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Table 4 Pollen development-related genes covalently modified by H3K4me3 and H3K27me3

From: Comparative transcriptome analysis and ChIP-sequencing reveals stage-specific gene expression and regulation profiles associated with pollen wall formation in Brassica rapa

Classification

Brassica rapa

Type

Arabidopsis

Locus

Fold enrichment

FDR (%)

Locus

Gene name

Description

References

Meiosis process

Bra015676

6.35

2.19

H3K4

AT1G77320

MEI1

BRCT-domain-containing protein

[38]

Bra029127

7.58

2.16

H3K4

AT5G52290

SHOC1

protein with similarity to XPF endonucleases

[39]

Bra017718

6.02

4.73

H3K4

AT4G35520

MLH3

DNA mismatch repair protein

[40]

Bra000955

9.92

1.61

H3K4

AT4G01370

MAPK4

MAP kinase

[41]

Bra019444

2.27

11.76

H3K27

AT3G43210

TES

ATP binding microtubule motor family protein

[42]

Bra023796

9.7

44.54

H3K27

AT3G22880

DMC1

DNA repair (Rad51) family protein

[43]

Bra001890

7.24

23.26

H3K27

AT3G22880

   

Tapetum development

Bra009277

10.25

1.91

H3K4

AT5G07280

EMS1

leucine-rich repeat receptor protein kinase

[44]

Bra002401

5.8

11.36

H3K27

AT5G22260

MS1

PHD-finger motif transcription factor

[17]

Bra000615

4.68

12.43

H3K27

AT5G50260

CEP1

papain-like cysteine protease

[45]

Bra013041

6.24

11.48

H3K27

AT2G16910

AMS

basic helix-loop helix transcription factor

[16]

Pollen exine formation

Bra014776

10.36

1.52

H3K4

AT3G55090

ABCG16

ABCG half-transporter

[22]

Bra024796

9.47

1.76

H3K4

AT2G02970

APY6

putative apyrase

[46]

Bra017147

7.5

1.52

H3K4

AT1G02050

LAP6

chalcone and stilbene synthase family

[25]

Bra008832

15.49

12.07

H3K4

AT5G13390

NEF1

membrane protein

[47]

Bra023407

15.38

5.03

H3K4

AT5G13390

   

Bra034054

6.58

2.42

H3K4

AT3G09090

DEX1

membrane associated protein

[48]

Bra029746

6.58

2.09

H3K4

AT3G09090

   

Bra038909

6.69

2.54

H3K4

AT3G51610

NPU

membrane protein

[49]

Bra014776

8.58

11.76

H3K27

AT3G55090

ABCG16

ABCG half-transporter

[22]

Bra025595

7.8

11.49

H3K27

AT5G40260

RPG1

a member of the MtN3/saliva gene family

[50]

Bra013442

4.12

15.6

H3K27

AT4G20050

QRT3

polygalacturonase

[51]

Pollen maturation

Bra029700

9.92

1.51

H3K4

AT3G08590

IPGAM2

phosphoglycerate mutase

[52]

Bra022067

7.76

1.59

H3K4

AT3G01780

TPLATE

cytokinesis protein

[53]

Bra037331

6.58

1.55

H3K4

AT4G00330

CRCK2

calmodulin-binding receptor-like cytoplasmtic kinase

[54]

Bra001510

5.46

2.32

H3K4

AT3G13530

MAP3KE1

epsilon protein kinase

[55]

Bra001358

4.9

3.06

H3K4

AT3G10405

vacuolar acid trehalase

[54]

Bra026579

4.57

5.65

H3K4

AT2G02810

UTR1

multitransmembrane hydrophobic protein

[56]

Bra008037

5.02

2.43

H3K4

AT1G72520

LOX4

PLAT/LH2 domain-containing lipoxygenase family protein

[57]

Bra024316

5.02

3.98

H3K4

AT5G64630

FAS2

chromatin assembly factor-1 p60 subunit

[58]

Bra029541

8.88

1.64

H3K4

AT4G04970

GSL1

callose synthase

[59]

Bra008722

3.01

17.63

H3K27

AT5G15100

PIN8

auxin transporter

[60]

Bra008615

9.47

14.76

H3K27

AT5G16530

PIN5

an atypical member of the PIN family

[61]

Bra039940

7.91

11.59

H3K27

AT2G22950

ACA7

putative auto-regulated Ca2+-ATPase

[62]

Bra033961

3.57

15.97

H3K27

AT1G68090

ANN5

calcium-binding protein

[63]

Bra007536

6.69

11.27

H3K27

AT3G60460

DUO1

R2R3 MYB transcription factor

[64]

Bra003413

5.57

14.1

H3K27

AT3G60460

   

Pollen maturation and anther dehiscence

Bra002816

11.48

1.82

H3K4

AT5G56450

PM-ANT

mitochondrial substrate carrier family protein

[65]

Bra004869

6.8

11.27

H3K27

AT2G44810

DAD1

alpha/beta hydrolases superfamily protein

[66]

Pollen development and tube growth

Bra040162

5.35

2.09

H3K4

AT4G17530

RAB1C

Rab GTPase

[67]

Bra009268

5.35

2.74

H3K27

AT5G07370

IPK2A

inositol polyphosphate kinase

[68]

Bra015643

3.68

14.95

H3K27

AT1G77980

AGL66

MADS transcription factor

[69]

Pollen germination and tube growth

Bra004738

5.24

4.14

H3K4

AT2G43040

NPG1

calmodulin-binding protein

[70]

 

Bra010936

4.9

5.3

H3K4

AT1G27460

NPGR1

calmodulin-binding protein

[70]

 

Bra011041

4.79

3.81

H3K4

AT4G28600

NPGR2

calmodulin-binding protein

[70]

 

Bra010358

4.57

5.02

H3K4

AT4G28600

   
 

Bra032785

4.57

5.35

H3K4

AT1G24620

CML25

EF-hand calcium-binding protein

[71]

 

Bra011622

10.36

1.5

H3K4

AT4G35540

PTF2

TFIIB-related protein

[72]

 

Bra039141

6.46

1.52

H3K4

AT3G01150

PTB1

polypyrimidine tract-binding protein

[73]

 

Bra003466

6.35

2.47

H3K4

AT3G61710

ATG6

autophagy protein

[74]

 

Bra005376

7.91

1.49

H3K4

AT2G34980

SETH1

phosphatidylinositol-glycan synthase subunit

[75]

 

Bra031332

4.57

5.25

H3K4

AT3G22200

POP2

gamma-aminobutyrate transaminase

[76]

 

Bra009450

10.59

1.52

H3K4

AT5G04480

BUP

putative glycosyltransferase

[77]

 

Bra000950

9.81

1.43

H3K4

AT4G01220

MGP4

Rhamnogalacturonan II xylosyltransferase

[78]

 

Bra015010

8.92

1.51

H3K4

AT4G38430

ROPGEF1

guanine nucleotide exchange factor

[79]

 

Bra023489

6.24

2.66

H3K4

AT5G14850

APTG1

mannosyltransferase

[80]

 

Bra008404

5.91

1.53

H3K4

AT1G79250

AGC1.7

AGC kinase

[81]

 

Bra014529

5.46

2.83

H3K4

AT3G59760

ATCS-C

O-acetylserine lyase

[82]

 

Bra008733

10.81

11.6

H3K27

AT5G14870

CNGC18

a member of the cyclic nucleotide gated channel family

[83]

 

Bra007785

7.91

14.93

H3K27

AT2G25600

SPIK

member of the Shaker family potassium ion (K+) channel

[84]

 

Bra000105

8.69

11.79

H3K27

AT2G38910

CPK20

calcium dependent protein kinase

[85]

 

Bra015442

6.91

11.81

H3K27

AT1G05580

CHX23

member of putative Na+/H+ antiporter family

[86]

 

Bra025052

4.79

14.1

H3K27

AT5G45810

CIPK19

CBL-interacting protein kinase

[87]

 

Bra022172

4.35

15.47

H3K27

AT3G16640

TCTP1

a protein homologous to translationally controlled tumor protein

[88]

 

Bra027968

4.01

17.49

H3K27

AT1G54560

XIE

myosin family protein with DIL domain-containing protein

[89]

 

Bra008656

4.01

14.78

H3K27

AT5G16020

GEX3

plasma membrane localized protein

[90]

  1. Genes were selected on the basis of previous reports of Arabidopsis mutants affecting anther or pollen development as well as pollen germination or pollen tube growth. The Brassica ID in bold means the gene showed differential expressional levels between the fertile and sterile floral buds at mature pollen development in our RNA-seq analysis