TRPLSC 1534 No.
of Pages 3
Forum
Are Circular RNAs
New Kids on the
Block?
Sang-Moo Lee,1,2,3 Hyun
Gi Kong,1,3 and Choong-
Min Ryu1,2,*
Circular [104_TD$IF]RNAs (circ[10_TD$IF]-RNAs), a novel
class of noncoding RNAs, are a
popular topic in animal research
because they have potential as
post-transcriptional regulators
and diagnostic markers. Research
in plants is only now emerging, but
indicates that circ[10_TD$IF]-RNAs could
also be a crucial class of noncod-
ing regulators.
In animals, many thousands of circ[10_TD$IF]-RNAs
have been identied, representing a rela-
tively unexplored class of noncoding
RNAs (see Glossary) compared to the
better-studied microRNAs (miRNAs)
and small interfering RNAs (siRNAs) [1].
The unique structure of circ[10_TD$IF]-RNAs, a
covalently closed continuous loop,
means that they are more resistant to
exonuclease attack than are linear RNAs
[1]. [105_TD$IF]circ-RNAs were initially thought to be
the result of splicing errors, but more
recently it has been shown that circ[10_TD$IF]-RNAs
can act as miRNA sponges or as
sponges for RNA-binding proteins, and
regulate post-transcriptional events [2].
A close association with human diseases,
including cancers and neurologic dis-
eases such as Alzheimer disease, has
been demonstrated, and circ[10_TD$IF]-RNAs are
currently being explored as diagnostic
biomarkers and therapeutic targets in
such diseases [2,3]. Recently, transcrip-
tome-wide sequencing studies have
revealed that circ[10_TD$IF]-RNAs are highly con-
served and many circ[10_TD$IF]-RNAs have also
been identied in plants [4], but insight
into their function is only now emerging.
We highlight here the distinct features of
plant circ[10_TD$IF]-RNAs and propose possible
functions.
Genesis and Exodus from the
Nucleus
The regulation and function of circ[10_TD$IF]-RNAs
in plants were largely unknown until
recently, whereas circ[10_TD$IF]-RNAs in human
cells were identied as far back as
1994 [5]. In plants, viroids pathogenic
viruses without capsids that were identi-
ed in the 1980s replicate using a roll-
ing-circle mechanism and self-cleavage
[6]. The circular structure and replication
mechanism of viroids are features shared
with intracellular circ[10_TD$IF]-RNAs. However, in
contrast to viroids, which enter cells from
the outside, computational and molecu-
lar techniques initially developed in ani-
mals revealed that circ[10_TD$IF]-RNAs are
generated from plant genomes and are
involved in cytosolic processes [4,79].
The genesis of circ[10_TD$IF]-RNAs is a conserved
feature in animal and plant cells, and
depends on transcription by RNA poly-
merase II and back-splicing reactions
of pre-messenger RNAs (pre-mRNAs).
Regulation of the back-splicing reaction
in the spliceosome requires a repeated
sequence and RNA-binding proteins
(Figure 1). Typically, spliceosome forma-
tion is initiated by the sequential assem-
bly of small nuclear ribonucleoproteins
(snRNPs) onto a specic region of the
pre-mRNA downstream of the [106_TD$IF]50 donor
splice site (GT) and upstream of the 30
acceptor site (AG). Depending on the
initial snRNP binding site, exonic or
intronic circ[10_TD$IF]-RNAs are generated [8].
In addition, RNA-binding proteins such
as serine/arginine-rich proteins (SR pro-
teins) play important roles in the back-
splicing reaction (Figure 1). In plants, circ[10_TD$IF]
-RNAs have a few repetitive elements
and relatively long reverse complemen-
tary anking introns for splicing knots
[4,7]. Thus, different endogenous
circRNA-silencing pathways may be
involved in regulatory processes in
plants.
Glossary
Back-splicing: the formation of a covalent bond
between 50 (splice donor) and 30 (splice
acceptor) splice-sites of a pre-mRNA, thereby
generating a circRNA.
Exonic circRNA: a circRNA spliced from an
exon sequence when inverted repeats within the
anking introns close to form a circle.
Intronic circRNA: an intron-derived circRNA
produced when lassos that escape the
debranching enzymes are processed by
exonucleases.
MicroRNAs (miRNAs): small noncoding RNAs
that regulate endogenous RNA expression by
RNA silencing and post-transcriptional regulation.
miRNA sponge: a decoy target of miRNAs
containing multiple, tandem binding sites that
regulate miRNA activity.
Noncoding RNAs: RNAs that do not encode
proteins, such as miRNAs, small interfering
RNAs (siRNAs), long noncoding RNAs (lncRNAs),
and circular RNAs (circ-RNAs).
RNase R: a potent magnesium-dependent 30 to
50 exoribonuclease which specically degrades
all linear RNAs, but not circ-RNAs.
Spliceosome: the complex machinery required
to remove intron sequences from primary
transcripts to produce mRNAs and noncoding
RNAs.
Viroid: a small, low molecular weight circRNA
that can infect plant cells, replicate itself, and
cause plant disease.
What Do circ[10_TD$IF]-RNAs Do?
Developmental Processes
Developmental regulation by circ[10_TD$IF]-RNAs is
poorly understood in plants, but has been
intensely studied in humans and animals;
for example, circ[10_TD$IF]-RNAs are known to be
involved in the epithelialmesenchymal
transition [2,7]. Interestingly, some plant
circ[10_TD$IF]-RNAs accumulate in a tissue- or
organelle-dependent manner [8,9].
Recently, 30 putative circ[10_TD$IF]-RNAs were
found to be differentially expressed in rice
(Oryza sativa) leaves and panicles [7]. In
Arabidopsis (A. thaliana), 6% and 1% of
putative circ[10_TD$IF]-RNAs are present in chlor-
oplasts and mitochondria, respectively
[8]. In addition, some barley (Hordeum
vulgare L.) circ[10_TD$IF]-RNAs involved in micro-
nutrient homeostasis are highly
expressed in mitochondria [9]. These
results indicate that plant circ[10_TD$IF]-RNAs con-
tribute to cellular development via tissue-
or organelle-specic expression (Figure 1).
However, there have been no reports
Trends in Plant Science, Month Year, Vol. xx, No. yy 1
 TRPLSC 1534 No. of Pages 3

Nucleus
5 3
Pol ll
1. snRNP 2. SR protein
3. Splicing
Cytoplasm knots
1. Development Back-splicing
process

3. miRNA
sponge
Mitochondria
Stress condion

Abioc stress
circRNA
2. Stress PO43
response Fe3+
Chloroplast
Chilling Drought Nutrient
imbalance
Plant cell Bioc stress

Viroid Bacteria Fungi?

(virus?)

Figure 1. B[10_TD$IF] iogenesis and Function of Circular RNAs (circ-RNAs) in Plant Cells. Functional processes inuenced by circ-RNAs (solid arrows), the origin of circ-
RNAs (broken arrows), unknown pathways (grey arrows), and stress conditions (red arrow) are shown. circ-RNAs may originate from the nucleus or an organelle
(mitochondria/chloroplast) or from outside the cell as in the case of viroids. circ-RNAs are produced from plant genomes via back-splicing by the spliceosome (snRNPs),
the action of RNA-binding proteins such as serine/arginine-rich proteins (SR proteins), and splicing knots from exonic (green, yellow, blue, and purple boxes) or intronic
regions (black lines between exon boxes). circ-RNAs affect developmental processes via their differential expression in leaves or owers, act as stress responsive
regulators against biotic (viroid, virus, bacteria, and fungi) and abiotic stresses (drought, chilling, and nutritional imbalance), undergo transfer to the cytosol, and play
roles as miRNA sponges sequestering miRNAs from endogenous targets. Abbreviations: Pol II, RNA polymerase II; snRNP, small nuclear ribonucleoprotein.

showing the involvement of circ[10_TD$IF]-RNAs involved in chilling injury regulation, such nutrients such as phosphate, iron, and
during plant development. as redox reactions and low temperature- zinc [4,9]. However, the detailed mecha-
induced transcription factors [10]. nism underlying circRNA-mediated regu-
Stress Responses Another 62 wheat circ[10_TD$IF]-RNAs are lation during abiotic stress has not been
Although functional studies are still lack- expressed under dehydration conditions studied. Meanwhile, some Arabidopsis
ing, some plant circ[10_TD$IF]-RNAs have been and target drought-specic miRNAs circ[10_TD$IF]-RNAs that regulate immunity against
identied under abiotic or biotic stress involved in photosynthesis and oxidative Pseudomonas syringae pv. tomato inu-
conditions (Figure 1). A total of 163 phosphorylation [11]. Some circ[10_TD$IF]-RNAs in ence biotic stress-related accumulation of
tomato circ[10_TD$IF]-RNAs were predicted to be rice and barley respond to imbalances in miRNAs by acting as a miRNA sponge [8].

2 Trends in Plant Science, Month Year, Vol. xx, No. yy

 TRPLSC 1534 No. of Pages 3

Collectively, these reports indicate that Specically four points stand out that Acknowledgments
plant circ[10_TD$IF]-RNAs can affect plant need to be addressed in this context. This research was supported by grants from BioNano
responses to abiotic and biotic stresses. Health-Guard Research Center funded by the Ministry

[108_TD$IF](i) Triggering signal: the triggering signals of Science[109_TD$IF], ICT, and Future Planning of Korea as a
Global Frontier Project ([10_TD$IF]Grant H-GUARD_2013-
miRNA Sponges that originate outside the plant cell and
M3A6B2078953), the Woo Jang-Choon Project
Functional studies of animal circ[10_TD$IF]-RNAs stimulate the accumulation of circ[10_TD$IF]-RNAs
[1_TD$IF](PJ010939)of the Rural Development Administration
showed that they modulate gene expres- in specic organelles or nucleus remain (RDA), and the KRIBB Initiative Program, South
sion via post-transcriptional regulation. elusive. (ii) Regulation: the mechanisms Korea[12_TD$IF].
For example, some circ[10_TD$IF]-RNAs act as involved in the degradation and reas-
1
miRNA sponges, as shown by the com- sembly of circ[10_TD$IF]-RNAs are unknown, but Molecular Phytobacteriology Laboratory, Korea Research
Institute of Bioscience and Biotechnology (KRIBB),
petition between a circRNA cIRS-7 and are likely to be novel given the unusual Daejeon 34141, South Korea
miR-7 in the regulation of brain develop- loop structure of these circ[10_TD$IF]-RNAs. (iii) 2Biosystems and Bioengineering Program, University of
ment in animals [2]. The rst genome- Mobile signal: recent ndings of small Science 3
and Technology, Daejeon 34141, South Korea
These authors contributed equally.
wide study of plant circ[10_TD$IF]-RNAs containing RNAs moving via the phloem suggest
miRNA-binding sites identied 6.6% and that they may act as signaling molecules. *Correspondence: cmryu@kribb.re.kr (C.-M. Ryu).
5.0% of putative circ[10_TD$IF]-RNAs in rice and Similarly, localization, lack of correlation http://dx.doi.org/10.1016/j.tplants.2017.03.007
Arabidopsis, respectively, as miRNA between circ[10_TD$IF]-RNAs, and their accumu-
sponges (Figure 1) [4]. Furthermore, lation in response to specic
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Although circRNA research in plants is still involved in their ne-tuning of RNA proc-
in its infancy, insights gained in the essing. We propose that circ[10_TD$IF]-RNAs could
circRNA eld in animals could lead to turn out to be a crucial class of noncoding
new directions in plant circRNA research. regulators in plant.

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