Antisense Oligo Pulldown of Circular RNA For Downstream Analysis
Antisense Oligo Pulldown of Circular RNA For Downstream Analysis
Antisense Oligo Pulldown of Circular RNA for Downstream Analysis. Bio-protocol 11(14): e4088. DOI:
10.21769/BioProtoc.4088.
Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha, India; 2School of Biotechnology, KIIT
1
[Abstract] Circular RNAs (circRNAs) are a large family of noncoding RNA molecules that have emerged
as novel regulators of gene expression by sequestering microRNAs (miRNAs) and RNA-binding
proteins (RBPs). Several computational tools have been developed to predict circRNA interaction with
target miRNAs and RBPs with a view to studying their potential effect on downstream target genes and
cellular physiology. Biochemical assays, including reporter assays, AGO2 pulldown, ribonucleoprotein
pulldown, and biotin-labeled RNA pulldown, are used to capture the association of miRNAs and RBPs
with circRNAs. Only a few studies have used circRNA pulldown assays to capture the associated
miRNAs and RBPs under physiological conditions. In this detailed protocol, the circRNA of interest (e.g.,
circHipk2) was captured using a biotin-labeled antisense oligo (ASO) targeting the circHipk2 backsplice
junction sequence followed by pulldown with streptavidin-conjugated magnetic beads. The specific
enrichment of circRNA was analyzed using reverse transcription quantitative PCR (RT-qPCR).
Furthermore, the ASO pulldown assay can be coupled to miRNA RT-qPCR and western blotting analysis
to confirm the association of miRNAs and RBPs predicted to interact with the target circRNA. In summary,
the specific pulldown of circRNA using this quick and easy method makes it a useful tool for identifying
and validating circRNA interaction with specific miRNAs and RBPs.
Keywords: CircRNAs, CircRNA pulldown, Antisense oligo, Biotin pulldown, RT-qPCR, miRNA, RNA-
binding proteins
[Background] The RNA family can be broadly classified into coding (mRNAs) and noncoding RNAs.
Interestingly, the vast majority of cellular RNAs are noncoding RNAs, including rRNA, lincRNA, miRNA,
snRNA, snoRNA, tRNA, piRNA, and poorly characterized circular (circ) RNAs (Palazzo and Lee, 2015).
The use of next-generation RNA sequencing and bioinformatics tools has uncovered more than a
hundred thousand circRNAs in humans (Vromman et al., 2020). CircRNAs are generated from pre-
mRNAs by head-to-tail splicing of specific exons by a process called backsplicing, which is regulated by
transcription speed, RBPs, and inverted repeat sequences. Their length can vary from less than 100
nucleotides to a few thousand nucleotides. Depending on the sequence of circRNA origin from the
parent gene, circRNAs have been classified into exonic circular RNA (circRNA), lariat-derived circular
intronic RNA (ci-RNA), stable intronic sequence RNA (sisRNA), and exonic-intronic circular RNA
(EIcircRNA) (Guria et al., 2019). Although a vast number of circRNAs have been identified in different
cellular systems and disease models, only a fraction of circRNAs has been functionally characterized
(Vromman et al., 2020). Recent evidence suggests that circRNAs play a critical role in regulating cellular
events by interacting with miRNAs and RBPs (Guria et al., 2019). The majority of studies use
computational tools to predict the association of circRNAs with cellular miRNAs and proteins that could
regulate the expression of downstream target genes (Dudekula et al., 2016). Several biochemical
techniques are currently used to analyze the circRNA-miRNA interaction, including luciferase reporter
assays, AGO2 pulldown, and fluorescence in situ hybridization (FISH). Similarly, ribonucleoprotein
pulldown assays using an antibody against the predicted RBP and biotin-labeled RNA pulldown assays
to capture the target RBPs are used to validate the interaction of circRNA with specific RBPs. However,
some of these methods are indirect assays to conclude whether the circRNA is associated with target
miRNAs or RBPs. Our previous studies have successfully used circRNA pulldown assays with biotin-
labeled antisense oligos targeting the circRNA backsplice junction sequence. Furthermore, circRNA-
pulldown followed by RT-qPCR and western blotting analysis identified the miRNA or RBP associated
with the circRNA of interest (Abdelmohsen et al., 2017; Panda et al., 2017; Pandey et al., 2020). Here,
we adapted the published method to successfully pull down circHipk2 in βTC6 cells. The detailed
protocol for the pulldown of circRNA to analyze the associated miRNA or RBP is described here.
Equipment
1. Manual pipette set, 2 µl, 20 µl, 200 µl, and 1 ml (various manufacturers)
2. Vortex mixer (Tarson, catalog number: 3001)
3. Magnetic stand (Tarson, catalog number: S1509S)
4. Tube rotator (Tarson, catalog number: 3071)
5. Refrigerated centrifuge (Eppendorf, model: 5810R)
6. Benchtop microfuge (Tarson, catalog number: 1010)
7. Thermomixer (Eppendorf, catalog number: 5384000012)
8. PCR machine (various manufacturers)
9. QuantStudio 3 real-time PCR system (Thermo Fisher Scientific, catalog number: A28567)
Software
Procedure
A. Oligo design
1. Obtain the mature sequence of the circRNA of interest from the RNA sequencing data or the
UCSC genome browser using the genome coordinates of backsplice sites. Here, we retrieved
the sequence of mouse circHipk2 (chr6|38818229|38819313|-) from the mouse mm10 UCSC
genome browser (Figure 1).
Note: The mature splice sequence of multiexonic circRNA can be obtained by combining all the
exon sequences between the genomic coordinates of the backsplice site.
Figure 1. Design of the divergent primers and biotin-labeled antisense oligo targeting
circHipk2
2. As shown in Figure 1, join the last 15 nucleotides of the circRNA sequence to the upstream of
the first 15 nucleotides to obtain the 30-nucleotide sequence spanning the circRNA backsplice
junction.
3. To design ASO, generate the reverse complement sequence of the 30-nucleotide junction
sequence using GeneRunner. Have this sequence synthesized with biotin-TEG added to the 3’
end by the preferred vendor.
4. Design primers for the target housekeeping gene mRNAs or rRNAs using the Primer 3 web tool.
5. Design the divergent primer for the target circRNA as described previously (Panda and Gorospe,
2018) or using the circinteractome website for human circRNAs (Dudekula et al., 2016).
B. Cell lysis
1. Take one 100-mm dish of ~70% confluent βTC6 cells and discard the culture media.
Note: A minimum of 5 million cells should be used for the pulldown assay. A higher amount of
cells may help to obtain better pulldown of rare or low copy number circRNAs.
2. Wash the cells three times with 5-10 ml ice-cold 1× PBS.
3. Harvest the cells by trypsinization or scraping with a cell scraper.
4. Pellet the cells by centrifuging at 1,000 × g for 2 min at 4°C and discard the supernatant.
5. Resuspend the cell pellet in 1 ml ice-cold polysome extraction buffer (PEB).
Note: Lysis with PEB releases the cytoplasmic fraction, not the nuclear fraction.
6. Immediately add 5 µl RNase inhibitor and 50 µl 20× protease inhibitor.
7. Mix well by pipetting ten times and keep on ice for 15 min, pipetting or vortexing for a few
seconds every 4-5 min until the cells are lysed.
8. Centrifuge the lysate at 12,000 × g for 10 min at 4°C.
9. Collect 900 µl supernatant and proceed to the hybridization step (Figure 2).
1. Add 50 µl washed magnetic streptavidin beads into each hybridization reaction tube (mentioned
in Step C4) after completing the 90-minute hybridization step.
2. Add 1 µl RNase inhibitor and 5 µl 20× protease inhibitor to the tubes and mix well by pipetting.
3. Rotate both the control and circRNA ASO tubes at room temperature for 30 min on a tube rotator
at 30 rpm.
4. Centrifuge the tubes briefly to bring all the liquid samples to the bottom of the tube without
pelleting the beads.
Note: High-speed centrifugation may pellet the beads, which may affect the washing steps.
5. Place the tubes on a magnetic rack for 30 s and discard the supernatant.
6. Resuspend the magnetic beads in 500 µl ice-cold 1× TENT buffer and place the tube on the
magnetic stand for 30 s.
7. Rotate the tube twice on the magnetic stand to wash the beads (Video 1).
8. Allow the beads to settle toward the magnet and discard the buffer.
9. Repeat the washing steps (steps 6-8) twice.
Note: The number of washes may be decided depending on the fold enrichment of the target
circRNA. We found that two to three washes are suitable to enrich circHipk2 in our pulldown
assays.
10. After the last wash, centrifuge the tube for a few seconds to settle the beads at the bottom.
11. Place the tube on the magnetic stand for 30 s and discard the remaining supernatant.
12. Resuspend the beads in 30 µl ice-cold PEB.
13. Take 15 µl beads to a fresh tube for RNA isolation and RT-qPCR to analyze the pulldown
efficiency of circRNA using the ASO and to detect the circRNA-associated miRNAs.
14. Add 7 µl 3× SDS loading dye to the remaining 15 µl beads and mix by pipetting, then heat at
95°C for 5 min. This sample can be immediately used for western blotting to identify interacting
RBPs or stored at -20°C.
Figure 3. Example data showing the percentage enrichment of circHipk2 in the circRNA-
ASO pulldown sample relative to the control ASO pulldown sample
Data analysis
This method describes circular RNA pulldown using an antisense oligo specifically targeting the
backsplice junction sequence of the target circRNA. However, the success of this pulldown assay
depends on the availability of the circRNA junction sequence, which may be inaccessible due to
secondary structures or junction-interacting RBPs, preventing the ASO from binding. Moreover, the
PEB used for cell lysis is good for releasing the cytoplasmic fraction, while lysis of the nucleus for
the pulldown of nuclear-localized circRNAs remains to be standardized. Since most circRNAs are
cytoplasmic in nature (Jeck et al., 2013), we used PEB for the cell lysis and pulldown assay. Use
the delta-Ct method to analyze the enrichment of target circRNA in the circRNA ASO pulldown
sample compared with the control pulldown using a loading control such as 18S rRNA or Gapdh
mRNA (Livak and Schmittgen, 2001). As shown in Figure 3, the circHipk2 levels are more than 2-
fold higher in the circHipk2 ASO pulldown than in the control ASO pulldown. Alternatively, the
efficiency of circRNA pulldown can be measured by comparing the pulldown samples with the flow
through or input. After checking the enrichment of circRNA in the pulldown samples, the remaining
RNA can be subjected to miRNA RT-qPCR analysis to check for the specific enrichment of miRNAs
predicted to interact with the circRNA of interest. Furthermore, the other half of the pulldown sample
may be used for western blotting analysis to evaluate the RBPs associated with the target circRNA.
This is a promising method to pulldown the circular RNA of interest and study the circRNA-
associated miRNAs and RBPs, which are critical factors for circRNA-mediated gene regulation.
Recipes
Acknowledgments
This research was supported by intramural funding from the Institute of Life Sciences and the
Wellcome Trust/DBT India Alliance Intermediate Fellowship (IA/I/18/2/504017) provided to ACP. DD
and AD were supported by Junior Research Fellowships from the University Grant Commission,
India. This protocol was adapted from previously published papers (Abdelmohsen et al., 2017 and
Panda et al., 2017). The authors thank our colleagues at the Institute of Life Sciences, Bhubaneswar,
for proofreading the article.
Competing interests
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