Genome-wide analyses of direct target genes of four rice NAC-domain transcription factors involved in drought tolerance

Chung, Pil Joong; Jung, Harin; Choi, Yang Do; Kim, Ju-Kon

doi:10.1186/s12864-017-4367-1

Table 1 Summary of the integration of RNA-Seq and chromatin immunoprecipitation (ChIP)-Seq data and gene ontology (GO) analysis. ¹AGRIGO (http://bioinfo.cau.edu.cn/agriGO/). V, vesicle related (GO:0031982, GO:0031988, GO:0016023, GO:0031410); M, membrane related (GO:0043231, GO:0043227). ²PANTHER (http://geneontology.org/). TA, transmembrane transport (GO:0055085, GO:0006810, GO:0005215); CM, carbohydrate metabolic process (GO:0005975). ³NBRP database (http://shigen.nig.ac.jp/rice/oryzabase/). DT, drought tolerance (Trait Ontology, TO:0000276); GY, grain yield (TO:0000396); RS, root system (Plant Ontology, PO:0025025). Black circle, detected in ChIP-Seq data; Black bold circle, detected in RNA-Seq; Black light circle, not detected in RNA-Seq

From: Genome-wide analyses of direct target genes of four rice NAC-domain transcription factors involved in drought tolerance

Locus	Description	Symbol	RNA-Seq/ChIP-Seq					¹AgriGO		⁴PANTHER			⁸Oryzabase
Locus	Description	Symbol	OsNAC	5	6	9	10	¹AgriGO		⁴PANTHER			⁸Oryzabase
Transmembrane / Transporter activity
Os01g0881300	MtN3 and saliva related transmembrane protein family	SWEET1A		Ο	Ο
Os02g0513100	MtN3 protein precursor	SWEET15		Ο	Ο			²V	³M	⁵T	⁶TA
Os11g0508600	MtN3 protein precursor	SWEET14			Ο	Ο	Ο			T	TA
Os05g0493800	MtN21 nodulin protein-like			Ο		Ο	Ο	V	M	T	TA
Os05g0409500	Usually multiple acids move in and out transporter 9	OsUMAMIT9		Ο	Ο	Ο	Ο			T	TA
Os06g0179200	Nodulin-like protein			Ο			Ο		M	T	TA
Os02g0227200	Early nodulin	ENOD93b		Ο		Ο			M	T
Os03g0115000	Cupredoxin domain	ENODL10		Ο			Ο		M
Os06g0681200	Cupredoxin domain	OsENODL18		Ο		Ο	Ο	V	M				⁹DT		¹¹RS
Os03g0146100	Tonoplast intrinsic protein	TIP1;1		Ο		Ο		V	M						RS
Os02g0658100	Tonoplast membrane integral protein ZmTIP2-1	TIP2;1					Ο			T	TA
Os01g0232000	Major intrinsic protein family	TIP4;3			Ο	Ο	Ο	V	M	T	TA
Os01g0685800	ATP synthase beta chain, mitochondrial precursor				Ο	Ο	Ο		M	T	TA
Os01g0239200	Phophate translocator	TPT1		Ο	Ο		Ο		M	T	TA
Os02g0496900	Mitochondrial import receptor, TOM9-2 subunit			Ο	Ο	Ο	Ο			T	TA
Os02g0773400	Cyclic nucleotide-binding domain containing protein	OsCNGC12, OsCNGC4			Ο		Ο		M	T	TA
Os02g0693700	ABC transporter superfamily ABCB subgroup member 11	OsABCB11			Ο	Ο				T	TA		DT		RS
Os04g0642000	ABC transporter superfamily ABCB subgroup member 16	OsABCB16			Ο		Ο			T	TA		DT
Os05g0424000	amino acid permease 11F	OsAAP11F			Ο		Ο			T	TA
Os11g0137000	PIN1-like auxin transport protein	OsPIN1B			Ο	Ο	Ο			T	TA
Os03g0216700	Citrate transporter	OsFRDL1				Ο				T	TA
Os03g0571900	Transparent testa 12 protein	OsPEZ1		Ο	Ο					T	TA
Os10g0195000	Multi antimicrobial extrusion protein MatE family	OsSTA240				Ο	Ο			T	TA				RS
Os06g0494400	Multi antimicrobial extrusion protein MatE family				Ο	Ο				T	TA
Os02g0510600	Heavy metal transport/detoxification protein domain						Ο			T	TA
Os03g0751600	Heavy metal transport/detoxification protein domain				Ο		Ο	V	M	T
Os08g0403300	Heavy metal transport/detoxification protein domain					Ο				T
Os10g0532300	Heavy metal transport/detoxification protein domain			Ο					M	T
Os01g0849000	non-specific lipid transfer protein d5	OsLTPd5			Ο	Ο				T					RS
Os01g0856600	Nsp1-like, C-terminal family			Ο	Ο	Ο	Ο	V	M	T
Os07g0198300	Bifunctional inhibitor/plant lipid transfer protein/seed storage domain containing protein.	OsLTPG19		Ο		Ο	Ο		M	T	TA
Os12g0104800	Clathrin heavy chain				Ο	Ο	Ο	V	M	T
Os03g0234000	Non-symbiotic hemoglobin 3 (rHb3)	OsNSHB3			Ο	Ο	Ο	V	M	T
Os04g0277400	Membrane bound O-acyl transferase, MBOAT family			Ο	Ο	Ο	Ο			T
Os03g0693700	Oxalate oxidase 1 (Germin)	OXO1		Ο				V	M						RS
Os02g0532500	Germin-like protein	OsGLP2-1		Ο				V	M
Os05g0277500	Germin-like protein subfamily 2 member 4 precursor	OsGLP5-2			Ο	Ο	Ο	V	M	T
Os08g0506400	Serine/threonine protein kinase domain containing protein	OsRLCK257			Ο		Ο	V	M				DT		RS
Os05g0371600	BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1	OsRLCK184					Ο	V	M				DT
Os04g0576900	Protein kinase-like domain	XIAO			Ο	Ο	Ο	V	M
Os03g0416200	BRITTLE CULM1, Cell Wall Architecture1	OsBC1			Ο	Ο	Ο	V	M					¹⁰GY	RS
Os10g0453900	Eggshell protein family	OsGRP7			Ο	Ο	Ο	V	M						RS
Os01g0668100	Arabinogalactan-like protein	OsFLA7		Ο	Ο		Ο	V	M						RS
Os02g0757100	Phi-1 protein	OsPHI-1			Ο	Ο	Ο	V	M						RS
Os02g0219800	Tetraspanin domain containing protein	OsTET2		Ο	Ο	Ο	Ο	V	M						RS
Os01g0699900	Plasma membrane associated protein-like				Ο	Ο	Ο	V	M
Os06g0634500	Leucine-rich repeat transmembrane protein kinase 1			Ο	Ο	Ο		V	M
Os08g0442700	SERK1	COE1		Ο	Ο		Ο	V	M
Os06g0269300	Soluble quinoprotein glucose dehydrogenase domain			Ο		Ο	Ο	V	M
Os12g0568900	Thaumatin, pathogenesis-related family			Ο	Ο		Ο	V	M
Os01g0631500	Beta-1,3-glucanase-like protein				Ο	Ο		V	M
Os04g0579200	Zinc finger, RING-type domain				Ο	Ο	Ο	V	M
Os01g0121800	Glycosyl transferase, family 14 protein			Ο	Ο		Ο	V	M
Os12g0611900	Glycosyl transferase, family 17 protein				Ο			V	M
Carbohydrate Metabolic Process
Os12g0512100	Sugar transporter family			Ο	Ο	Ο					TA	⁷CM
Os02g0575800	Aldose 1-epimerase family			Ο	Ο			V	M			CM
Os07g0539400	Glycoside hydrolase, family 17 protein, β-1, 3-glucanase 12	Gns12			Ο			V	M			CM
Os04g0376400	Glycoside hydrolase, family 18 protein			Ο	Ο		Ο	V	M			CM
Os02g0790500	Trehalose-6-phosphate synthase	OsTPS5			Ο	Ο	Ο		M			CM
Os05g0247100	Drought-induced protein 3, Xylanase inhibitor protein 2	DIP3, OsHI-XIP		Ο			Ο	V	M			CM	DT		RS
Os07g0646800	Avr9/Cf-9 rapidly elicited protein 231	OsSTA2		Ο		Ο	Ο		M			CM			RS
Os01g0675500	Glycoprotein-specific UDP-glucuronyltransferase-like protein	OsGT43F				Ο	Ο					CM
Os08g0237800	Xyloglucan endotransglycosylase	OsXTH8		Ο	Ο		Ο	V	M			CM			RS
Os06g0356800	Xylanase inhibitor protein I precursor			Ο				V	M			CM
Os02g0764200	Xyloglucan fucosyltransferase-like					Ο			M			CM
Os06g0212300	Xyloglucan fucosyltransferase-like			Ο	Ο		Ο		M			CM
Os01g0944700	Beta-1,3-glucanase precursor	OsGLN2			Ο		Ο	V	M			CM
Os07g0480800	Xyloglucan endotransglucosydase / hydrolase 21	OsXTH21		Ο	Ο	Ο		V	M			CM
Os04g0556400	UDP-glycosyltransferase	UGT93B9		Ο	Ο	Ο	Ο					CM
Os04g0486950	Malate synthase						Ο					CM
Os07g0490100	UDP-glucuronosyl / UDP-glucosyltransferase family	UGT709A4		Ο	Ο		Ο	V	M			CM
Os01g0276800	Mannose-6-phosphate receptor, binding domain containing protein						Ο	V	M			CM
Os01g0329300	Pectin lyase fold domain containing protein				Ο	Ο			M			CM
Os03g0421800	X8 domain containing protein			Ο			Ο	V	M
Auxin / Hormon related
Os08g0109400	AUX/IAA protein family	OsIAA25			Ο	Ο			M
Os02g0769100	Auxin responsive SAUR protein family	OsSAUR12		Ο	Ο		Ο		M
Os06g0714300	Auxin responsive SAUR protein family	OsSAUR29			Ο	Ο	Ο		M
Os02g0167600	Auxin responsive SAUR protein family	OsSAUR6		Ο			Ο
Os05g0381400	ABA induced plasma membrane protein PM 19	OsPM19L1		Ο	Ο	Ο	Ο	V	M				DT		RS
Os01g0859300	ABA response element binding factor	OsABI5		Ο	Ο	Ο			M						RS
Os03g0760800	GAST1 protein precursor	OsGASR1		Ο			Ο	V	M						RS
Os05g0432200	Gibberellin-regulated protein 2 precursor			Ο	Ο	Ο	Ο	V	M
Transcription factors
Os07g0227600	Pathogenesis-related transcriptional factor and ERF domain	OsERF57				Ο			M
Os01g0657400	Ethylene-responsive transcription factor 5	OsERF54			Ο				M
Os03g0263000	TINY-like protein	OsERF9					Ο		M
Os02g0521100	Non-protein coding transcript, unclassifiable transcript	OsERF107				Ο
Os06g0222400	Conserved hypothetical protein	OsERF120					Ο		M
Os04g0429050	Ethylene response factor 100	OsERF100		Ο
Os05g0541400	Helix-loop-helix DNA-binding domain containing protein	OsbHLH119			Ο
Os05g0139100	Helix-loop-helix DNA-binding domain containing protein	OsbHLH106			Ο	Ο			M
Os03g0782500	Phytochrome-interacting factor-like bHLH protein, Stress-responsive transcription factor	OsbHLH152		Ο					M
Os10g0376900	Helix-loop-helix DNA-binding domain containing protein	OsbHLH045			Ο	Ο	Ο		M
Os06g0613500	Helix-loop-helix DNA-binding domain containing protein	OsbHLH095				Ο	Ο		M
Os04g0641700	INCREASED LEAF INCLINATION 1	OsbHLH154		Ο	Ο	Ο	Ο							GY	RS
Os01g0854500	Homeobox domain containing protein	OsWOX5			Ο		Ο		M				DT		RS
Os01g0182700	WRKY GENE 102	WRKY102			Ο	Ο			M				DT
Unclassified
Os07g0604433	Glycosyltransferase family-37			Ο	Ο		Ο
Os05g0370300	C2 calcium/lipid-binding region, CaLB domain			Ο			Ο		M
Os03g0161400	IQ calmodulin-binding region domain			Ο	Ο	Ο	Ο		M
Os01g0833800	IQ calmodulin-binding region domain				Ο		Ο
Os07g0619400	Calcium-binding EF-hand domain			Ο	Ο	Ο	Ο
Os07g0622700	Alpha/beta hydrolase fold-1 domain containing protein				Ο	Ο	Ο		M
Os12g0119800	Harpin-induced 1 domain					Ο	Ο		M
Os09g0419200	NAD-dependent epimerase/dehydratase family			Ο	Ο	Ο			M
Os03g0136900	Aconitate hydratase, cytoplasmic			Ο	Ο	Ο			M
Os01g0330100	GDSL ESTERASE/LIPASE PROTEIN 15	OsGELP15		Ο	Ο		Ο		M
Os09g0527500	MEG5				Ο	Ο	Ο		M
Os07g0601000	NADPH HC toxin reductase			Ο		Ο	Ο		M
Os01g0618700	Lipase, class 3 family			Ο		Ο	Ο		M
Os01g0745400	Sec34-like protein family	Sec34-like			Ο	Ο	Ο
Os08g0545200	Alcohol dehydrogenase superfamily	OsDH1		Ο	Ο		Ο
Os06g0727200	Catalase isozyme B	OsCAT1B		Ο	Ο		Ο
Os03g0110500	KIP1-like domain			Ο	Ο	Ο	Ο
Os06g0704500	Leucine-rich repeat, plant specific				Ο	Ο	Ο
Os01g0613500	Peptidase C1A, papain family			Ο	Ο	Ο	Ο
Os12g0613600	Remorin, C-terminal region domain containing protein	OsREM6.3		Ο		Ο	Ο
Os01g0695300	Farnesyl pyrophosphate synthetase	FPS			Ο	Ο	Ο
Os01g0634500	Laccase-2				Ο	Ο	Ο
Os03g0392050	Oligosaccaryltransferase domain containing protein			Ο	Ο	Ο	Ο
Os07g0605350	Protein EGG APPARATUS-1				Ο	Ο	Ο
Os12g0127650	Ulp1 protease family, C-terminal catalytic domain			Ο	Ο	Ο	Ο

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