Plant non-coding RNAs and epigenetics
Plant non-coding RNAs and epigenetics
Yijun Qi 0 3
0 Center for Plant Biology, School of Life Sciences, Tsinghua University , Beijing 100084 , China
1 ShanghaiTech University , Shanghai 200031 , China
2 National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Shanghai Institutes for Biological Sciences (SIBS) , Shanghai 200032 , China
3 Tsinghua-Peking Center for Life Sciences , Beijing 100084 , China
THEMATIC ISSUE: Plant non-coding RNAs and epigenetics . . . . . . . . . . . . . . . . . . . . . . . . . . . February 2018 Vol.61 No.2: 135-137 •EDITORIAL• . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . https://doi.org/10.1007/s11427-017-9244-0
NON-CODING RNAS: THE
SHORT OF THEM
LONG AND THE
MicroRNAs (miRNAs) are a class of endogenous sRNAs
that are processed from hairpin-structured precursors.
miRNA expression often exhibits spatial and temporal
specificity. Xu et al. present an expression atlas of Arabidopsis
miRNAs by sequencing sRNA libraries generated from 27
different organ/tissue types
(Xu et al., 2018)
. They found that
different miRNA members within the same family have
distinct spatial and temporal expression patterns and some
miRNAs are produced from different arms of their hairpin
precursors at different developmental stages. This work
provides a rich resource for future investigation of miRNA
functions in Arabidopsis. A subset of miRNAs has been
identified to target the transcripts encoding plant resistance
(R) proteins, the immune receptors that recognize pathogen
effectors and trigger rapid defense responses. Li summarizes
the recent progress in our understanding of how plant
miRNAs reduce R gene levels under normal conditions and allow
induction of R gene expression under stress conditions
Y. et al., 2018)
Phased siRNAs (phasiRNAs) are generated from long
RNA precursors (transcripts from protein-coding or
noncoding genes) targeted by miRNAs at intervals of 21 or 24 nt
in plants. Interestingly, grass phasiRNAs are specifically
expressed in reproductive organs. Yu et al. summarize
current knowledge on phasiRNAs in male germ cells and their
possible biological functions and mechanisms in anther
development and male fertility
(Yu et al., 2018)
RNAderived small RNAs (tsRNAs) are generated from precursor
or mature tRNAs. Zhu et al. review the recent progress in the
discovery, biogenesis, and function of tsRNAs in higher
plants (Zhu et al., 2018).
In addition to sRNAs, lncRNAs play critical roles in plant
development and environmental acclimation. Deng et al.
systematically analyze lncRNAs in five monocot and five
(Deng P. et al., 2018)
. They found that the
majority of lncRNAs have high sequence conservation at the
intra-species and sub-species levels, similar to mRNAs.
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triguingly, they demonstrate that although highly diverged at
the nucleotide level, some lncRNAs are conserved by
position in the genome at the inter-species level and they are
often co-expressed with their adjacent protein-coding genes.
Wang et al. show that a lncRNA, named HID1 (hidden
treasure 1), acts as a negative regulator of cotyledon greening
in addition to its role in photomorphogenesis
(Wang et al.,
. HID1 acts downstream of phytochrome-interacting
factors 3 (PIF3) during the dark-to-light transition. Genetic
ablation of HID1 resulted in the elevated transcript levels of
the protochlorophyllide oxidoreductases known to catalyze
Pchlide to chlorophyllide conversion, and subsequently
leading to an increased greening rate of etiolated seedlings.
Lariat-derived circular RNAs (laciRNAs) are produced
during pre-mRNA splicing. They are previously thought as
by-products of mRNA processing in higher eukaryotes.
Cheng et al. identify an Arabidopsis laciRNA that plays an
essential role in gene regulation and plant development,
suggesting that the production of laciRNAs may have
(Cheng J. et al., 2018)
RNA editing is a type of post-transcriptional modification
that includes nucleotide insertion/deletion or conversion. In
higher plants, RNA editing usually occurs in plastids and
mitochondria and plays important roles in organelle
biogenesis, environmental adaptation and development. Yan et
al. discuss the divergent roles of the plant RNA editing
factors such as pentatricopeptide repeat (PPR) proteins,
multiple organelle RNA editing factors (MORF, also known
as RIP), organelle RNA recognition motif (ORRM)
containing proteins, protoporphyrinogen IX oxidase 1 (PPO1)
and organelle zinc finger 1 (OZ1)
(Yan et al., 2018)
HISTONE AND DNA MODIFICATIONS:
EVER-GROWING PUZZLE AN
In eukaryotes, epigenetic inheritance is mainly established
by histone modification and DNA methylation. The covalent
modifications on histone can be “read” by specific protein
domains and subsequently trigger downstream signaling
events. Liu et al. review recent structural studies on the
recognition of the epigenetic marks on histones by reader
proteins, and summarize the general and unique features of
histone mark readers in plants
(Liu et al., 2018)
EARLY FLOWERING IN SHORT DAYS (EFS, also
known as SDG8) is the major contributor for H3K36
methylation in Arabidopsis
(Kim et al., 2005; Zhao et al., 2005)
Cheng et al. uncover a novel function of EFS/SDG8 in
(Cheng L. et al., 2018)
. They found that the
mutation in EFS/SDG8 causes large embryo and altered
histone modification at an imprinted gene called MOP9.5.
Lin et al. show that overexpression of the mutated forms of
histone H3 (H3.1K36M and H3.3K36M) causes serious
(Lin et al., 2018)
. The H3K36M
mutation inhibits the activity of EFS/SDG8 and changes the
modifications of endogenous histone H3, including
acetylation at lysine 9 (H3K9ac), trimethylation at lysine 27
(H3K27me3), di- and tri-methylation at lysine 36
(H3K36me2 and H3K36me3).
The SU(VAR)-3-9-related protein family member SUVR2
is involved in transcriptional gene silencing in both
RNAdependent and -independent pathways
(Thorstensen et al.,
. Luo et al. demonstrate that SUVR2 is
mono-sumoylated in planta
(Luo et al., 2018)
. The sumoylation of
SUVR2 is required for the interaction of SUVR2 with the
chromatin-remodeling proteins CHR19, CHR27, and
CHR28 and transcriptional gene silencing.
In addition to histone modification, DNA methylation
plays a vital role in gene expression and plant development.
Chen et al. performed genome-wide profiling of DNA
methylation at single-base resolution by whole-genome bisulfite
sequencing in tomatoes
(Chen et al., 2018)
. Taking the
advantage of the tomato epimutant colourless non-ripening
(Cnr) and virus-induced gene silencing (VIGS) technology,
they found that two genes, named SlDET1 and SlPDS, are
involved in the pigmentation in Cnr fruits.
These review and research articles underscore the
importance of epigenetic mechanisms that regulate a variety of
biological processes in plants. Our understanding of the
functions and mechanisms of chromatin modifications and
noncoding RNAs is still very limited. Further efforts and
resources are needed to solve these ever-growing puzzles.
Compliance and ethics
The author(s) declare that they have no conflict
3. . . . . . . . . . . . . . . . . . . . . . . Wang, J.W., et al. Sci China Life Sci February (2018) Vol.61 No.2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137
Dr. Jia-Wei Wang was born in Shanghai and graduated from the Department of Life Science and
Technology, Shanghai Jiao Tong University in 1999. He received a Ph.D. degree at Shanghai
Institutes for Biological Sciences, Chinese Academy of Sciences (CAS) in 2005. He went to
Germany as a postdoc in 2005 and received postdoctoral training at Max Planck Institute for
Developmental Biology. His independent research began from 2011 and he is currently a
principal investigator at National Key Laboratory of Plant Molecular Genetics (NKLPMG),
CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and
Ecology (SIPPE), CAS. The main research focus of his group is plant life cycle and
Dr. Yijun Qi is a Professor in School of Life Sciences and Center for Plant Biology at Tsinghua
University in Beijing. He completed a Ph.D. in plant virology at Zhejiang University. He is an
expert on RNA silencing in plants. Work in his laboratory includes investigating the functions
of small RNAs and long non-coding RNAs, biochemical and molecular analysis of Argonaute
complexes, and RNA-directed repair of DNA double-strand breaks.
Chen , W. , Yu , Z. , Kong , J. , Wang , H. , Li , Y. , Zhao , M. , Wang , X. , Zheng , Q. , Shi , N. , Zhang , P. , Zhong , S. , Hunter , P. , Tör , M. , and Hong , Y. ( 2018 ). Comparative WGBS identifies genes that influence non-ripe phenotype in tomato epimutant Colourless non-ripening . Sci China Life Sci 61 , 244 - 252 .
Cheng , L., Shafiq , S. , Xu , W. , and Sun , Q. ( 2018 ). EARLY FLOWERING IN SHORT DAYS (EFS) regulates the seed size in Arabidopsis . Sci China Life Sci 61 , 214 - 224 .
Cheng , J., Zhang, Y. , Li , Z. , Wang , T. , Zhang , X. , and Zheng , B. ( 2018 ). A lariat-derived circular RNA is required for plant development in Arabidopsis . Sci China Life Sci 61 , 204 - 213 .
Deng , P. , Liu , S. , Nie , X. , Weining , S. , and Wu , L. ( 2018 ). Conservation analysis of long non-coding RNAs in plants . Sci China Life Sci 61 , 190 - 198 .
Deng , Y. , Liu , M. , Li , X. , and Li , F. ( 2018 ). microRNA-mediated R gene regulation: molecular scabbards for double-edged swords . Sci China Life Sci 61 , 138 - 147 .
Kim , S.Y. , He , Y. , Jacob , Y. , Noh , Y.S. , Michaels , S. , and Amasino , R. ( 2005 ). Establishment of the vernalization-responsive, winter-annual habit in Arabidopsis requires a putative histone H3 methyl transferase . Plant Cell 17 , 3301 - 3310 .
Lin , G. , Zhou , Y. , Li , M. , and Fang , Y. ( 2018 ). Histone 3 lysine 36 to methionine mutations stably interact with and sequester SDG8 in Arabidopsis thaliana . Sci China Life Sci 61 , 225 - 234 .
Liu , R. , Li , X. , Chen , W. , and Du , J. ( 2018 ). Structure and mechanism of plant histone mark readers . Sci China Life Sci 61 , 170 - 177 .
Luo , Y.X. , Han, Y.F. , Zhao , Q.Y. , Du , J.L. , Dou , K. , Li , L. , Chen , S. , and He , X.J. ( 2018 ). Sumoylation of SUVR2 contributes to its role in transcriptional gene silencing . Sci China Life Sci 61 , 235 - 243 .
Thorstensen , T. , Fischer , A. , Sandvik , S.V. , Johnsen , S.S. , Grini , P.E. , Reuter , G. , and Aalen , R.B. ( 2006 ). The Arabidopsis SUVR4 protein is a nucleolar histone methyltransferase with preference for monomethylated H3K9 . Nucleic Acids Res 34 , 5461 - 5470 .
Wang , Y. , Li , J. , Deng , X. W. , and Zhu , D. ( 2018 ). Arabidopsis noncoding RNA modulates seedling greening during deetiolation . Sci China Life Sci 61 , 199 - 203 .
Xu , L. , Hu , Y. , Cao , Y. , Li , J. , Ma , L. , Li , Y. , and Qi , Y. ( 2018 ). An expression atlas of miRNAs in Arabidopsis thaliana . Sci China Life Sci 61 , 178 - 189 .
Yan , J. , Zhang, Q. , and Yin , P. ( 2018 ). RNA editing machinery in plant organelles . Sci China Life Sci 61 , 162 - 169 .
Yu , Y. , Zhou , Y. , Zhang , Y. , and Chen , Y. ( 2018 ). Grass phasiRNAs and male fertility . Sci China Life Sci 61 , 148 - 154 .
Zhao , Z. , Yu , Y., Meyer, D. , Wu , C. , and Shen , W.H. ( 2005 ). Prevention of early flowering by expression of FLOWERING LOCUS C requires methylation of histone H3 K36 . Nat Cell Biol 7 , 1256 - 1260 .
Zhu , L. , Ow , D.W. , and Dong , Z. ( 2018 ). Transfer RNA-derived small RNAs in plants . Sci China Life Sci 61 , 155 - 161 .