. 2009 Jun;150(2):879–888. doi: 10.1104/pp.109.137240

Table I.

Genes identified by microarray analysis as consistently up- or down-regulated in the cia2 mutant

AGI Code	Gene Description	PSL^a	Expression Ratio cia2:Wild Type		RT-PCR^b	ChIP^c
AGI Code	Gene Description	PSL^a	Slide 1	Slide 2	RT-PCR^b	ChIP^c
I. Genes up-regulated in cia2
Ribosome biosynthesis
AT2G07696	Ribosomal protein S7 (RPS7)	N^d/M^e ^f ^g	1.76	1.62
Male gametophyte development
AT3G13400	Multicopper oxidase (SKS13)	EX^d/ER^e ^f ^g	1.62	1.52
II. Genes down-regulated in cia2
Protein chloroplast targeting
AT1G02280	GTP-binding protein (Toc33)	CP^d ^e/other^f ^g	0.54	0.64	+	+
AT3G46740	Translocon of outer membrane (Toc75)	CP^d ^e ^f ^g	0.65	0.61	+	+
Ribosome biosynthesis
AT1G32990	Ribosomal protein L11 (RPL11)	CP^d ^e ^f ^g	0.56	0.58	+	+
AT1G48350	Ribosomal protein L18 (RPL18)	CP^d ^e ^f ^g	0.63	0.47	+	+
AT2G33450	Ribosomal protein L28 (RPL28)	CP^d ^e ^f ^g	0.61	0.49	+	+
AT3G17170	Ribosomal protein S6 (RPS6)	CP^d ^e ^f ^g	0.60	0.55	+	+
AT3G25920	Ribosomal protein L15 (RPL15)	CP^d ^e ^f ^g	0.54	0.64	+	+
AT5G65220	Ribosomal protein L29 (RPL29)	CP^d ^e ^f ^g	0.66	0.56	+	+
AT2G38140	Ribosomal protein S31 (PSRP4)	CP^d ^e ^f ^g	0.64	0.50	+	−
AT1G35680	Ribosomal protein L21 (RPL21)	CP^d ^e ^f ^g	0.52	0.46	−
AT1G74970	Ribosomal protein S9 (RPS9)	CP^d ^e ^f ^g	0.66	0.43	−
AT1G75350	Ribosomal protein L31 (RPL31)	CP^d ^e ^f ^g	0.58	0.54	−
AT2G43030	Ribosomal protein L3 (RPL3A)	CP^d ^e ^f ^g	0.67	0.62	−
AT3G15190	Ribosomal protein S20 (RPS20)	CP^d ^e ^f ^g	0.57	0.48	−
AT3G44890	Ribosomal protein L9 (RPL9)	CP^d ^e ^f ^g	0.55	0.45	−
AT3G54210	Ribosomal protein L17 (RPL17)	CP^d ^e ^f ^g	0.54	0.64	−
AT4G01310	Ribosomal protein L5 (RPL5)	CP^d ^e ^f ^g	0.52	0.52	−
AT5G47190	Ribosomal protein L19 (RPL19-2)	CP^d ^e ^f ^g	0.66	0.56	−
AT5G51610	Ribosomal protein L11-like (RPL11-like)	CP^d ^e ^f ^g	0.53	0.64	−
RNA binding
AT3G53460	RNA-binding protein (CP29)	CP^d ^e ^f ^g	0.66	0.41	+	+
AT3G52150	RNA-binding protein (CP33)	CP^d ^e ^f ^g	0.61	0.56	−
AT4G38160	Transcription terminator (PDE191)	CP^d ^f ^g/other^e	0.50	0.63	−
Protein folding
AT2G44650	Chaperonin 10 (CPN10)	CP^d ^e ^f ^g	0.59	0.45	+	+
Porphyrin biosynthesis
AT1G03475	Coproporphyrinogen III oxidase (CPO1)	CP^d ^e ^f ^g	0.60	0.61	+	−
AT5G08280	Hydroxymethylbilane synthase (HemC)	CP^d ^e ^f ^g	0.66	0.59	−
Removal of superoxide radicals
AT5G23310	Fe-superoxide dismutase (FSD3)	CP^d ^e ^f ^g	0.52	0.65	−	−
AT4G25100	Fe-superoxide dismutase (FSD1)	CP^d ^e ^f ^g	0.55	0.62	−
Electron transport
AT1G60600	Aberrant chloroplast development (ABC4) CP^b ^c ^d ^e		0.59	0.41	−
ATP binding
AT5G63310	Nucleotide diphosphate kinase2 (NDPK2) CP^b ^d ^e/N^c		0.60	0.64	−
Aldo-keto reductase
At1G04420	Aldo/keto reductase (KAB1)	CP^d ^e ^f ^g	0.66	0.65	−
Unknown function
AT5G58250	Expressed protein	CP^d ^e ^f ^g	0.63	0.46	+	+
AT5G58260	Expressed protein	CP^d ^e ^f ^g	0.56	0.64	+	+
AT3G12930	Expressed protein	CP^d ^e ^f ^g	0.58	0.49	−
AT4G34290	SWIB BAF60b-containing protein	CP^d ^f ^g/N^e	0.67	0.40	−
AT2G01620	Expressed protein	ER^d/other^e ^f ^g	0.63	0.65
AT4G21030	Zinc finger domain-containing protein	CY^d/other^e ^f ^g	0.65	0.44
AT5G05250	Expressed protein	N^d/other^e ^f ^g	0.58	0.44
AT5G48210	Expressed protein	ER^d ^f ^g/other^e	0.64	0.63

PSL, Predicted subcellular location; CP, chloroplast; CY, cytosol; ER, endoplasmic reticulum; EX, extracellular; M, mitochondrion; N, nucleus.

RT-PCR symbol denotation: +, cia2:wild type transcript ratio <67%; −, cia2:wild type transcript ratio between 67% and 100%.

ChIP symbol denotation: +, determined positively; −, determined negatively.

WoLF PSORT, prediction of protein localization (Horton et al., 2007).

Gene Ontology cellular component, predicting cellular component of protein on gene ontology (Ashburner et al., 2000).

Predotar, prediction of organelle targeting sequences (Small et al., 2004).

TargetP, predicting subcellular localization of proteins (Emanuelsson et al., 2000).