L6. Control of Gene Expression Flashcards
how do cells differentiate
cells make and accumulate different sets of RNA and protein molecules
what are housekeeping genes
- genes that are common to all the cells of a multicellular organism
- cells contain ~50% of these genes
- they are used to characterize the differential expression of genes
what are examples of house keeping genes
- structural proteins of chromosomes
- ribosomal proteins
- enzymes involved in basic metabolic pathways
- cytoskeleton
- and more
how is gene expression regulated
- it is regulated at every step from DNA to protein:
1. transcriptional control
2. RNA processing control
3. mRNA transport and localization control
4. mRNA degradation control
5. translation control
6. protein degradation control
7. protein activity control
regulation of gene expression - transcriptional control
controlling when and how often a given gene is transcribed
regulation of gene expression - RNA processing control
controlling how an RNA transcript is sliced or otherwise processed
regulation of gene expression - mRNA transport and localization control
selecting which mRNAs are exported from the nucleus to the cytosol
regulation of gene expression - mRNA degradation control
regulating how quickly certain mRNAs molecules are degraded
regulating gene expression - translation control
selecting which mRNAs are translated into proteins by ribosomes
regulating gene expression - protein degradation control
regulating how rapidly specific proteins are destroyed after they have been made
transcriptional control - switches
- promoters
- regulatory DNA sequences
- transcription regulator proteins
transcriptional control: switches - promoters
they contain recognition sites for proteins that associate with the sigma factor (bacteria) or general transcription factors (eukaryotes)
transcriptional control: switches - regulatory DNA sequences
- used to switch the gene on or off
- can be upstream or downstream of the promoter
- they attract transcription regulator proteins
transcriptional control: switches - explain regulatory DNA sequences in prokaryotes vs eukaryotes
- prokaryotes: regulatory sequences are short and simple
- eukaryotes: sequences are longer and integrates multiple signals
transcriptional control: switches - transcription regulator proteins
these bind to the regulatory DNA sequence to act as the switch to control transcription
transcriptional control: switches - transcriptional regulator-DNA binding
- the transcription regulator positions itself within the major DNA groove as a dimer
- alpha-helices will tightly associate with DNA
bacterial mRNA - define polycistronic
prokaryotic mRNA can encode for several different proteins which are translated from the same mRNA molecule
bacterial mRNA - how are the different coding regions recognized
- they do not have a 5’ cap to tell the ribosome where to begin
- they instead have ribosome-binding sequences upstream the start codon
explain simple transcription switches in bacteria
- polycistronic transcripts and operon
- their gene regulation is dependent on the environment and available food sources
simple transcription switches in bacteria - define operon
- genes that are arranged in a cluster
- they are transcribed by a single promoter as one mRNA molecule
- the mRNA molecule then gives rise to multiple different proteins
simple transcription switches in bacteria - define operator
present within the operon’s promoter and it is recognized by a transcription regulator
transcription switches in bacteria - tryptophan transcription repressor
- when tryptophan repressor binds to the operator, it blocks access of RNA pol to the promoter
- preventing transcription of the operon and tryptophan-producing enzymes
transcription switches in bacteria - how is the tryptophan repressor controlled
- it only is able to bind to the operator if it has a tryptophan bound to it
- prevents the cell from making more when tryptophan is already present
transcription switches in bacteria: tryptophan transcription - what happens when tryptophan is low
- no tryptophan is available to bind to the repressor, making it inactive
- this allows the repressor to unbind from the operator
explain how transcription is activated in bacteria
- transcription activator proteins bind and position RNA pol on their own
- but need help from a second molecule to bind to DNA
transcription switches in bacteria - Lac operon activation
- the operon is controlled by the Lac repressor and the CAP activator
- it encodes proteins required to import and digest lactose
Lac operon - what does the presence or absence of glucose do
- glucose absent: CAP activator with cAMP bound is present
- glucose present: CAP activator is not bound to the operon
Lac operon - what does the presence or absence of lactose do
- lactose absent: repressor is present
- lactose present: repressor is absent
Lac operon activation - when is the operon off
- when both glucose and lactose is present
- when glucose is present but lactose is absent
- when both glucose and lactose is absent
Lac operon activation - when is the operon active and why
- when glucose is absent and lactose is present
- this is bc the presence absence of glucose allows the activator protein to binds RNA pol and the presence of lactose removes the repressor allowing RNA pol to express the gene
explain eukaryotic gene expression
- activator proteins recognize and bind to enhancers
- this attracts RNA pol and general transcription factors which form a large transcription complex
eucaryotic gene expression - large transcription complex
composed of a mediator, general transcription factors, and RNA pol
eucaryotic gene expression - enhancer
- enhances the rate of transcription
- can be several nucleotides away from the gene (either upstream or downstream)
eukaryotic gene expression - how can the transcription complex interact with the enhancer is it is upstream of downstream
the DNA forms 3D structures and this allows the activator protein on the enhancer to bind with the mediator of the transcription complex
eukaryotic gene expression - example of cooperative regulation in humans
- cortisol receptor protein
- a transcript regulator must form a complex with cortisol in order to bind to DNA sites
- this then coordinates the expression of many genes at once
explain how chromatin remodeling can impact the regulation gene expression
- transcriptional regulators on histone tails attract chromatin remodeling complexes
- these complexes modulate the accessibility of the promoter and the gene
- the complexes do this through covalent histone modification
- regulators may function at gene or loci levels
chromatin remodeling - examples
- histone acetyl-transferases
- histone deacetylase
chromatin remodeling - histone acetyl-transferases
- attaches acetyl group to histone tail
- causes that gene to have greater accessibility
- acetyls attract transcriptional activator proteins
chromatin remodeling - histone deacetylase
- removes acetyl groups
- results in less accessibility to the gene
chromatin remodeling - how can it work in loci levels
- X-chromosome
- heterochromatin and histone deacetylase is found in inactive X chromosomes in female mammals
what does the level of gene expression depend on
the sum effect of the combinations of regulatory mechanisms
how can a cell be converted into another cell type
- a small number of transcription regulators can initiate differentiation
- a combination of few transcription regulators can generate many cell types
explain induced de-differentiation
- the artificial expression of four genes, each encoding a transcriptional regulator, can reprogram a fibroblast into a stem cell
- can be differentiated into almost any cell with appropriate stimuli
how can a cell have memory
- positive feedback
- DNA methylation
- histone modifications
cell “memory” - positive feedback
- descendant cells will ‘remember’
- a transcription regulator activates a regulatory factor
- the factor controls its own expression and cell fate of that cell lineage creating a positive feedback
cell “memory” - DNA methylation
- turns off genes by attracting proteins to bind to methylated cytosines and block gene transcription
- DNA methylation is passed on during DNA replication
cell “memory”: DNA methylation - epigenetic inheritence
transmission of information without altering DNA
cell “memory” - inherited histone modifications
- histones are distributed randomly to daughter cells
- histone modification enzymes will bind and spread its state to other unmodified histones
- occurs to some, but not all histones
- epigenetic effect
regulatory RNA
- microRNA
- small interfering RNAs (RNAi)
- long non-coding RNAs
regulatory RNA - microRNA
- packed in a “RISC” (RNA-induced Splicing Complex)
- once a target mRNA is bound to it, the mRNA is degraded
- one miRNA can regulate several genes
regulatory RNA - RNAi (interference)
- part of a host’s defense against viruses
- Dicer protein cuts up foreign DNA
- those fragments are called small interfering RNAs (siRNA)
- RISC processes those fragments to detect and target the foreign mRNA to degrade it
regulatory RNA - long non-coding RNA
- roles are poorly understood
- 2 examples:
1. Xist
2. antisense transcripts
regulatory RNA: long non-coding RNAs - Xist
- involved in X chromosome inactivation
- it is produced by one of the X chromosome
- Xist transcripts coat the chromosome
- it is thought to promote chromatin remodeling: heterochromatin formation
regulatory RNA: long non-coding RNAs - antisense transcripts
- arise from protein coding regions of the “wrong” opposite strand
- they bind to mRNA, affect translation and stability, some may also function as miRNAs
