limited oxygen reaching organs

where is sickle cell anaemia most common

Africa

india

caribbean

middle east

mediterranean

cause of sickle cell anaemia

single mutation in beta-globin gene

normal RBC to sickled RBC due to clumped haemoglobin

beta thalassaemia cause

defects production or function of beta globin gene

beta thalassaemia - mutation types

no beta globin B0, diminished beta globin B+(mild or severe)

patient severity depends on what combinations of what class of mutations they have

beta-thalassaemia - severe clinical phenotype

homozygous or heterozygous for rither B0 mutant alleles and the more severe B+ allele

patients display severe transfusion-dependent anaemia

untreated child would die by age 5

beta thalassaemia - intermediate clinical phenotype (1)

mutant allele combination involving a more mild B+ allele that still allows some beta-globin production

beta thalassaemia - mild clinical phenotype (1)

one more copy of beta globulin gene present

severe beta-thalassaemia genotype (3)

B+ (severe)/ B+ (severe)

B+ (severe)/ B0

B0/ B0

intermediate beta-thalassaemia genotype (3)

B+ (mild)/ B+ (mild)

B+ (mild)/ B0

B+ (mild)/ B+ (severe)

mild beta-thalassaemia genotype (2)

B+/ B

B0/ B

epigenetics (def)

study of mitotically heritable changes in gene expression and therefore cellular phenotypes that do not involve changes to the sequence of DNA

important epigenetic gene regulation to be maintained during mitosis (3)

constitutive heterochromatic regions of chromosomes → eg. centromeres

patterns of gene expression that determine cell type

choice of which X chromosome is inactivated in a female cell

histone modification - opening for transcription steps (2)

1. transcription regulator recruits chromatin remodelling complexes to alter chromatin so that it opens up → nucleosome slides along DNA to expose regions like the TATA box

2. transcription regulator can recruit histone-modifying complexes to mark histones and create more open chromatin

complexes transcription repressor can recruit to compact DNA (3)

chromatin remodelling complex

histone deactylase

histone methylase

DNA methylation occurs…

at CpG dinucleotides (palindromic)

impact of DNA methylation to silence genes

does not affect base pairing

inhibits gene expression by preventing transcription factors from binding

causes compaction of chromatin by recruiting histone modifying enzymes

writers, erasers and readers

writers add marker via acetylation or methylation

erasers remove marker

reader binds to histone mark

transcription factors - writers and readers steps (4)

1. transcription factor binds to specific DNA sequence

2. histone modifying enzyme (writer) is recruited and adds histone mark

3. histone (reader) binds to histone mark and recruits another writer which marks the next nucleosome

4. sequence repeatsmi with new reader-writer complex binding → spreading wave of chromatin condensation

conservation of histone marks during mitosis

heterochromatin can cause other nucleosomes to also become heterochromatic → marked histones will recruit histone modifying enzymes to add histones to others

conservation of DNA methylation during mitosis

de novo DNMTa/b can take unmethylated DNA and put down a methyl mark onto the cytosines

maintenance methylase recognises hemi-methylated sequences and methylates cytosine that is not methylated

methylation preserved form one cell type to the next

cooperation of histone and DNA marks

spreading heterochromatin can be achieved by both histone modifying enzymes and DNA methylation cooperating

Spreading heterochromatin example (1 recruits 3)

HP1 binds to H3K9me and recruits KMT, DNMT1, HDAC

KMT = lysine methyl transferase and methylates H3K9 → puts down methylation mark on neighbouring nucleosome

DNMT1 = methylates DNA

HDAC = histone deacetylase → removes acetylation