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In This Article

  • Summary
  • Abstract
  • Introduction
  • Protocol
  • Representative Results
  • Discussion
  • Disclosures
  • Acknowledgements
  • Materials
  • References
  • Reprints and Permissions

Summary

Circular RNAs (circRNAs) are non-coding RNAs that may have roles in transcriptional regulation and mediating interactions between proteins. Following assessment of different parameters for construction of circRNA sequencing libraries, a protocol was compiled utilizing stranded total RNA library preparation with RNase R pre-treatment and is presented here.

Abstract

Circular RNAs (circRNAs) are a class of non-coding RNAs involved in functions including micro-RNA (miRNA) regulation, mediation of protein-protein interactions, and regulation of parental gene transcription. In classical next generation RNA sequencing (RNA-seq), circRNAs are typically overlooked as a result of poly-A selection during construction of mRNA libraries, or are found at very low abundance, and are therefore difficult to isolate and detect. Here, a circRNA library construction protocol was optimized by comparing library preparation kits, pre-treatment options and various total RNA input amounts. Two commercially available whole transcriptome library preparation kits, with and without RNase R pre-treatment, and using variable amounts of total RNA input (1 to 4 µg), were tested. Lastly, multiple tissue types; including liver, lung, lymph node, and pancreas; as well as multiple brain regions; including the cerebellum, inferior parietal lobe, middle temporal gyrus, occipital cortex, and superior frontal gyrus; were compared to evaluate circRNA abundance across tissue types. Analysis of the generated RNA-seq data using six different circRNA detection tools (find_circ, CIRI, Mapsplice, KNIFE, DCC, and CIRCexplorer) revealed that a stranded total RNA library preparation kit with RNase R pre-treatment and 4 µg RNA input is the optimal method for identifying the highest relative number of circRNAs. Consistent with previous findings, the highest enrichment of circRNAs was observed in brain tissues compared to other tissue types.

Introduction

Circular RNAs (CircRNAs) are endogenous, non-coding RNAs that have gained attention given their pervasive expression in the eukaryotic transcriptome1,2,3. They are formed when exons back-splice to each other and hence were initially considered to be splicing artifacts4,5. However, recent studies have demonstrated that circRNAs exhibit cell type, tissue, and developmental stage specific expression3,6 and are evolutionarily conserved2

Protocol

This research has been performed in compliance with all institutional, national and international guidelines for human welfare. Brain tissues were obtained from the Banner Sun Health Research Institute Brain and Body Donation Program in Sun City, AZ. The operations of the Brain and Body Donation Program are approved by the Western Institutional Review Board (WIRB protocol #20120821). All subjects or their legal representatives signed the informed consent. Commercial (non-brain) biospecimens were purchased from Proteogenex.

1. RNase R Treatment

NOTE: In the following steps, the reaction volume is ad....

Representative Results

Data generated using a commercially available universal control RNA (UC) and using two library preparation kits, both of which include a ribo-depletion step in their protocols, was first assessed. Using an analytical workflow (Data analysis workflow, section 4), overall, a higher number of circRNAs was detected in the TruSeq datasets compared to the Kapa ones (Figure 1). Although the ribosomal RNA (rRNA) percentages were below 5% in datasets from both kits for lower input amounts (1, 2 ug), .......

Discussion

In this study, two commercially available library preparation kits, pre-treatment options, and input RNA amounts were tested in order to optimize a circRNA enrichment protocol for construction of circRNA sequencing libraries. Based on this study’s assessments, a number of key aspects and critical steps in creating circRNA sequencing libraries are apparent. Our evaluation confirms the utility of RNase R pre-treatment, as reflected by the increased number of circRNAs detected. Overall, a higher diversity of circRNAs .......

Disclosures

The authors have nothing to disclose.

Acknowledgements

We are grateful to the Banner Sun Health Research Institute Brain and Body Donation Program (BBDP) of Sun City, Arizona for the provision of human brain tissues. The BBDP has been supported by the National Institute of Neurological Disorders and Stroke (U24 NS072026 National Brain and Tissue Resource for Parkinson's Disease and Related Disorders), the National Institute on Aging (P30AG19610 Arizona Alzheimer's Disease Core Center), the Arizona Department of Health Services (contract 211002, Arizona Alzheimer's Research Center), the Arizona Biomedical Research Commission (contracts 4001, 0011, 05-901 and 1001 to the Arizona Parkinson's Disease Consortium) and the M....

Materials

NameCompanyCatalog NumberComments
1000 µL pipette tipsRaininGP-L1000F
20 µL pipette tipsRaininSR L 10F
200 µL pipette tipsRaininSR L 200F
2200 TapeStation Accessories (foil covers)Agilent Technologies5067-5154
2200 TapeStation Accessories (tips)Agilent Technologies5067-5153
Adhesive Film for MicroplatesVWR60941-064
AMPure XP Beads 450 mLBeckman CoulterA63882PCR purification
Eppendorf twin.tec 96-Well PCR PlatesVWR951020401
High Sensitivity D1000 reagentsAgilent Technologies5067-5585
High Sensitivity D1000 ScreenTapeAgilent Technologies5067-5584
HiSeq 2500 Sequencing SystemIlluminaSY-401-2501
HiSeq 3000/4000 PE Cluster KitIlluminaPE-410-1001
HiSeq 3000/4000 SBS Kit (150 cycles)IlluminaFC-410-1002
HiSeq 4000 Sequencing SystemIlluminaSY-401-4001
HiSeq PE PE Rapid Cluster Kit v2IlluminaPE-402-4002
HiSeq Rapid SBS Kit v2 (50 cycle)IlluminaFC-402-4022
Kapa Total RNA KitRocheKK8400
Molecular biology grade ethanolFisher ScientificBP28184
Qubit Assay TubesSupply Center by Thermo FischerQ32856
Qubit dsDNA High Sense Assay KitSupply Center by Thermo FischerQ32854
RNA cleanup and concentrator - 5ZymoRCC-100Contains purification columns, collection tubes
RNAClean XP beadsBeckman Coulter GenomicsRNA Cleanup beads
Rnase RLucigenRNR07250
SuperScript II Reverse Transcriptase 10,000 unitsThermoFisher (LifeTech)18064014
TapeStation 2200Agilent TechnologiesNucleic Acid analyzer
TElowEVWR10128-588
TruSeq Stranded Total RNA Library Prep KitIllumina20020596Kit used in section 3
Two-Compartment Divided TrayVWR3054-1004
UltraPure WaterSupply Center by Thermo Fischer10977-015
Universal control RNAAgilent740000

References

  1. Salzman, J., Gawad, C., Wang, P. L., Lacayo, N., Brown, P. O. Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types. PloS One. 7 (2), e30733 (2012).
  2. Jeck, W. R., et al.

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