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Table 1 Transcriptome profiles for 33 transcription factor genes with potential relevance to a pollen HSR

From: A comparison of heat-stress transcriptome changes between wild-type Arabidopsis pollen and a heat-sensitive mutant harboring a knockout of cyclic nucleotide-gated cation channel 16 (cngc16)

Gene ID

Description

WT Norm Avg.

WT Heat Avg.

log2-CHG

Sig. adj p-val.

Mut Norm Avg.

Mut Heat Avg.

log2-CHG

Sig. adj p-val.

HS- seedling log2- CHGb

Ratio of pollen to seedling c

Reference Genes

 AT3G48010

CNGC16, cNMP-gated channel

539

733

0.43

N

98e

94

−0.08

N

0.23

284

 AT5G14870

CNGC18, cNMP-gated channel

3741

4158

0.15

N

2989

2620

−0.19

N

−0.08

185

 AT5G52640

HSP90, heat shock protein

8.3

739

5.40

Y

6.2

489

5.03

Y

5.94

0.010

 AT5G59720

HSP18.2, heat shock protein

26

309

3.27

Y

29

257

2.89

Y

6.38

0.314

 AT3G08770a

LTP6, Lipid transfer protein

41

108

1.31

Y

153

31

−2.11

Y

−0.53

0.005

 AT3G20210a

DELTA-VPE, endopeptidase

5.7

31

2.08

Y

5.8

3.7

−0.54

N

0.07

2644

 AT5G07690a

MYB29, myb domain protein

1.5

1.0

−0.27

N

< 0.43

13

2.65

Y

−0.89

NA

 AT5G66300a

NAC105, NAC domain

38

1.0

−1.12

N

207

74

−0.88

N

0.15

2

27 transcription factors with heat-altered expression in WT and preferential expression in pollen

 AT3G05860

AGL45, MADS-box

1.9

47

3.51

Y

5.0

16

1.28

N

−0.05

14

 AT5G37800

RSL1, RHD SIX-LIKE 1

15

208

3.45

Y

4.8

101

3.60

Y

NA

43

 AT5G58010

LRL3, LJRHL1-like 3

40

345

3.00

Y

47

186

1.91

Y

0.48

1308

 AT1G49120

CRF9, Integrase-type

5.7

50

2.67

Y

6.2

29

1.85

Y

NA

21

 AT5G17320

HDG9, Homeodomain

6.4

37

2.19

Y

6.8

12

0.56

N

0.24

120

 AT3G53790

TRFL4, TRF-like 4

3.0

17

1.93

Y

6.9

22

1.39

N

0.19

104

 AT4G00120

IND1, Basic helix-loop-helix

7.6

33

1.80

Y

6.6

33

1.91

Y

NA

16

 AT2G24681

REM11, AP2/B3-like

2.6

13

1.71

Y

4.3

12

1.19

N

NA

3

 AT5G50480

NFYC6, Nuclear factor Y

4.2

16

1.56

Y

3.5

8.8

0.97

N

0.18

270

 AT5G60480

HB26, Homeobox protein 26

344

876

1.29

Y

331

868

1.33

Y

NA

30246d

 AT4G26440

WRKY34, WRKY DNA-binding

59

147

1.27

Y

61

114

0.86

Y

−0.04

155

 AT5G61620

MYB-like

51

113

1.10

Y

37

78

1.00

Y

−0.06

185

 AT1G26610

C2H2-like zinc finger protein

50

23

−1.06

Y

48

19

−1.25

Y

0.13

8

 AT4G16110

ARR2, Response regulator 2

3705

1723

−1.07

Y

3475

1282

−1.40

Y

−0.44

8

 AT3G22760

SOL1, Tesmin/TSO1-like

8947

4051

−1.10

Y

10,247

3080

−1.66

Y

0.04

12

 AT5G27090

AGL54, AGAMOUS-like 54

179

79.8

−1.12

Y

300

104

−1.47

Y

NA

5382

 AT3G57390

AGL18, AGAMOUS-like 18

17,513

7358

−1.23

Y

18,821

5458

−1.75

Y

0.06

42

 AT2G20110

TCX6, Tesmin/TSO1-like

325

120

−1.39

Y

265

52

−2.25

Y

0.20

3

 AT5G55020

MYB120, myb domain

458

158

−1.42

Y

404

123

−1.59

Y

0.18

61

 AT4G08250

SCL26, GRAS family

70

23

−1.53

Y

99

25

−1.92

Y

0.10

5

 AT4G37940

AGL21, AGAMOUS-like 21

124

37

−1.66

Y

186

37

−2.24

Y

0.04

3468

 AT5G17430

BBM, Integrase-type

62

15

−1.77

Y

57

8.6

−2.31

Y

0.07

77

 AT2G37000

TCP11, TCP family

128

33

−1.82

Y

99

20

−2.14

Y

0.05

22

 AT5G65330

AGL78, AGAMOUS-like 78

137

34

−1.90

Y

130

20

−2.51

Y

0.04

301

 AT1G72350

MADS-box

164

38

−2.01

Y

150

29

−2.26

Y

0.18

402

 AT1G66370

MYB113, myb domain

13

1.2

−2.41

Y

24

1.5

−3.12

Y

0.17

4

 AT5G21120

EIL2, Ethylene insensitive

182

23

−2.48

Y

219

20

−2.85

Y

0.48

18

6 transcription factors without a WT HS-response, but still showing a significant > 2-fold difference between cngc16 and WT

 AT5G24610

cAMP-response element-binding

7.6

16

0.91

N

12

43

1.73

Y

−0.17

0.041

 AT2G34440

AGL29, AGAMOUS-like 29

6.8

11

0.68

N

< 0.43

< 0.43

0.00

N

0.17

52

 AT1G78080

DREB subfamily A-6, RAP2.4

26

42

0.61

N

19

106

2.28

Y

1.57

0.002

 AT1G10200

GATA-type Zn finger protein

8.32

12.2

0.43

N

10

46

1.85

Y

−0.04

NA

 AT1G12260

NAC 007, NAC-domain protein

801

1002

0.30

N

529

422

−0.31

N

0.25

9

 AT1G10610

bHLH DNA-binding protein

245

190

−0.35

N

521

296

−0.79

N

−0.20

1.4

  1. Eight reference genes are shown at the top, including the four genes marked with (a) which were chosen for verification by Q-PCR
  2. aGenes used for RNA-Seq validation by Q-PCR
  3. bHS-dependent changes in transcript abundance in seedlings (aerial parts) based on publically available data using the AtGenExpress Visualization Tool (AVT) (http://jsp.weigelworld.org/expviz/expviz.jsp) [33] for seedlings exposed to one hour HS at 38 °C. The log2-fold change was calculated based on a comparison of means of normalized values for two heat-stressed and two non-stressed seedling samples
  4. cRatio of expression between pollen and seedling is based on [22]. NA stands for not applicable because it was not possible to calculate based on the information available
  5. dBecause seedling value was below the limit of detection (< 0.0019), a minimal value of 0.0019 was used in its place as a denominator (0.0019 was the RPKM for ATCG00860 and was the lowest value reported in Loraine et al., 2013 (PMCID: PMC3668042 [22])
  6. ecngc16 read counts were restricted to the 5′ end of a truncated transcript (see Additional file 6 and text for more details)
  7. Norm Normal, Avg Average, log2-CHG log2-fold change, Sig. adj. p-val significance based on adjusted p-value ≤0.01, Mut cngc16, N No, Y Yes, cNMP cyclic-nucleotide monophosphate, Ez Enzyme
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BMC Genomics

ISSN: 1471-2164

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