This protocol describes a novel rAAV-based transient enhancer-reporter assay. This assay can be used to induce enhancer-driven expression in vivo in the mouse brain.
Enhancers are binding platforms for a diverse array of transcription factors that drive specific expression patterns of tissue- and cell-type-specific genes. Multiple means of assessing non-coding DNA and various chromatin states have proven useful in predicting the presence of enhancer sequences in the genome, but validating the activity of these sequences and finding the organs and developmental stages they are active in is a labor-intensive process. Recent advances in adeno-associated virus (AAV) vectors have enabled the widespread delivery of transgenes to mouse tissues, enabling in vivo enhancer testing without necessitating a transgenic animal. This protocol shows how a reporter construct that expresses EGFP under the control of a minimal promoter, which does not drive significant expression on its own, can be used to study the activity patterns of candidate enhancer sequences in the mouse brain. An AAV-packaged reporter construct is delivered to the mouse brain and incubated for 1-4 weeks, after which the animal is sacrificed, and brain sections are observed under a microscope. EGFP appears in cells in which the tested enhancer is sufficient to initiate gene expression, pinpointing the location and developmental stage in which the enhancer is active in the brain. Standard cloning methods, low-cost AAV packaging, and expanding AAV serotypes and methods for in vivo delivery and standard imaging readout make this an accessible approach for the study of how gene expression is regulated in the brain.
Enhancers are genomic cis-regulatory elements that serve as transcription factor binding sites and can drive the expression of a target gene in a spatiotemporally specific manner1,2. They are differentially active in different cell types, tissues, and stages of development and can be substrates of disease risk-related genomic variation3,4. Thus, the need to understand the dynamics of enhancer function is critical to progress in both translational and basic science applications within genomics. In silico predictions of enhancer activity can serve as excellent resources for generating hypotheses as to enhancer capability5,6. Such predicted enhancer activity can require additional validation and interrogation for a full understanding of the functional activity. Enhancer reporter assays have proved valuable for this purpose across a variety of systems, from cells to animals7,8,9. Towards extending these studies in a flexible and cost-effective transient in vivo context, this protocol describes the use of in vivo AAV-based methods to test putative enhancer sequences for their ability to drive the expression of an ectopic reporter gene in the postnatal mouse brain. This family of methods has utility for interrogating single candidate sequences or parallel library screening and is relevant for basic and translational research.
This method combines in a single plasmid a putative enhancer candidate DNA sequence with a reporter gene (here EGFP), under the control of a minimal promoter that alone does not drive significant expression. The plasmid is packaged into recombinant AAV (rAAV) and injected into an animal model. While the application here is to the brain, various rAAV serotypes enable infection across different tissue types so that this approach can be extended to other systems10. After a period of time, the brain can be collected and assayed for the expression of the reporter gene. Strong expression, compared with controls, indicates that the tested candidate sequence was able to "enhance" the expression of the gene (Figure 1). This simple design offers an easy and clear approach to test a sequence for enhancer activity in vivo in the brain.
In addition to testing for enhancer capability of a sequence, this method can be combined with techniques to determine cell-type enhancer activity. In sequence-based approaches to determining differential enhancer activity, sorting cells on cell-type-specific markers prior to DNA and RNA sequencing can allow researchers to determine if different cell types show differential enhancer activity, as was described in Gisselbrecht et al.11. In imaging-based approaches, co-labeling images with cell-type-specific markers allows examination of whether cells exhibiting enhancer-driven fluorescence also display cell-type markers of interest12,13,14,15,16. Enhancer reporter assays enable direct testing of risk-associated allelic variation in enhancers for effects on enhancer capability. The vast majority of risk loci identified in genome-wide association studies (GWAS) lie in non-coding regions of the genome17. Functional annotation studies of these risk loci indicate that a large portion likely act as enhancers18,19,20. MPRA deployment in vivo can allow testing of these risk-associated variants for enhancer activity in brain12,21. Finally, delivery and collection at different time points can offer insights into the developmental stages during which an enhancer is active.
Enhancer-reporter plasmid designs are diverse and can be customized to suit experimental goals. There are several options for minimal promoters that have been used in enhancer research, such as the human β-globin minimal promoter22 and the mouse Hsp68 minimal promoter23. These promoters are known to drive low levels of expression unless coupled with an enhancer element to activate them. In contrast, constitutive promoter elements drive strong expression of the transgene, useful for positive control or to test for enhancer function against a background of robust expression. Common choices for constitutive promoters include CAG, a hybrid promoter derived from the chicken β-actin promoter and the cytomegalovirus immediate-early enhancer24, or human EF1α25. Since enhancers are known to work bidirectionally26, the orientation and location of the enhancer relative to the minimal promoter are flexible (Figure 2A). Traditional enhancer-reporter assays place the enhancer upstream of the promoter and, in library deliveries, include a barcode sequence downstream of the reporter gene to associate sequencing reads with the tested enhancer27. However, enhancers can also be placed in the open reading frame of the reporter gene and serve as their own barcode sequence, as is done in STARR-seq28. The protocol described here utilizes the STARR-seq assay design, placing the candidate enhancer sequence into the 3' UTR of the reporter gene. While the STARR-seq orientation offers the benefit of more streamlined cloning, it is less well understood than the conventional approach and may induce variable RNA stability between constructs. The described methods can be easily adapted to either the STARR-seq or conventional orientation with minor alterations to the cloning process that have been described elsewhere27,29.
Different methods of AAV delivery can be employed to further customize this technique to fit experimental goals (Figure 2B). Direct intracranial injections, described further in this protocol, deliver a high concentration of virus directly to the brain30. This gives a high transduction efficiency centered at the site of injection, making this an excellent technique for experiments looking to maximize the density of transduced cells over an area of tissue. Stereotactic injection can help standardize the site of injection across animals for reproducible localized transduction. Intracranial injections are most straightforward in early postnatal animals. As an alternative technique, systemic injections can deliver transgenes using AAVs with serotypes capable of crossing the blood-brain barrier31. Tail-vein injections allow the virus to circulate throughout the body, enabling generalized delivery across many tissues10. Retro-orbital injections are another systemic injection technique that delivers the virus behind the eye into the retro-orbital sinus32. This offers a more direct route for the AAV from the venous system to the brain, resulting in a higher concentration of transduced cells in the brain than injections into more peripheral blood vessels33.
Another flexible aspect of this technique is the method of readout. Broadly, options can be described as reporter-based or sequencing-based (Figure 2C). Incorporating a fluorescent reporter such as GFP into the open reading frame of the construct results in the expression of the fluorescent protein in any transduced cells where the candidate enhancer drove expression. Labeling and imaging techniques such as immunohistochemistry enable signal amplification. Sequencing-based readout techniques involve identifying sequences from the delivered construct in RNA collected from the tissue. By quantifying the amount of viral DNA that was initially delivered, the comparison of expressed RNA versus delivered DNA can be used to determine the degree to which a tested enhancer sequence was capable of driving increased expression of the transgene, for example, in the context of a massively parallel reporter assay (MPRA). MPRAs offer a powerful expansion of these techniques to test up to thousands of candidate enhancers for activity simultaneously and have been described extensively in genomics research12,27,34,35,36. Higher throughput screening is achieved by executing cloning, packaging, delivery, and sequencing steps for candidate enhancers in batch rather than individually.
Candidate enhancer selection provides another opportunity for flexibility (Figure 2D). For example, this assay can be used to identify enhancers of a specific gene, to ascertain the function of non-coding DNA regions of interest, or to determine specific cell types or developmental stages during which an enhancer is active – all of which serve goals both in basic science and in disease research. Generally, candidate enhancer selection is driven by in silico predictions of enhancer activity. Commonly, in silico predictions include ChIP-seq for histone modifications that indicate likely enhancers, such as H3K27ac37 and chromatin accessibility mapping38. Finally, a growing area of research is the function-based screening of synthetically designed enhancer elements, enabling studies of how enhancer sequence directs function39 and the design of enhancers with specific properties40.
This protocol has been approved by the UC Davis Institutional Animal Care and Use Committee (Protocol #22339) and the UC Davis Institutional Biosafety Committee (BUA-R1903). This protocol has been tested on C57BL/6J mice of both sexes at postnatal day 0-1.
1. Clone the enhancer candidate sequence into the AAV vector plasmid.
NOTE: The representative protocols are given, but the cloning strategy has a high degree of flexibility.
2. Obtain packaged rAAV.
3. Intracranially inject rAAV-packaged plasmid into neonatal mice.
4. Collect tissue and perform immunohistochemistry.
5. Image and analyze brain tissue sections for enhancer activity.
Using these methods, a 915 bp sequence in the psychiatric risk-associated third intron of the gene CACNA1C19,49,50 was tested for enhancer activity in the postnatal mouse brain. This sequence was discovered in an MPRA of 345 candidate enhancer sequences centered on psychiatric and neurological risk SNPs12 and characterization experiments are described here as a general example. C57BL/6 mice were injected at P0 with an AAV9 construct packaged as a self-complementary vector51 containing EGFP under the control of the Hsp68 minimal promoter and a single candidate enhancer sequence (Figure 3A). Additional mice were injected with constructs that contained a negative control sequence that was predicted to have no regulatory activity (Figure 3B). Viral titers for these constructs were normalized to 6.85 x 1010 vg/mL. All injected mice were co-injected with an AAV9-packaged construct containing mRuby3 under the control of the constitutive CAG promoter to visualize the area that was successfully transduced and control for potential variability in the site and spread of infection. Brains were collected at postnatal day (P)28 for immunohistochemistry and imaging. These experiments confirmed that this candidate enhancer region in CACNA1C drove expression of EGFP in P28 mouse brain (Figure 3A), while a negative control sequence did not (Figure 3B). These results demonstrate the application of enhancer-reporter assays in the mouse brain, enabling in vivo study of enhancers during conditions that cannot be recapitulated using traditional in vitro models.
These methods can also be used to test libraries of candidate enhancer sequences for activity using AAV-based delivery methods, such as in MPRAs. Representative images of library-based reporter expression at different titers demonstrate the flexibility of this assay and the effect of viral titer on transduction efficiency. High-titer (Figure 4A) versus low-titer (Figure 4B) viral preparations result in differences in the amount of transduced cells, as evidenced by both positive control mRuby3 expression driven by a CAG promoter and EGFP expression produced from the candidate enhancer libraries in postnatal mouse brain. There are situations where either high titer and broad transduction or low titer and sparse transduction may be preferred.
Figure 1: Overview of the protocol. Key elements of this assay include a candidate enhancer element, a minimal promoter, a reporter gene, and, depending on assay design, a barcode sequence for unique tagging. These elements are cloned into an AAV plasmid backbone and packaged into AAV. The virus is delivered to the animal and left to incubate for a number of days or weeks. Finally, the tissue of interest is collected and enhancer activity is ascertained via imaging or sequencing. Enhancer-driven transgene expression can produce expression with cell-type, regional, and temporal specificity, in contrast to constitutive drivers. Please click here to view a larger version of this figure.
Figure 2: Flexibility in assay design. (A) Plasmid orientation can place the enhancer upstream of the minimal promoter or downstream of the reporter gene, as in STARR-seq28. For sequence-based readouts, a barcode is included downstream of the reporter gene, or the enhancer can serve as its own barcode in the second orientation. (B) Common viral delivery techniques to the brain include intracranial injections, retro-orbital injections, or tail-vein injections, which may result in different densities of transduced cells in different tissues. (C) Readouts can be sequencing-based or imaging-based. In sequencing-based readouts, enhancer activity is defined by a relative increase of RNA sequence versus input DNA sequence (controlling for AAV delivery). In imaging readouts, expression of the reporter gene is increased where the enhancer is active. (D) Potential intronic enhancers in the psychiatric risk-associated gene CACNA1C are highlighted. In the top image, a broad region is selected that shows strong associations to GWAS-tested traits and interactions with the CACNA1C promoter via PLAC-seq20. In the inset, smaller candidate regions are identified that are evolutionarily conserved at the sequence level, are in areas of open chromatin, and show epigenetic marks indicative of enhancers. Please click here to view a larger version of this figure.
Figure 3: Enhancer in CACNA1C drives EGFP expression in P28 mouse brain. (A) A mouse injected intracranially at P0 with an enhancer-reporter construct (scAAV9-Hsp68-EGFP-CACNA1C_3) and constitutively expressed injection control (AAV9-CAG-mRuby3) shows enhancer-driven EGFP expression in the middle-lower layers of the cortex at P28. (B) A mouse injected at P0 with a negative control construct (scAAV9-Hsp68-EGFP-NEG_4) and injection control does not show expression of EGFP at P28. Whole-brain images were taken at 5x magnification and insets show zoomed-in view of the boxed region. Please click here to view a larger version of this figure.
Figure 4: AAV-delivered enhancer-reporter libraries of different titers show activity in mouse brain. (A) Commercially packaged, high-titer AAV-PHP.eB library of candidate enhancers drives broad EGFP expression in P7 mouse brain. (B) Lower-titer AAV9 library of candidate enhancers precipitated from conditioned media of the packaging cells drives sparse EGFP expression in P7 mouse brain. Images were taken at 5x magnification. Please click here to view a larger version of this figure.
PCR Reaction Mix | |
5x reaction buffer | 10 µL |
dNTPs | final concentration of 200 µM each |
Cloning primers | final concentration of 0.2 µM each |
Template DNA | 50 ng |
High fidelity polymerase | final concentration of 0.02 U/µL |
Nuclease-free water | to reach 50 µL final reaction volume |
Thermocycling conditions | |||
30 cycles of the following: | Notes | ||
Step | Temperature | Time | |
Denature | 98 °C | 10 s | |
Anneal | 60 °C | 20 s | Optimal temperature may vary based on primers. |
Extend | 72 °C | 30 s | Optimal temperature and duration may vary based on polymerase. |
Final Extension | 72 °C | 2 min | Optimal temperature and duration may vary based on polymerase. |
Hold | 4 °C |
Table 1: PCR reaction mix and thermocycling conditions.
Thermocycling conditions | |||
30 cycles of the following: | Notes | ||
Step | Temperature | Time | |
Cell Lysis | 98 °C | 5 min | |
Denature | 98 °C | 10 s | |
Anneal | 55 °C | 15 s | Optimal temperature may vary depending on primers. |
Extend | 72 °C | 30 s | Optimal temperature and duration may vary depending on polymerase. |
Hold | 4 °C |
Table 2: Thermocycling conditions for colony PCR.
Buffers for immunohistochemistry | |
Buffer | Composition |
1x PBS | 137 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO4, 1.8 mM KH2PO4 |
1x Citrate Antigen Retrieval Buffer (ARB ), pH 6.0 | Proprietary, see table of materials |
Permeabilization Buffer (PB) | 1x PBS + 0.5% Triton X100 |
Wash Buffer (WB) | 1x PBS + 0.1% Triton X100 |
Blocking Buffer (BB) | WB + 5% milk |
Table 3: Buffers for immunohistochemistry.
This protocol describes an rAAV-based method for the deployment of enhancer-driven transgenes in the postnatal mouse brain. In this generalized protocol, a candidate enhancer, a minimal promoter, a reporter gene, and an optional barcode sequence are cloned into an AAV plasmid backbone. These experiments can be done with a single candidate enhancer sequence or with many sequences in parallel. The plasmid is packaged into an rAAV and delivered to the postnatal mouse brain. After a period of time to allow for virus transduction, the brain is collected and imaged for reporter gene expression. A constitutively expressed reporter virus (CAG-mRuby3) is included as an injection control. Using this assay, enhancer elements are shown to drive transcription of EGFP in the mouse brain, demonstrating enhancer activity in vivo.
The primary targets for troubleshooting and optimization of this assay include viral titer, injection technique, and transduction time frame. Different viral titers can have a strong effect on the density of transduced cells. While a higher transduction efficiency is likely preferable for most research, the optimal level of transduction is highly dependent on experimental goals. Intracranial injections offer a high density of transduced cells, but are likely to be more focal at the site of injection, though the spread of infection may depend on viral serotype and age of the animal52. Retro-orbital injections may show more even distribution of transduced cells throughout the brain but are less likely to give any area of high infection. Tail-vein injections can more effectively transduce other tissues in addition to the brain but will likely give still lower densities of transduced cells in the brain. Similarly, a variety of time-frames for virus transduction in the brain can serve different purposes. Robust scAAV expression can occur in the brain as early as seven days after intracranial injection, though periods of 28 days or longer are more typically used and yield strong expression. As enhancers can be temporally specific in their activity, it is important to consider the predicted activity of the tested enhancers when determining study design.
There are some limitations associated with these methods that might make other options a more suitable choice, depending on experimental goals. Since AAVs exhibit low integration into the genome, tissues are most effectively transduced when they are mature and there is a high density of postmitotic cells, as a large amount of continued cell divisions will lower the density of transgene-expressing cells. For viral delivery of a transgene to a less mature model, such as tissues that are still growing, lentiviruses may be a more appropriate choice, as they integrate into the genome and will be inherited by all daughter cells of a transduced proliferating cell. Additionally, while the reporter assay described here is a widely used technique for the functional study of cis-regulatory activity, it cannot provide a complete picture of how the regulatory element acts within its native context. For example, this assay does not provide information on what genes may be targeted by the regulatory element in the genome. However, if the enhancer's target genes are known, this information can be leveraged to determine if the cell types showing expression in this assay are the same as those known to express the enhancer's targeted genes, which would lend high biological validity to the interpretation of results. The assay also may not completely recapitulate the effects that the surrounding genomic sequence or normal biological and behavioral activity of the animal may have on the activity of the tested regulatory element. Finally, this protocol describes the STARR-seq reporter assay design, in which the candidate enhancer element is cloned downstream of the reporter gene in the ORF, in contrast to upstream of the promoter, as in the conventional reporter assay cloning orientation. Including long variable sequences in the ORF of the reporter gene may cause reduced RNA stability due to factors such as RNA binding protein motifs, alternate splice sites, or variable GC content 36,53, and statistical methods have been developed to account for sequence-based biases when analyzing STARR-seq data54,55. Despite these considerations, STARR-seq MPRAs have been widely used in recent years to successfully identify cis-regulatory elements56,57,58,59. The methods described here can be easily adapted for use with the conventional MPRA orientation.
The cell-type specificity of enhancers makes this assay a powerful tool in driving the cell-type-specific expression of genes of interest in vivo. Current techniques for cell-type-specific expression of a desired gene can be limited by the availability of conditional expression constructs or require the generation of new transgenic mouse lines. Using an rAAV-based enhancer-driven system, a gene of interest can be expressed in a spatiotemporally specific manner by using validated cell-type-specific enhancers or promoters to drive expression13,14,15. Recent developments in this technology have shown that combining cell-type-specific enhancers with rAAV serotypes with tropisms for cells or tissues of interest can show similar specificity of transgene expression as in transgenic animal models60. This offers a cheap, fast, and potentially high-throughput method for sequence screening and specific induction of transgene expression in vivo in animal models.
This technology also has therapeutic potential. Clinical studies have found that rAAV-based delivery of a transgene in vivo can induce the expression of healthy copies of a gene in cases where only a defective copy is present, or the gene is not being transcribed at a sufficient rate61,62,63. The selection of a driving enhancer element has the potential to enable generalized delivery but expression induction in a cell-type-specific manner. Finally, delivering the transgene via rAAV also confers significant benefits; AAVs have lower immunogenicity than other viruses often used in transgene delivery64, making this a potentially safe viral vector to be employed for clinical use.
Specific deployment of in vivo rAAV-based enhancer-reporter assays is customizable and can be modified to suit a range of experimental goals. Different tissues and cells can be targeted by selecting AAV serotypes or enhancers that have cell type or spatiotemporal specificity. Anywhere from one to thousands of enhancer-reporter constructs can be delivered in vivo, and activity can be assayed using a number of imaging- and sequencing-based readouts, as have been shown in an emerging set of studies using this approach15,16,65,66,67,68. The range of options for construct design and delivery enables this technique to be modified for a variety of uses in both translational and basic science, making this a powerful new tool for genomics and neuroscience research.
The authors have nothing to disclose.
Sequencing was performed at the UC Davis DNA Technologies Core. We thank the lab of Lin Tian at UC Davis for training on rAAV packaging and generously gifting us AAV helper and rep/cap plasmids. This work was supported by NIH/NIGMS R35GM119831.
10x Citrate Buffer | Sigma-Aldrich | C9999-1000ML | |
5'-gatcactctcggcatggac-3' | Integrated DNA Technologies | N/A: Custom designed | Forward primer for verifying clones after transformation. These primers are specific to the vector used and were designed for the specific vector used in our experiments. |
5'-gatggctggcaactagaagg-3' | Integrated DNA Technologies | N/A: Custom designed | Reverse primer for verifying clones after transformation. These primers are specific to the vector used and were designed for the specific vector used in our experiments. |
Agarose | VWR | VWRVN605-500G | |
Aspirator tube assemblies | Sigma-Aldrich | A5177-5EA | for mouth-driven delivery of rAAV |
Bacteriological petri dishes | Thermo Fisher Scientific | 08-757-100D | |
Carbenicillin | Sigma-Aldrich | C1389-5G | |
Chicken IgY anti-GFP | Thermo Fisher Scientific | A10262 | |
Confocal microscope | Zeiss | LSM900 | The images were taken on the LSM800 model, but Zeiss launched the LSM900 model in recent years to replace LSM800. |
Conical centrifuge tubes 15 mL | Thermo Fisher Scientific | 12-565-269 | |
Cryomolds | Thermo Fisher Scientific | NC9806558 | These molds are suitable for P28 mouse brain. Other sizes may be more suitable for larger or smaller tissues. |
DAPI | Sigma-Aldrich | D9542-10MG | |
Dissecting scissors, 4.5" | VWR | 82027-578 | |
Donkey anti-chicken AlexaFlour-488 | Jackson ImmunoResearch | 703-545-155 | |
Dulbecco's PBS 1x | Thermo Fisher Scientific | MT21031CV | |
Eppendorf Microcentrifuge tubes 2.0 mL | Thermo Fisher Scientific | 22431048 | |
Falcon round-bottom tubes 14 mL | Thermo Fisher Scientific | 352059 | |
Fast Green dye | Grainger | F0099-1G | |
Fine detail paint brush set | Artbrush Tower | B014GWCLFO | |
Gibson Assembly Master Mix | NEB | E2611S | |
Glass capillary tubes | Drummond Scientific Company | 5-000-2005 | |
HiSpeed Plasmid Maxi Kit | QIAGEN | 12663 | Commercial plasmid maxi prep kit |
HyClone HyPure Molecular Biology Grade Water | VWR | SH30538.03 | |
IV butterfly infusion set with 12" tubing and 25G needle | Thermo Fisher Scientific | 26708 | |
Kimwipes | Kimberly Clark | 34155 | Lint-free wipe |
LB Agar | Thermo Fisher Scientific | BP1425-500 | LB agar pre-mix for selective media |
McPherson Vannas iris scissor | Integra LifeSciences | 360-215 | |
Mineral oil | Sigma Life Science | 69794-500ML | |
NEB Stable Competent E. coli | NEB | C3040I | |
NucleoSpin Gel and PCR Clean-Up | Takara | 740609.5 | Kit for enzymatic reaction cleanup and gel extraction |
OCT medium | VWR | 25608-930 | |
Orbital shaker | Cole Parmer | 60-100 | |
Paraformaldehyde | Sigma-Aldrich | 158127-500G | |
PCR strip tubes 0.2 mL | VWR | 490003-692 | |
Peristaltic pump | Gilson | F155005 | |
Phosphate buffered saline (PBS) 10x | Thermo Fisher Scientific | 70011044 | |
Phusion Hot Start II High Fidelity DNA Polymerase | Thermo Fisher Scientific | F549L | |
Powdered milk | Sunny Select | ||
ProLong Gold Antifade Mountant | Thermo Fisher Scientific | P36934 | |
QIAquick PCR Purification Kit | QIAGEN | 28106 | |
rCutSmart Buffer | NEB | B6004S | Buffer for restriction digest with PacI, AscI, and XmaI |
Restriction enzyme: AscI | NEB | R0558L | |
Restriction enzyme: PacI | NEB | R0547L | |
Restriction enzyme: XmaI | NEB | R0180L | |
SOC outgrowth medium | NEB | B0920S | Recovery medium after transformation |
Sucrose (RNase/DNase free) | Millipore Sigma | 033522.5KG | |
TAE buffer | Apex | 20-194 | |
Transfer tubing | Gilson | F1179941 | For peristaltic pump |
Triton X100 | Sigma-Aldrich | X100-100ML | |
Wizard Plus SV Minipreps DNA Purification System | Thermo Fisher Scientific | A1460 | Plasmid mini prep kit |