Plant miRNA biogenesis
The major difference between plants and metazoans is all of the pri-and premiRNA processing steps occur in the nucleus (mediated by DCL1) whereas in
metazoans it is segregated in the nucleus and then cytoplasm. The second major
difference is 2-O- methylation of the initial miRNA/miRNA duplex by HEN1
Figure 1. Plant miRNA biogenesis (from Xie, et.al.,(2015); DOI 10.1007/s00018014-1728-7)
Name
Desc.
CC
BP
MF
RNA polymerase II
Transcription factor
GO:0005634 nucleus
;DNA-directed RNA
polymerase II, core
complex
GO:0061614 pri-miRNA
transcription from RNA
polymerase II promoter
GO:0001055
RNA polymerase
II activity
GO:0034518 RNA cap
binding complex;
GO:0031053 primary miRNA
processing;
GO:0035196 production of
miRNAs involved in gene
silencing by miRNA
GO:0010445 nuclear
dicing body,
GO:0035196 production of
miRNAs involved in gene
silencing by miRNA;
GO:0035195 gene silencing by
miRNA
Cap Binding Complex
(CBP20 and CBP80)
DCL1 (dicer like 1)
Cleavage of pri-mRNA then
cleavage of pre-miRNA
hairpin-to form miRNA
miRNA duplex. A
GO:0035198 miR
NA
binding;GO:0090
502 RNA
phosphodiester
bond hydrolysis,
endonucleolytic
SE
Cleavage of pri-mRNA to
pre-mRNA
GO:0010445 nuclear
dicing body,
GO:0031053 primary miRNA
processing
GO:0070878 pri
mary miRNA
binding
AGO1
miRNA carrier and slicer to
cleave target mRNAs
GO:0005737 cytoplas
m
GO:0035196 production of
miRNAs involved in gene
silencing by miRNA;
GO:0035195 gene silencing by
miRNA
GO:0035198 miR
NA binding;
GO:0090624
endoribonucleas
e activity,
cleaving miRNApaired mRNA;
GO:0035279
mRNA cleavage
involved in gene
silencing by
miRNA
HSY
Export of miRNA from
nucleus to cytoplsam
GO:0005635 nuclear
envelope;
GO:0005737 cytoplas
m;
GO:0005634 nucleus
GO:1990428 miRNA transport
GO:0005487
nucleocytoplasm
ic transporter
activity
HYL
pri-premiRNA processing
(lke DCL1)
GO:0005737 cytoplas
m;GO:0010445
nuclear dicing body,
GO:0005634 nucleus
GO:0031054 pre-miRNA
processing
GO:0035196 production of
miRNAs involved in gene
silencing by miRNA;
GO:0035195 gene silencing by
miRNA
GO:0003725
double-stranded
RNA binding;
GO:0070883 premiRNA binding;
GO:0035279
mRNA cleavage
involved in gene
silencing by
miRNA
DDL
stabilizes miRNA in Dbody
for excision
GO:0010445 nuclear
dicing body,
GO:0035196 production of
miRNAs involved in gene
silencing by miRNA
HSP90/SQN
Interact with AGO1, may
be involved in strand
selection
HEN1
miRNA duplex methylation
at 3’ end.
GO:0005737 cytoplas
m
GO:0044747 mature miRNA
3'-end processing
GO:0008757 Sadenosyl
methoninedependent
methyltransferas
e
CDC25
Interacts with RNA pol II
and MIR promoter.
GO:0005634 nucleus
GO:1902893 regulation of primiRNA transcription from
RNA polymerase II promoter;
GO:0001085
RNA polymerase
II transcription
GO:0035279 mRNA cleavage
involved in gene silencing by
miRNA
Increase transcription
GO:0035196 production of
miRNAs involved in gene
silencing by miRNA
factor binding;
GO:0000976
transcription
regulatory
region sequencespecific DNA
binding
NOT2B
Increase transcription of
pri-miRNA, miRNA
processing
GO:0005634 nucleus
GO:1902893 regulation of primiRNA transcription from
RNA polymerase II promoter;
GO:0035196 production of
miRNAs involved in gene
silencing by miRNA
GO:0001085
RNA polymerase
II transcription
factor binding
TGH
miRNA processing
GO:0010445 nuclear
dicing body
GO:0035196 production of
miRNAs involved in gene
silencing by miRNA
GO:0070883 premiRNA binding
;GO:0070878
primary miRNA
binding
Mediator Complex
proteins (MED21;
STRUWWELPETER
/MED14;PHYTOCHRO
ME AND FLOWERING
TIME1
/MED25
;At2g28230/
MED20a;At4g09070
MED20b;At2g28020/
Med20c)
Recruits RNA pol II to miR
promoters
GO:0005634 nucleus
GO:1902893 regulation of primiRNA transcription from
RNA polymerase II promoter
GO:0001085
RNA polymerase
II transcription
factor binding;
miPEP
Peptides encoded at miR
loci that appear to
regulate the expression of
the miRNA. Recent so not
clear if they all act in this
way.
GO:1902895, positive
regulation of pri-miRNA
transcription from RNA
polymerase II promoter;
GO:0010628 positive
regulation of gene expression
with annotation extension to:
regulates_levels_of_product_
of: miRNA or pri-miRNA
GO:0001085
RNA polymerase
II transcription
factor binding;
Table 1. Suggested annotations for components of plant miRNA biogenesis
pathway. Note, that this does not exactly reflect the status of current annotations
in TAIR.
References:
Rogers, K and Chen, X., (2013) The Plant Cell 25: 2383-2399
(http://dx.doi.org/10.1105/tpc.113.113159)
Xie, e.al., (2015) , Cell. Mol. Life Sci. 72:87–99
(DOI 10.1007/s00018-014-1728-7 )
Lauressergues (2015) Nature 520, 90–93 (doi:10.1038/nature14254)
Axtell MJ et al.,( 2011), Genome Biology 12:221 (doi:10.1186/gb-2011-12-4-221
)