An in vivo strategy for knockdown of circular RNAs

Nagarjuna Reddy Pamudurti,Sebastian Kadener,Aishwarya Krishnamoorthy,Osnat Bartok,Reut Ashwal-Fluss,Ines Lucia Patop

doi:10.1038/s41421-020-0182-y

Nagarjuna Reddy Pamudurti, Sebastian Kadener + Show 4 more

Open Access

https://doi.org/10.1038/s41421-020-0182-y

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Journal: Cell Discovery	Publication Date: Aug 11, 2020
Citations: 32	License type: open-access

Affiliation: Brandeis University, Hebrew University of Jerusalem

Abstract

Exonic circular RNAs (circRNAs) are highly abundant RNAs generated mostly from exons of protein-coding genes. Assaying the functions of circRNAs is not straightforward as common approaches for circRNA depletion tend to also alter the levels of mRNAs generated from the hosting gene. Here we describe a methodology for specific knockdown of circRNAs in vivo with tissue and cell resolution. We also describe an experimental and computational platform for determining the potential off-target effects as well as for verifying the obtained phenotypes. Briefly, we utilize shRNAs targeted to the circRNA-specific back-splice junction to specifically downregulate the circRNA. We utilized this methodology to downregulate five circRNAs that are highly expressed in Drosophila. There were no effects on the levels of their linear counterparts or any RNA with complementarity to the expressed shRNA. Interestingly, downregulation of circCtrip resulted in developmental lethality that was recapitulated with a second shRNA. Moreover, downregulation of individual circRNAs caused specific changes in the fly head transcriptome, suggesting roles for these circRNAs in the fly nervous system. Together, our results provide a methodological approach that enables the comprehensive study of circRNAs at the organismal and cellular levels and generated for the first time flies in which specific circRNAs are downregulated.

Highlights

1234567890():,; 1234567890():,; 1234567890():,; 1234567890():,; Introduction Exonic circular RNAs are a highly abundant type of RNA produced through circularization of specific exons in a process known as back-splicing1–4. circRNAs are expressed in tissue- and development stage-specific ways, independently of the expression of the hosting gene[5]
Results circRNAS can be downregulated by miRNAderived shRNAs in vivo To knockdown circRNAs in vivo, we generated flies that express shRNAs directed against individual circRNAspecific back-splicing junctions (Fig. 1a)
We found that expression of the second shRNA construct targeting circCtrip resulted in developmental lethality when expressed under the actin-Gal[4] driver (Fig. 4d)

Summary

Introduction

Introduction Exonic circularRNAs (circRNAs) are a highly abundant type of RNA produced through circularization of specific exons in a process known as back-splicing1–4. circRNAs are expressed in tissue- and development stage-specific ways, independently of the expression of the hosting gene[5]. CircRNAs are expressed in tissue- and development stage-specific ways, independently of the expression of the hosting gene[5]. CircRNA levels increase with age in the brains of mice and flies as well as in worms[18,20,21] and are affected by neuronal activity[19]. These observations suggest important roles for circRNAs in the brain. Mice depleted of the circRNA CDR1as have abnormal gene expression in the brain and specific behavioral defects[22]. Other circRNAs titrate or transport proteins and might be important for cancer development6,26,27. circRNAs can mediate responses to viral infections[28,29,30,31]

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