The sequence of the promoter region controls the binding of the RNA polymerase and transcription factors, therefore promoters play a large role in determining where and when your gene of interest will be expressed. Thus, promoter selection has received greatest attention in the literature.
Usually, the promoter region is immediately upstream of the coding sequence. This region can be short (only a few nucleotides in length) or quite long (hundreds of nucleotides long). The longer the promoter, the more available space for proteins to bind. This also adds more control to the transcription process. The length of the promoter is gene-specific and can differ dramatically between genes. Consequently, the level of control of gene expression can also differ quite dramatically between genes.
A major limitation of AAV as a gene therapy vector is the restricted ~5 kb packaging capacity. This has largely prevented the use of large regulatory elements to control transgene expression with AAV vector systems. Customers should pay attention to this limitation and determine which expression strategies can be used.
Steps to consider when selecting a promoter for AAV vectors
Understand Your Goals: What is the therapeutic goal of your gene therapy? Are you aiming for widespread or targeted expression? Different promoters have varying strengths and tissue specificity.
Promoter Strength: Promoters have different levels of activity, often described as strong, moderate, or weak. Choose a promoter strength that matches the desired expression level of your therapeutic gene.
Tissue Specificity: Some promoters are specific to certain tissues or cell types. Choose a promoter that drives expression in the tissues where you want your therapeutic gene to be active.
Safety Considerations: Some promoters may cause unintended immune responses or off-target effects. Choose a promoter with a known safety profile, especially if you’re working with human subjects.
Transcriptional Regulation: Consider whether you need tight control over gene expression. Some promoters can be regulated by specific factors or inducible systems.
Size and Compatibility: Remember that the promoter sequence adds to the overall size of the expression cassette. Make sure the chosen promoter, along with other elements, fits within the packaging capacity of your AAV vector.
Literature Review: Look for promoters that have been successfully used in similar contexts. This can give you insights into their performance and suitability.
Consult Experts: If you’re uncertain, consult with colleagues, experts in the field, or professionals experienced in gene therapy vector design. Please do not hesitate to contact AAVnerGene, our scientists have widely experiences in gene therapy and AAV vector design.
Experimental Validation: Test your chosen promoter in relevant cell lines or animal models before proceeding to clinical applications. AAVnerGene provides AAV optimization services to customer. This can be extremely valuable in ensuring that the AAV vector and the chosen promoter function optimally for the specific therapeutic goals.
Consider Combinations: In some cases, using a combination of promoters (hybrid promoters) can provide a tailored expression pattern that suits your therapeutic goals.
Common eukaryotic promoters
Models of gene therapy generally employ expression cassettes containing strong viral promoters that are constitutively active in a wide spectrum of cells. Such generic vectors have been popular because of their broad utility, and have typically proved extremely powerful in vitro and in some pre-clinical models in vivo. Common eukaryotic promoters used in research are listed below. It should be a good place to start when trying to pick your promoter.
CMV (Cytomegalovirus) Promoter:
- One of the most widely used promoters for high-level, constitutive expression.
- Provides strong expression across a range of cell types.
- May not be suitable for all tissues due to its ubiquitous nature.
EF1α (Elongation Factor 1 Alpha) Promoter:
- Offers strong and constitutive expression in a variety of cell types.
- Relatively less influenced by the host cell’s differentiation status.
PGK (Phosphoglycerate Kinase) Promoter:
- Exhibits strong and constitutive expression across different cell types.
- Commonly used for viral vectors and transgenic animals.
CAG (CMV enhancer, chicken beta-actin promoter, rabbit beta-globin splice acceptor) Promoter:
- Combines elements from the CMV enhancer and chicken beta-actin promoter.
- Drives high-level expression in various cell types.
SV40 (Simian Virus 40) Promoter:
- A strong constitutive promoter derived from the SV40 virus.
- Widely used for high-level gene expression.
Rous Sarcoma Virus (RSV) Promoter:
- A strong viral promoter that works in a wide range of cell types.
- Used for constitutive gene expression.
CMV (Cytomegalovirus) Enhancer/Chicken β-Actin(CB) Promoter:
- Combines the enhancer from CMV and the promoter from chicken β-actin.
- Provides high and constitutive gene expression.
- Ubiquitin C (UBC) Promoter:
- Constitutively active in various cell types.
- Used for stable gene expression.
- Tet-Off/Tet-On Promoters:
- Inducible promoters regulated by the presence or absence of doxycycline (Tet-On) or its removal (Tet-Off).
- Allow tight control over gene expression, which can be useful for specific applications.
Liver Specific Promoter
Certainly, here are a few liver-specific promoters that are commonly used to drive gene expression specifically in hepatocytes (liver cells):
Albumin Promoter: A widely used liver-specific promoter; Drives expression in hepatocytes, the main functional cells of the liver; Well-established and offers strong and consistent expression in the liver.
Alpha-1-Antitrypsin (AAT) Promoter: Drives expression in hepatocytes; Often used in gene therapy targeting liver-related diseases.
Transthyretin (TTR) Promoter: Active in hepatocytes; Used for liver-specific gene expression and gene therapy applications.
Phosphoenolpyruvate Carboxykinase (PEPCK) Promoter: Primarily found in liver cells; Can be used for liver-specific expression, especially in metabolic studies.
C/EBPα (CCAAT/Enhancer-Binding Protein Alpha) Promoter: Drives expression in hepatocytes; Can be used to study liver-related processes.
UDP-Glucuronosyltransferase 1A1 (UGT1A1) Promoter: Active in liver cells; Used for studying liver metabolism and for targeting liver diseases.
Human Apolipoprotein E (APOE) Promoter: Expressed in hepatocytes; Often used for studying lipid metabolism and related disorders.
Cytochrome P450 (CYP) Promoters (e.g., CYP2B6, CYP3A4): These are a family of liver-specific promoters that drive the expression of enzymes involved in drug metabolism; Used for studying drug metabolism and liver-specific effects.
Liver-Specific MicroRNA Promoters (e.g., miR-122 Promoter): miR-122 is highly expressed in the liver; Used for liver-specific modulation of gene expression.
Factor IX (FIX) Promoter: Liver-specific promoter that is commonly used in hemophilia B gene therapy; Drives expression of the blood clotting factor IX in hepatocytes.
HNF4α (Hepatocyte Nuclear Factor 4 Alpha) Promoter: Regulatory factor in liver development and function; Its promoter can be used for liver-specific expression.
Remember that the specificity and strength of these promoters can vary depending on the experimental context and the exact sequence used. Always validate the performance of the chosen promoter in your specific model system before proceeding with gene therapy or other applications.
Lung Specific promoter
Lung-specific promoters are important for achieving targeted gene expression in lung cells. Here are a few examples of lung-specific promoters that are commonly used:
- Surfactant Protein C (SP-C) Promoter: Specific to alveolar type II cells in the lungs; Used for lung-specific gene expression.
- Clara Cell Secretory Protein (CCSP) Promoter: Active in Clara cells, which are non-ciliated cells in the bronchiolar epithelium; Can be used for lung-specific expression.
- Aquaporin 5 (AQP5) Promoter: Expressed in alveolar type I cells and other lung cells; Used for lung-specific gene expression.
- Mucin 1 (MUC1) Promoter: Found in various epithelial tissues, including the respiratory tract; Can be used for lung-specific expression.
- T1α (Podoplanin) Promoter: Expressed in alveolar type I cells and some bronchiolar epithelial cells; Used for lung-specific gene expression.
- SP-B (Surfactant Protein B) Promoter: Specific to alveolar type II cells; Used for targeting gene expression to lung tissue.
- CC10 (Club Cell Secretory Protein, also known as CCSP) Promoter. Active in Clara cells and other non-ciliated epithelial cells; Can drive lung-specific expression.
- HOPX (HOP Homeobox) Promoter: Expressed in distal airway epithelial cells; Can be used for lung-specific gene expression.
- Napsin-A Promoter: Found in alveolar type II cells; Used for driving gene expression in lung tissue.
These promoters are valuable tools for researchers aiming to study lung biology or develop lung-specific gene therapies. As with any promoter, it’s important to validate their specificity and activity in your experimental system before proceeding with applications.
CNS promoter
Central Nervous System (CNS) promoters are essential for achieving targeted gene expression in the brain and spinal cord. Here are a few examples of CNS-specific promoters that are commonly used:
Synapsin Promoter:Active in neurons throughout the brain; Drives gene expression in the central nervous system.
Neuron-Specific Enolase (NSE) Promoter:Expressed in neurons and neuroendocrine cells;Used for gene expression in the CNS.
CamKII (Calcium/Calmodulin-Dependent Kinase II) Promoter: Active in excitatory neurons; Used for neuronal gene expression in the CNS.
Thy1 Promoter: Drives expression in subsets of neurons; Used for targeting specific neuronal populations.
Human Glial Fibrillary Acidic Protein (hGFAP) Promoter: Active in astrocytes, which are a type of glial cell in the CNS; Used for glial cell-specific expression.
Nestin Promoter: Active in neural stem cells and some progenitor cells; Used for gene expression in developing and regenerating CNS.
NeuroD Promoter: Expressed in neuronal precursors and mature neurons; Used for gene expression in the CNS.
Human Dopamine Beta-Hydroxylase (DBH) Promoter: Found in catecholaminergic neurons; Used for targeting gene expression to specific neuronal populations.
Myelin Basic Protein (MBP) Promoter: Active in oligodendrocytes, cells responsible for myelination; Can be used for glial cell-specific expression.
Enkephalin Promoter: Expressed in certain neurons, including those involved in pain regulation; Used for targeted gene expression in the CNS.
Thyroglobulin Promoter: Expressed in the choroid plexus cells of the brain; Used for gene expression in the brain’s ventricular system.
Neuronal Pentraxin (NPTX2) Promoter: Active in excitatory neurons; Used for neuronal gene expression in the CNS.
Glutamate Decarboxylase (GAD) Promoter: Expressed in inhibitory GABAergic neurons; Used for targeting inhibitory neurons in the CNS.
Choline Acetyltransferase (ChAT) Promoter: Found in cholinergic neurons, including motor neurons; Used for gene expression in specific neuronal populations.
Proopiomelanocortin (POMC) Promoter: Expressed in neurons within the hypothalamus; Used for targeting gene expression in specific hypothalamic nuclei.
Reelin Promoter: Active in various neuronal populations during development and in the adult brain; Used for CNS-specific gene expression.
Gfap (Glial Fibrillary Acidic Protein) Promoter: Specific to astrocytes in the CNS; Used for targeting gene expression to astrocytes.
VGlut2 (Vesicular Glutamate Transporter 2) Promoter: Expressed in excitatory glutamatergic neurons;Used for gene expression in specific glutamatergic populations.
Purkinje Cell-Specific Promoters (e.g., Pcp2, L7): Active in cerebellar Purkinje cells; Used for targeted gene expression in the cerebellum.
Parvalbumin Promoter: Expressed in certain subtypes of GABAergic interneurons; Used for targeting specific inhibitory neuron populations.
These CNS-specific promoters are valuable tools for studying neurobiology and developing therapies for neurological disorders. Always ensure to validate their specificity and activity in your specific experimental system before using them for gene therapy or other applications.
Retina specific promoter
Retina-specific promoters are essential for achieving targeted gene expression in the cells of the retina. Here are a few examples of retina-specific promoters that are commonly used:
- Rhodopsin Promoter: Active in rod photoreceptor cells; Used for targeting gene expression specifically to rods.
- IRBP (Interphotoreceptor Retinoid-Binding Protein) Promoter: Drives expression in both rod and cone photoreceptor cells; Used for targeting gene expression to photoreceptors.
- Cone Arrestin Promoter: Specific to cone photoreceptor cells; Used for cone cell-specific gene expression.
- Opsin Promoters (e.g., Blue, Green, Red Opsin Promoters): Drive expression in specific cone photoreceptor subtypes; Used for targeting different cone populations.
- Chx10 Promoter: Expressed in retinal progenitor cells and bipolar cells; Used for targeting gene expression in developing retina.
- Nrl Promoter (Neural Retina Leucine Zipper): Active in rod photoreceptor cells; Used for driving gene expression in rods.
- Pde6b Promoter (Phosphodiesterase 6B): Expressed in rods and cones; Used for retina-specific gene expression.
- Prph2 Promoter (Peripherin 2, also known as RDS): Found in photoreceptor cells; Used for gene expression in photoreceptors.
- Thy1.2 Promoter (Thy-1 Cell Surface Antigen): Can target ganglion cells in the retina; Used for ganglion cell-specific expression.
- Crx (Cone-Rod Homeobox) Promoter: Active in photoreceptors; Used for retina-specific gene expression.
- Vsx2 Promoter (Visual System Homeobox 2, also known as Chx10): Expressed in bipolar cells and retinal progenitor cells; Used for bipolar cell-specific expression.
- Sncg (or γ-synuclein) promoter: mouse γ-synuclein (mSncg) promoter is retina ganglion cell-specific promoter.
These retina-specific promoters are valuable tools for studying retinal development, function, and diseases, as well as for gene therapy applications targeting retinal disorders. Always validate the specificity and activity of the chosen promoter in your specific experimental system before proceeding with gene expression studies or gene therapy.
Muscle-specific promoter
Muscle-specific promoters are crucial for achieving targeted gene expression in muscle cells, which can be important for studying muscle biology or developing therapies for muscle-related disorders. Here are some examples of muscle-specific promoters:
- Muscle Creatine Kinase (MCK) Promoter: Active in skeletal muscle cells; Used for muscle-specific gene expression.
- Myosin Light Chain (MLC) Promoter: Drives expression in both cardiac and skeletal muscle cells; Used for muscle-specific gene delivery.
- Desmin Promoter: Specific to muscle cells, including cardiac, skeletal, and smooth muscle cells; Used for muscle-specific gene expression.
- Troponin Promoters (e.g., cTnT, cTnI, cTnC Promoters): Drive expression in cardiac muscle cells; Used for targeting gene expression to the heart.
- α-Actin Promoter: Active in smooth muscle cells, including those in blood vessels and the gastrointestinal tract; Used for smooth muscle-specific gene expression.
- Myogenin Promoter: Expressed during muscle differentiation. Used for gene expression in developing muscle cells.
- Titin Promoter: Active in both cardiac and skeletal muscle cells; Used for muscle-specific gene expression.
- α-Myosin Heavy Chain (α-MHC) Promoter: Specific to cardiac muscle cells; Used for cardiac muscle-specific gene expression.
- Slow Troponin I Promoter (ssTnI): Drives expression in slow-twitch skeletal muscle fibers Used for targeting specific muscle fiber types.
- Fast Troponin I Promoter (ffTnI): Expressed in fast-twitch skeletal muscle fibers; Used for targeting specific muscle fiber types.
These muscle-specific promoters are valuable tools for studying muscle development, function, and diseases, as well as for gene therapy applications targeting muscle disorders. Always validate the specificity and activity of the chosen promoter in your specific experimental system before using it for gene expression studies or therapeutic applications.
Kidney-specific promoter
Kidney-specific promoters are essential for achieving targeted gene expression in kidney cells. Here are a few examples of kidney-specific promoters that are commonly used:
Renin Promoter: Drives expression in cells of the juxtaglomerular apparatus in the kidney; Used for kidney-specific gene expression.
Aquaporin-2 (AQP2) Promoter: Specific to collecting duct cells in the kidney. Used for targeting gene expression to these cells.
Nephron-Specific Promoters (e.g., Slc12a1, Slc12a3): Drive expression in specific segments of the nephron. Used for kidney-specific gene delivery.
Glutamate Transporter (EAAT1) Promoter: Expressed in certain types of kidney cells, including proximal tubules. Used for targeting gene expression to these cells.
Sodium-Phosphate Cotransporter (NaPi-IIa) Promoter: Found in proximal tubule cells. Used for gene expression in these cells.
Podocin Promoter: Expressed in podocytes, specialized cells in the glomerulus. Used for gene expression in these cells.
Ksp-Cadherin (Cadherin-16) Promoter: Active in collecting duct cells and distal tubules. Used for kidney-specific gene expression.
Wilms’ Tumor-1 (WT1) Promoter: Expressed in podocytes and some mesangial cells. Used for targeting gene expression to these cells.
Renal Tubule-Specific Promoters (e.g., Slc22a6, Slc34a1): Drive expression in specific segments of the renal tubules. Used for kidney-specific gene delivery.