Table 1 Chromatin-associated proteins identified by ChEP

 At4g21710.1

NRPB2

DNA-templated transcription

6

WT; al6

 At4g09000.2

GRF1

Regulation of transcription

13

WT; al6

 At1g14410.1

WHY1

Regulation of transcription

5

WT; al6

 At2g02740.1

WHY3

Regulation of transcription

8

WT; al6

 At4g24800.1

MRF3

Regulation of transcription

13

WT; al6

 At1g77180.1

SKIP

Regulation of transcription

3

WT; al6

 At5g65430.3

GRF8

Regulation of transcription

7

WT; al6

 At1g22300.1

GRF10

Regulation of transcription

15

WT; al6

 At1g09770.1

CDC5

Regulation of transcription

8

WT; al6

 At5g63190.1

MRF1

Regulation of transcription

6

WT; al6

 At5g38480.1

GRF3

Regulation of transcription

14

WT; al6

 At5g65410.1

ZHD1

Regulation of gene expression

4

WT; al6

 At1g15750.1

TPL

Regulation of transcription

7

WT; al6

 At5g04430.2

BTR1

Regulation of transcription

16

WT; al6

 At2g32080.1

PUR-ALPHA-1

Regulation of transcription

3

WT; al6

 At2g45640.1

SAP18

Regulation of transcription

4

WT; al6

 At2g42560.1

LEA25

Unknown function

7

al6

 AT3G58680.1

MBF1b

Transcriptional coactivator

4

al6

 At3g05060.1

SAR DNA-binding protein

Box C/D RNP complex

12

WT; al6

 At1g76010.1

ALBA1

Chromatin structure

9

WT; al6

 At1g20220.1

ALBA2

Chromatin structure

5

WT; al6

 At2g32080.1

PUR ALPHA-1

DNA replication

3

WT; al6

 At1g48610.1

AT-hook motif

DNA binding

11

WT; al6

 At3g42170.1

DAYSLEEPER

Transposase-like

8

WT; al6

 At3g10690.1

GYRA

DNA topological change

12

WT; al6

 At5g04130.1

GYRB2

DNA topological change

7

WT

 At4g25210.1

DNA-binding storekeeper protein-related

Mediator complex

2

WT; al6

 At4g39680.1

SAP domain-containing protein

Nucleic acid binding (nucleus)

18

WT; al6

 At4g36020.1

CSP1

DNA duplex unwinding

7

WT; al6

 At4g26110.1

NAP1;1

DNA repair

8

WT; al6

 At5g10010.1

HIT4

Negative regulation of gene silencing

7

WT; al6

 At3g49601.1

pre-mRNA-splicing factor

mRNA splicing

5

WT; al6

 At2g18510.1

JANUS

mRNA splicing

3

WT

 At2g37340.1

RSZ33

mRNA splicing

4

WT

 At3g55460.1

SCL30

mRNA splicing

6

WT; al6

 At3g55220.1

SAP130B

mRNA splicing

9

WT; al6

 At1g09760.1

U2A’

mRNA splicing

4

WT; al6

 At3g61240.1

RH12

mRNA binding (nucleus)

2

WT; al6

 At2g14880.1

SWIB2

Regulation of transcription by RNA polymerase II

5

WT; al6

 At4g17520.1

HLN

mRNA binding (nucleus)

12

WT; al6

 At5g39570.1

PLDRP1

mRNA binding (nucleus)

11

WT; al6

 At4g34110.1

PAB2

mRNA binding (nucleus)

15

WT; al6

 At2g23350.1

PAB4

mRNA binding (nucleus)

17

WT; al6

 At5g47210.1

Hyaluronan

mRNA binding (nucleus)

18

WT; al6

 At1g51510.1

Y14

mRNA binding (nucleus)

3

WT; al6

 At5g42820.2

U2AF35B

mRNA splicing

3

WT; al6

 At1g02140.1

HAP1

mRNA splicing

3

WT; al6

 At3g49430.1

SRP34A

mRNA splicing

6

WT; al6

 At1g49760.1

PAB8

mRNA binding (nucleus)

13

WT; al6

 At1g04080.3

PRP39

mRNA splicing

10

WT; al6

 At5g04280.1

RZ1C

mRNA splicing

7

WT; al6

 At3g13570.1

SLC30A

mRNA splicing

4

WT; al6

 At3g26560.1

ATP-dependent RNA helicase

mRNA splicing

2

WT

 At2g33340.1

MAC3B

mRNA splicing

12

WT; al6

 At1g80070.1

SUS2

mRNA splicing

22

WT; al6

 At4g31580.1

RSZ22

mRNA splicing

7

WT; al6

 At4g39260.1

CCR1

mRNA splicing

11

WT; al6

 At2g24590.1

RSZ22A

mRNA splicing

3

al6

 At1g16610.3

SR45

mRNA splicing

3

WT; al6

 At1g14650.1

SWAP

mRNA splicing

4

WT; al6

 At2g13540.1

ABH1

mRNA splicing

4

WT; al6

 At5g64270.1

Splicing factor

mRNA splicing

11

WT; al6

 At2g38770.1

MAC7

mRNA splicing

7

WT; al6

 At1g20960.1

BRR2

mRNA splicing

34

WT; al6

 At5g41770.1

Crooked neck protein

mRNA splicing

3

WT; al6

 At5g52040.2

RS41

mRNA splicing

6

WT; al6

 At5g54900.1

RBP45A

mRNA binding (nucleus)

8

WT; al6

 At1g11650.2

RBP45B

mRNA binding (nucleus)

5

WT

 At2g42520.1

RH37

mRNA binding (nucleus)

6

WT; al6

 At3g58510.1

RH11

mRNA binding (nucleus)

9

WT; al6

 At1g29250.1

ALBA1

mRNA-binding (nucleus)

5

WT; al6

 At2g33410.1

RBGD2

mRNA-binding (nucleus)

4

WT; al6

 At4g00830.1

LIF2

mRNA-binding (nucleus)

5

WT; al6

 At5g07350.2

TSN1

mRNA binding (nucleus)

25

WT; al6

 At1g13190.1

RNA-binding (RRM/RBD/RNP motifs) family protein

mRNA binding (nucleus)

2

WT; al6

 At5g61780.1

TSN2

mRNA binding (nucleus)

22

WT; al6

 At3g04610.1

FLK

mRNA binding, regulation of gene expression

4

WT; al6

 At1g48920.1

PARL1

rRNA processing

24

WT; al6

 At5g52470.1

FIB1

RNA methylation

10

WT; al6

 At2g21660.1

CCR2

mRNA export from the nucleus

10

WT; al6

 At3g10650.1

NUP1

mRNA export from the nucleus

6

WT; al6

 At2g05120.1

NUP133

mRNA export from the nucleus

4

WT; al6

 At1g14850.1

NUP155

Nucleoporin

12

WT; al6

 At1g69250.1

NTF2

mRNA export from the nucleus

4

al6

 At2g16950.1

TRN1

Nuclear import

4

al6

 At3g06720.1

IMPA-1

Nuclear import

3

WT; al6

 At4g16143.1

IMPA-2

Nuclear import

9

WT; al6

 At1g09270.1

IMPA-4

Nuclear import

5

WT; al6

 At1g75660.1

XRN3

miRNA catabolic process

4

WT; al6

 At1g26110.1

DCP5

mRNA decapping

3

al6

 AT5G25757.1

RNA polymerase I-associated factor PAF67

RNA polymerase I-associated

9

WT; al6

 At2g06990.1

HEN2

mRNA processing

3

WT; al6

 At3g03920.1

H/ACA ribonucleoprotein complex

snoRNA guided rRNA pseudouridine synthesis

4

al6

 At3g57150.1

NAP57

mRNA pseudouridine synthesis

12

WT; al6

 At3g02540.1

RAD23C

DNA repair

3

al6

 At5g38470.1

RAD23D

DNA repair

3

WT; al6

 At4g31880.1

PDS5C

DNA repair

15

WT; al6

 At5g55660.1

DEK domain-containing chromatin associated protein

DNA repair

10

WT; al6

 At2g36060.2

MMZ3

DNA repair

4

WT; al6

 At2g29570.1

PCNA2

DNA repair

2

WT; al6

 At5g47690.1

PDS5A

DNA repair

11

WT; al6

 At3g04880.1

DRT102

DNA repair

5

WT; al6

 At1g74560.3

NRP1

Nucleosome assembly

1

WT; al6

 At3g18035.1

HON4

Nucleosome assembly

9

WT;al6

 At2g19480.1

NAP1;2

Nucleosome assembly

11

WT; al6

 At5g56950.1

NAP1;3

Nucleosome assembly

3

WT; al6

 At1g20693.1

HMGB2

Chromatin assembly/disassembly

2

WT; al6

 At1g48620.1

HON5

Nucleosome assembly

7

WT; al6

 At5g58230.1

MSI1

Chromatin assembly

3

WT; al6

 At1g27970.2

NTF2B

Nucleocytoplasmatic transport

5

WT; al6

 At1g65440.1

GTB1

Regulation of transcription; chromatin assembly

5

WT; al6

 At4g26630.1

DEK3

Chromatin remodeling

10

WT; al6

 At3g06400.3

CHR11

Chromatin remodeling

2

WT; al6

 At5g67630.1

ISE4

Chromatin remodeling

9

WT; al6

 At1g67230.1

LINC1

Nuclear structure

18

WT; al6

 At4g31430.2

KAKU4

Nuclear membrane organization

5

WT; al6

 At5g55190.1

RAN3

Nuclear transport of proteins

8

WT; al6

 At2g47970.1

NPL4

Nuclear pore localization protein

5

WT; al6

 At4g15900.1

PRL1

Protein binding (nucleus)

6

al6

 At5g17020.1

XPO1

Nuclear export

7

WT; al6

 At3g44110.1

ATJ

DNA replication

4

WT; al6

 At2g46520.1

XPO2

Protein export from nucleus

5

WT; al6

 At1g79280.2

NUA

Nuclear transport of proteins

22

WT; al6

 At5g43960.1

Nuclear transport factor 2 (NTF2) family protein

Nuclear transport of proteins

6

WT; al6

 At1g56110.1

NOP56

snoRNA binding

11

WT; al6

 At1g14900.1

HMGA

Chromosome condensation

3

WT; al6

 At5g20200.1

Nucleoporin-like protein

Nuclear membrane organization, DNA replication

6

WT; al6

 At5g60980.2

NTF2

Nuclear transport

4

WT; al6

 At3g51050.1

NERD1

Unidimensional cell growth

2

WT; al6

 At1g19880.1

RCC1

Chromosome condensation

3

WT; al6

 At5g11170.1

UAP56A

RNA-directed DNA methylation

19

WT; al6

 At3g15670.1

LEA76

Nuclear protein

9

WT; al6

 At1g15340.1

MBD10

Methyl-CpG-binding domain

7

WT; al6

 At1g61000.1

NUF2

Kinetochore organization

1

WT; al6

 At5g63860.1

UVR8

Chromatin binding

7

al6

 At1g47200.1

WPP2

Mitosis

6

WT; al6

 At5g03740.1

HDT3

Histone deacetylation

7

WT; al6

 At2g19520.1

NFC4

Histone modification

8

WT; al6

 At5g22650.1

HAD4

Histone deacetylation

5

WT; al6

 At5g08450.1

HDC1

Histone deacetylation

4

WT; al6

 At4g38130.1

HD1

Histone deacetylation

2

al6

 At5g45690.1

Histone acetyltransferase

Histone acetylation

13

WT; al6

 At1g08880.1

HTA5

Histone superfamily protein

1

WT; al6

 At5g65360.1

HRT1

Histone superfamily protein

4

WT; al6

 At2g30620.1

H1.2

Histone superfamily protein

8

WT; al6

 At3g46030.1

HTB11

Histone superfamily protein

1

WT; al6

 At1g01370.1

HTR12

Histone superfamily protein

2

al6

 At5g59970.1

Histone superfamily protein

Histone superfamily protein

14

WT; al6

 At1g61730.1

DNA-binding storekeeper protein-related transcriptional regulator

Regulation of transcription

6

al6

 At3g01540.2

RH14¹

rRNA processing

9

al6

 At5g02530.1

ALY2

mRNA binding (nucleus)

3

al6

 At2g20490.1

EDA27

rRNA pseudouridine synthesis

3

WT

 At1g80930.1

MIF4G domain-containing protein / MA3 domain-containing protein

mRNA splicing

1

al6

 At4g35800.1

NRBP1¹

RNA polymerase II

8

WT; al6

 At3g62310.1

DEAH RNA helicase homolog PRP43

mRNA binding (nucleus)

2

al6

 At3g50670.1

U1SNRNP¹

mRNA splicing

3

WT; al6

 At1g65090.2

Nucleolin²

Nucleolar protein

3

al6

 At1g06760.1

HON1¹

Nucleosome positioning

3

WT; al6

 At3g11200.1

AL2¹

Histone binding

2

WT

 At1g14510.1

AL7¹

Histone binding

1

WT; al6

 At3g18165.1

MOS4²

Protein binding (nucleus)

5

WT; al6

 At4g05420.1

DDB1A

Regulation of transcription

2

WT; al6

 At5g27670.1

HTA7²

Histone H2A.5 protein

2

WT; al6

 At3g44600.1

CYP71

Chromatin binding

5

WT

 At3g50670.1

U1SNRNP¹

mRNA splicing

3

WT; al6

 At4g32720.1

LA1

rRNA processing

2

al6

 At4g35800.1

NRBP1¹

RNA polymerase II

7

al6

 At3g01540.2

RH14¹

rRNA processing

4

WT

 At5g53620.1

MNC6.16

RNA polymerase II degradation

2

al6

 At4g24270.2

EMB140

RNA processing

3

al6

 At1g33240.1

GTL1

Negative regulation of transcription

3

al6

 At5g28040.1

VFP4

Regulation of transcription

1

al6

 At3g50370.1

Hypothetical protein

mRNA binding (nucleus)

 At2g27100.1

SE³

mRNA splicing

8

WT; al6

 At1g06760.1

HON1¹

Nucleosome positioning

3

al6

 At3g11200.1

AL2¹

Histone binding

3

WT; al6

 At3g42790.1

AL3

Histone binding

2

al6

 At1g14510.1

AL7¹

Histone binding

1

WT; al6

 At4g27000.1

RBP45C

mRNA binding (nucleus)

4

WT

 At1g23860.1

RSZ21

mRNA splicing

1

al6

 At1g65010.1

Microtubule-associated protein

Reciprocal meiotic recombination

10

al6

 At5g37720.1

ALY4

mRNA export from the nucleus

5

al6

 At2g15430.1

NRPB3

RNA polymerase II, IV and V

2

al6

 At4g36690.1

U2AF65A

mRNA splicing

5

al6

 At2g27100.1

SE³

mRNA splicing

8

al6

 At5g27670.1

HTA7²

Histone H2A protein

2

al6

 At1g65090.2

Nucleolin²

Nucleolar protein

3

al6

 At2g02470.1

AL6

Histone binding

1

al6

 At2g41620.1

Nucleoporin interacting component

mRNA export from the nucleus

2

al6

 At3g18165.1

MOS4²

Protein binding (nucleus)

5

al6

 At3g11450.1

ZRF1A

Chromatin silencing

3

al6

 At1g18800.1

NRP2

Chromatin assembly

1

al6

 At5g22880.1

HTB2

Histone family protein

1

WT;al6