4 - Regulation of Gene Expression Flashcards
Gene expression
- The process by which the information stored in our DNA is converted into a functional product (protein)
- The expression of specific genes determines the identity of the cell
Mechanisms of regulation
- Transcription
- Post-transcription
- Translation
- Post-translation
- Epigenetic
Cis-regulating elements
DNA in the vicinity of the structural portion of a gene that are required for gene expression
Trans-activating factors
- Factors that bind to the cis-acting sequences to control gene expression (transcription factors)
- Help position RNA polymerase at promoter site and initiate transcription (positive regulators of gene expression)
Transcription factors
- Specific
- Combination of transcription factors is necessary to initiate transcription of a gene.
- Presence/availability of the required transcription factors regulate transcription initiation
- Transcription factors are also themselves regulated by signals produced from other molecules
Spatial regulation
expressed in a tissue-specific manner
Temporal regulation
expressed at a specific time in development
Activity regulation
- Protein modification (e.g. phosphorylation)
- Activated by ligand binding
- May be sequestered until an appropriate environmental signal allows it to interact with the nuclear DNA
Transcription factor binding sites
- Bind to enhancer
- Certain proteins assist in bending the DNA so that the enhancer is near the promoter
- Transcription factors and other proteins attach to form an initiation complex, transcription now begins.
What is transcription elongation tightly coupled to
RNA processing (post transcriptional regulation)
Post-transcriptional regulation
- Further processing of the RNA
- The transcript is capped (5’ cap) and poly-adenylated (poly A tail)
- RNA splicing then removes the non-coding parts of the transcript (introns) so that only the coding sections (exons) remain
Function of 5’ cap
Stabilize and mark transcript as mature to prevent degradation
Function of poly A tail
Helps ribosome attach to begin translation
Alternative splicing
- Post-transcriptional regulation
- Variations in mRNA (and proteins)
- One gene can encode for more than one protein
- Grants genetic diversity
Example of alternative splicing
Calcitonin is alternatively spliced in the thyroid and neurons (same gene, different protein)
Varying longevity of mRNA
- Can last a long time and can continue to produce protein in the absence of DNA
- E.g. mammalian red blood cells eject their nucleus but continue to synthesise haemoglobin for several months
Examples of post transcriptional regulation
- 5’ capping and poly A tail
- Alternative splicing
- Varying rate of transport of mRNA through
the nuclear pores
Degradation of mRNA
- Ribonucleases destroy mRNA
- Hormones stabilise certain mRNA transcript
miRNA
- Micro RNAs
- Inhibit translation
rRNA
- Ribosomal RNAs
- Invloved in mRNA translation
lincRNA
- Long non coding RNAs
- Protein scaffolding, guidance, mRNA stability
circRNA
- Circular RNA
- RNA binding protein and miRNA decoy
miRNA and post-transcriptional regulation
- 22bp ssRNA
- Can bind to protein complexes to form RNA‐Induced Silencing Complexes (RISC) to inhibit mRNA translation
- RISC binding interferes with translation, resulting in down-regulation of gene expression
Regulation of Gene Expression via translational control
- Physical regulation (blockage)
- Initiation factors
- tRNA heterogeneity and codon usage bias
Physical regulation (blockage)
Proteins (even miRNA) that bind to mRNA (via specific sequences) can prevent ribosomes from attaching and thus prevent translation of
certain mRNA molecules
Initiation factors
- These bind to and help assemble the ribosome complex to initiate translation
- The availability of these factors are also regulated and are produced when certain
proteins are needed
tRNA heterogeneity and codon usage bias
- The relative abundance of tRNA can vary between tissues
- Coupled with preferential use of specific codons, this can regulate the rate of
translation
Post-translational modifications
- Increases the functional diversity of the proteome
- Molecular chaperones help guide the folding of many proteins
- Post-translational modifications can result in protein activation
What do translational modifications include
- Covalent addition of functional groups or proteins
- Proteolytic cleavage of regulatory subunits
- Degradation of entire proteins (proteasomes bind ubiquitinated proteins and degrade them)
Proteome complexity
The myriad of different post-translational modifications exponentially increases the complexity of the proteome relative to both the transcriptome and genome
Name 3 examples of post translational modifications
- Phosphorylation: phosphate group, usually to Ser, Tyr, Thr or His
- Glycosylation: carbohydrates, usually Asn, hydroxylysine, Ser, or Thr
- Methylation: methyl group, usually at Lys or Arg residues
Epigenetics
Alterations that cause a change in gene expression but doesn’t involve any changes in the DNA sequence
Examples of epigenetic regulation
DNA methylation and histone modification
DNA methylation
- Addition of a methyl group to cytosine at CpG islands (regions of the genome with high frequency of CG sites)
- Inhibits transcription by preventing access to promoters
- Plays a role in silencing tissue-specific genes
Histone modifications
- Acetylation or deacetylation
- Histone acetyltransferases, histone deacetylases (HDACs) and others regulate these modifications
- Some cancer cells overexpress or aberrantly recruit HDACs
- HDAC inhibitors are valuable cancer therapeutics, they can increase transcription, and lead to cell cycle arrest and apoptosis
Some cancer cells overexpress or aberrantly recruit HDACs
Hypoacetylation, condensed chromatin structure and reduced transcription
Acetylation
Associated with euchromatin (“open for transcription“ or active)
Deacetylation
Associated with heterochromatin (“closed“ or tightly wound DNA)
Are epigenetic alterations heritable
Yes
Cancer
- Cancer cells reproduce without restraint and colonise foreign tissues
- Most cancers derive from a single abnormal cell (epigenetic or genetic)
- Single mutation is not enough to cause cancer
Multiple stages of tumour development
- Initiation (genetically abnormal cell)
- Promotion (selective clonal expansion)
- Progression (additional mutations affecting polarity and communication)
- Invasion and metastasis (Invasion and colonisation of
secondary site)
Gene expression and cancer
- Cancer is a disease of dysregulated gene expression that imparts a survival advantage to the cell
- Alterations can occur at all levels of gene expression (e.g. histone acetylation, activation of transcription factors)
Proto-oncogenes
- Genes that stimulate cell growth and division in normal cells
- Become oncogenes through gain of function mutations
Tumour suppressor genes
- Genes that inhibit cell division in response to DNA damage and allow repair to occur
- Usually lose their function in cancer (loss-of-function)
Epithelial-mesenchymal transition (EMT)
- The process by which epithelial cells lose their cell polarity and cell-cell adhesion, and gain migratory and invasive properties
- Occurs naturally (e.g. tissue repair), but also important for initiation of metastasis in cancer
How do cells lose control of cell growth and/or death?
- Proto-oncogene gain of function mutations
- Tumour supressor gene loss of function mutations
How do cells lose cell polarity and miscommunicate?
Epithelial-mesenchymal transition (EMT)
What are the practical applications of studying gene expression in cancer?
Gene expression profiling
Gene expression profiling
- Capturing total gene activities, both increases
and decreases, across a genome as patterns of gene expression - Allows us to define different subtypes of cancer based on their gene expression profiles
What is gene expression profiling useful for
- Treatment selection (identify which specific pathways are deregulated in the tumour and treat with therapies that target that pathway)
- May predict cancer patient survival and prognosis
- Increasing understanding the molecular pathways that underlie cancer
Gene expression profiling and treatment selection in breast cancer
- A heterogeneous group of cancers with characteristic molecular features, prognosis and responses to available therapy
- three types based on gene expression profiling
Three types of breast cancer classifications
- Luminal (ER and PR positive, hormonal intervention)
- HER2+ (ERBB2 overexpression, Anti-HER2
therapy) - Basal like (Triple negative, Most difficult to treat)
Inter-tumour heterogeneity
- Variation between patients
- Different morphology types, expression subtypes, or gene expression
Intra tumour heterogeneity
- Variation within a tumour
- Different morphology AND different at the molecular level (tumour subpopulations)
Why do cancer cells frequently display startling heterogeneity for various traits related to tumourigenesis (e.g. angiogenic, invasive, and metastatic potential)
Clonal and cellular diversity for genetic and epigenetic alterations, Adaptive responses or fluctuation in protein levels and activity of signalling pathways
Gene expression profiling in
myelofibrosis
- Myelofibrosis is a bone marrow cancer where there is extensive scarring in the marrow that results in an inability to make blood cells
- Myeloproliferative
neoplasm - Diagnosis anad monitoring requires invasive bone marrow exam
Benefits of gene expression profiling
- Improved diagnosis, prognosis, treatment
- Personalised medicine
- Provides framework for testing targeted therapies
