miRNAomic Approach to Plant Nitrogen Starvation

Table 1

Differentially expressed miRNAs under nitrogen starvation condition.

miRNA	Target/function	Mode of regulation	References
miR156	Squamosa promoter binding protein-like (SPL) transcription factors	Up	[119–128]
miR159	MYB, TCP transcription factors/peptidase C48, SUMO/sentrin/Ubl1	Up	[119, 124–126, 129–134]
miR160	Serine carboxypeptidase; transcription factor; auxin-responsive factors (ARF10)	Up	[119, 120, 123, 125, 135–137]
miR162	Dicer-like proteins	Up	[138, 139]
miR164	NAC transcription factors	Up	[119, 135, 136, 140]
miR166	HD-ZIP transcription factors	Down	[135, 138, 141, 142]
miR166a-3p	Kinesin-1-like protein PSS1; transport		[129]
miR167	Auxin-responsive factors (ARF8)/cation/H+ exchanger	Up/down	[125, 126, 130, 136–140, 143]
miR167c-5p	SCF ubiquitin ligase complex		[129]
miR167f-3p_L-1R+1	Ubiquitin ligase complex; lysosomal alpha-mannosidase		[129]
miR168	ARGONAUTE1 (AGO1)	Up/down	[119, 125, 136, 138, 140]
miR168a-5p	WRKY; Cul4-RINGE3 ubiquitin ligase		[129]
miR168a-3p-L-3	Ubiquitin domain containing protein DSK2b		[129]
miR169	HAP2 transcription factors CAAT-binding factor/NFYA/MDIS1-interacting receptor-like kinase 1/protein high chlorophyll fluorescent 107	Up/down	[117, 119, 124–126, 130, 136, 137, 139, 141, 142, 144, 145]
miR169o	NF-YA1, NF-YA4, NF-YA10, NF-YA11, and TRA		[146]
miR169d-5p	Protein serine/threonine kinase; ABC transporter; C family member 13		[129]
miR169d-3p-L-2R+2	Galactinol-sucrose galactosyltransferase 2; E3 ubiquitin-protein ligase		[129]
miR169f-5p	NF-YA2		[119]
miR169(n, o)-5p	NF-YA4/NF-YA10		[119]
miR169r-5p	NF-YA1/NF-YA3		[119]
miR170	NSP2 transcription factor protein		[147]
miR171	Scarecrow-like transcription factors (SCL)/GAGA binding-like	Up/down	[121, 123, 125, 126, 130, 138]
miR171a	DELLA proteins RGL2; malate dehydrogenase		[129]
miR171a-3p	GRAS transcription factor/similar to scarecrow-like 6		[119]
miR171i-3p	GRAS transcription factor		[119]
miR171e-5p_2ss2GA21AG	Protein binding		[129]
miR172	AP2 like transcription factors	Up	[136–138]
miR172b-5p			[129]
miR172(a, d)-3p	AP2/EREBP family transcription factor		[119]
miR262	F-box/kelch-repeat protein	Down	[120]
miR319	TCP transcription factors/MYB transcription factor; Dnaj protein	Up/down	[125, 126, 129, 133, 136, 143]
miR319a-3p.2-3p_R+1	SCF ubiquitin ligase complex; MYB		[129]
miR319(a-3p.2,b)-3p	OsPCF6/TCP21		[119]
miR393(a, b)-5p	Auxin signaling F-box 2/OsTIR1		[119]
miR393-5p_L-1R+1	Auxin-activated signalling; protein transport inhibitor response 1; LRR kinase		[129]
miR393	Auxin receptors (TIR1/F-box AFB)/cyclin-like F-box	Up	[125, 126, 130, 133, 137, 138, 147]
miR394	F-box protein	Up/down	[139]
miR394-5p	SCF ubiquitin ligase complex; glutathione transferase activity		[129]
miR395	ATP sulfurylase; sulfate transporters (APS/AST)	Up/down	[120, 123, 125, 133, 136, 146]
miR396	Growth regulating factor (GRF)	Up/down	[121, 125, 138, 143, 148]
miR396a-5p	Phosphatidylinositol 4-phosphate 5-kinase 1; glutamate dehydrogenase; response to GA		[129]
miR396(a, b)-5p	OsGRF7		[119]
miR396c-5p	GTPase activity; HSP protein; RPM1		[129]
miR396e-5p	Transcription factor TFIID; ribonuclease P activity		[129]
miR396ef	s growth-regulating factors (OsGRFs)		[149]
miR397	Laccases, beta-6-tubulin/L-ascorbate oxidase/LAC17	Up/down	[120, 125, 127, 133, 136, 139, 147, 148]
miR398	COX5b-1; CCS1 COX (CSD)/IAA-amino acid hydrolase ILR1/GATA31	Up	[121, 123, 126, 136, 139, 147, 148, 150–153]
miR399	Ubiquitin conjugase E2/UBC24	Up/down	[123, 125, 129, 131, 136, 138, 143, 154, 155]
miR399a	Oxidoreductase; transcription factor		[129]
miR408	Plantacyanin laccases/superoxide dismutase [Cu–Zn]1A/SOD1A	Up/down	[120, 123, 125, 128, 131, 133, 136, 139, 147]
miR408_L-1	L-ascorbate oxidase; LPEAT1-like		[129]
miR408-p5_1ss20GA	Brassinosteroid insensitive 1		[129]
miR414	bZIP transcription factor	Down	[120]
miR419	Organic anion transporter		[147]
miR1425-5p	PPR domain-containing protein		[119]
miR444	MADS-box	Up	[119]
miR528	POD, SOD	Up	[136, 139, 140]
miR528-5p	Lectin-rich repeat receptor kinase		[129]
miR530-5p-R+1	Fructose-bisphosphate adolase; HSP70		[129]
miR530-5p_R+1_1ss20AG			[129]
miR530-5p-L+1	Fructose-bisphosphate aldolase; SCF ubiquitin ligase complex		[129]
miR531_L-4R+1-1ss5CT	NAD(P)H dehydrogenase; ABC transporter		[129]
miR780	Na^+/H^+ antiporter	Up	[123]
miR815c-p5_2ss6CT21CT	UDP-arabinose 4-epimerase 1-like; transcription factor TGA2-like; Dnaj		[129]
miR826	Alkenyl hydroxyalkyl producing 2	Up	[123]
miR827	Ubiquitin E3 ligase with RING and spx-domain-contain; phenylalanyl-tRNA synthetase; WPP domain-interacting protein 2; BTB/POZ domain-containing protein	Down	[123, 129, 136, 139, 147]
miR829	AP2 domain ethylene response	Up	[123, 133, 156]
miR839		Up	[123]
miR840	Basic helix-loop-helix (bHLH) DNA-binding protein		[147]
miR846	Jacalin lectin family protein	Up	[123, 156]
miR850		Down	[123]
miR854	UDP-glucuronic acid decarboxylase 2/ethylene-responsive transcription factor/GRAS transcription factor		[147]
miR857	Laccase	Down	[123]
miR858	Myb transcription factor		[130]
miR863	Transducin/WD40 repeat-like other RNA	Up
miR1040	Acylsphingosine kinase/hypersensitive-induced response protein 1	Down	[120]
miR1074	LRR receptor-like serine/threonine-protein kinase		[147]
miR1088	CoA ligase-like 3		[147]
miR1127b-3p-1ss12TC	UDP-glucuronate decarboxylase; SCF ubiquitin ligase complex		[129]
miR1127b-p5-1ss3TC			[129]
miR1133	bZIP transcription factor superfamily protein		[147]
miR1137a-p3_1ss9CT			[129]
miR1137a-p5_2ss9GA20GC	DNA mismatch repair protein MSH6		[129]
miR1214	Peroxidase 2-like/F-box domain containing protein		[147]
miR2097	Translation initiation factor eIF-2B subunit delta		[147]
miR2199	MDIS1-interacting receptor-like kinase 1		[147]
miR2275-p5	LRR receptor-like serine/threonine-protein kinase FLS2; brassinosteroid insensitive 1/stress response gene TaPRP/signal transduction-associated genes TaWRK and TaSPK/trafficking genes TaAAT, TaNTA, and TaIM		[129, 157]
miR2630	Leucine-rich repeat receptor-like serine/threonine-protein kinase		[147]
miR2864	Sphingosine kinase 1		[147]
miR2916-p3-2ss2TC17CA	Fructose-bisphosphate aldolase; PRM1; peroxidase		[129]
miR2916-p5-2ss2AG17TG	Protein serine/threonine kinase; glutathione S-transferase (GSTF) 1; DELLA		[129]
miR2919	F-box protein		[147]
miR2948	LRR receptor-like serine/threonine-protein kinase	Down	[120]
miR3454	Protein kinase family protein		[147]
PC-5p-3645-2157	Metalloendopeptidase; SCF ubiquitin ligase		[129]
miR3706	Pentatricopeptide repeat-containing protein		[147]
miR3946	ABC transporter G family member 41/SBP-transcription factor 5		[147]
miR3979-3p	PPR domain-containing protein		[119]
miR4350	Cyclin-A2/putative ubiquitin-like-specific protease 1B		[147]
PC-3p-4780_1750	Aspartic endopeptidase; transcription factor		[129]
miR5059	Glycosyltransferase family 61 protein		[147]
miR5070	Transport inhibitor response 1 protein		[147]
miR5262	F-box/kelch-repeat protein	Down	[120]
miR5301	Harbinger transposase-derived nuclease	Down	[120]
miR5384-p5	UDP-glycosyltransferase 83A1-like; ethylene-responsive transcription factor 1B		[129]
miR5721	Auxilin-related protein 2	Down	[119]
miR6148	Hydroxycinnamoyl transferase	Down	[119]
miR6224	RNA-directed RNA polymerase	Down	[119]
miR6300-p5	Protein RPM1; response to nitrate		[129]
miR9652-5p	Retrograde transport		[129]
miR9653b-p3	Protein binding		[129]
miR9655-p5	Transcription factor; oxidation-reduction		[129]
miR9657a-3p	Serine-type endopeptidase inhibitor activity; amino acid transport; WRKY		[129]
miR9658-3p	SCF ubiquitin ligase complex; RPM1		[129]
miR9664–3p-L-1	RPM1 protein; zinc finger CCCH domain-containing glucosidase		[129]
miR9666a-3p	Alternative splicing regulator; regulator protein NPR5		[129]
miR9666b-3p	DNA-directed RNA polymerase II subunit I/stress response		[129]
miR9672a-3p-L+2R-2	Replication factor C subunit 1		[129]
miR9672b-p5	LRR receptor-like serine/threonine-protein kinase FLS2-like		[129]
miR9674b-5p	SCF ubiquitin ligase complex; calcium-dependent protein kinase 20-like		[129]
miR9772a-5p-L-2R+2	SCF ubiquitin ligase complex		[129]
miR9776-L-1R+1-1ss18AG	Cell division; O-methyltransferase		[129]
miR9779-p3	Hexose transmembrane transport		[129]