dnase-seq data correlation among different biological genome … · 2012-06-19 · supplemental...

Supplemental Figure 1. DNase-seq data correlation among different biological replicates and different technical replicates. The entire A. thaliana genome was divided into 100 bp non-overlapping windows. The number of DNase-seq reads in the windows were used to calculate the Pearson Correlation Coefficient between replicates.

Supplemental Data. Zhang et al. (2012). Plant Cell 10.1105/tpc.111.098061

Supplemental Figure 2. DNase I sensitivity along all five A. thaliana chromosomes. Each Y axis represents normalized DNase-seq read counts in 100 kb windows. The X axes show the DNA sequence position on the chromosomes. The red horizontal bars mark the positions of pericentromeric heterochromatin along each chromosome.


Supplemental Figure 3. Distribution of DH sites along A. thaliana chromosomes. The Y axes represent the log2 fold change (log2FC) of normalized DNase-seq read counts between ddm1 and wild type tissues (ddm1/WT) in 100 kb windows. Red, blue and green lines indicate CG, CHG and CHH methylation, respectively, in 100 kb windows (data from wild type leaf tissue). The X axes show the DNA sequence position on each chromosome.


Supplemental Figure 4. Network of biological processes of Gene Ontology (GO) categories for genes associated with flower specific DH sites. GO categories with significant enrichment (adjusted P-value <0.0001) are highlighted with color. This figure was generated by Cytoscape 2.8.1 and BinGO version 2.44 (Shannon et al. 2003, Genome Res. 13: 2498-2504; Maere et al. 2005, Bioinformatics 21: 3448-3449; Cline et al. 2007, Nat. Protoc. 2: 2366-2382.)


Supplemental Figure 5. Distribution of the top 1000 tissue-specific DH sites from leaf vs. ddm1 leaf, and flower vs. ddm1 flower comparisons. The blue bars represent the DNase-seq read number from DH sites specific to wild type tissues. The red bars represent the DNase-seq read number from DH sites specific to ddm1 tissues. Data are in 100 kb windows. The X axes show the DNA sequence position on the chromosomes.


Supplemental Figure 6. Mean nucleotide-level accessibility within DNA sequences associated with DH sites that contain the ABRE-binding motif (C/T)ACGTGGC. The X axis represents the distance from the motif and the Y axis represents the DNase I cut per nucleotide (mean).


Table S1. Summary of the sequence data from the five DNase-seq libraries Total Reads Mappable Readsc Unique Readsc

ddm1 flower 25839040 25268585 (97.79%) 18104538 (70.07%) ddm1 leaf replicate 1a 27097776 25071893 (92.52%) 13672688 (50.46%) ddm1 leaf replicate 1a 27405446 25378890 (92.61%) 13820632 (50.43%) WT flower replicate 1b 19437602 18122924 (93.24%) 13758923 (70.79%) WT flower replicate 2b 22764905 22625493 (99.39%) 17354880 (76.24%) WT leaf replicate 1a 14790933 14656981 (99.09%) 9691173 (65.52%) WT leaf replicate 2a 14662909 14598780 (99.56%) 9081078 (61.93%) WT leaf replicate 3a 27945904 27793554 (99.45%) 18299371 (65.48%) a Sequencing replicates derived from the same DNase-seq library. b Biological replicates from the same type of tissue. c Mappable reads: reads that have perfect sequence matches in the rice genome; Unique reads: reads that have a single sequence match in the rice genome.


Table S2. Footprints within the DH sites containing known cis-regulatory DNA elements

Motif Name Title of publication Reference Motif

number in Genome

Motif in regions associated with

DH sites

DH sites with footprint

Motif SeqLogo Footprint

ARF1 binding site motif Dimerization and DNA binding of auxin response factors

Plant J 19:309-319 (1999)

17312

Flower: 5048 Flower: 1757

1 2 3 4 5 6

Position

0

0.5

1

1.5

2

Info

rmation c

onte

nt

−500 −400 −300 −200 −100 100 200 300 400 500

0.5

1.0

1.5

2.0

Flower footprinting

Leaf footprinting

−500 −400 −300 −200 −100 100 200 300 400 500

0.5

1.0

1.5

2.0

Leaf: 4609 Leaf: 1839

ATHB1 binding site motif

The Athb-1 and -2 HD-Zip domains homodimerize forming complexes of different DNA binding specificities

EMBO J 12:3507-3517 (1993)

1580


1 2 3 4 5 6 7 8 9

Position

0

0.5

1

1.5

2

Info

rmation c

onte

nt

−500 −400 −300 −200 −100 100 200 300 400 500

0.5

1.0

1.5

2.0

Flower footprinting

Leaf footprinting

−500 −400 −300 −200 −100 100 200 300 400 500

0.5

1.0

1.5

2.0

Leaf: 618 Leaf: 212


The Athb-1 and -2 HD-Zip domains homodimerize forming complexes of different DNA binding specificities

EMBO J 12:3507-3517 (1993)

4388


1 2 3 4 5 6 7 8 9

Position

0

0.5

1

1.5

2

Info

rmation c

onte

nt

−500 −400 −300 −200 −100 100 200 300 400 500

0.4

0.8

1.2

Flower footprinting

Leaf footprinting

−500 −400 −300 −200 −100 100 200 300 400 500

0.4

0.8

1.2

Leaf: 976 Leaf: 251


DNA-binding and dimerization preferences of Arabidopsis homeodomain-leucine zipper transcription factors in vitro

Plant Mol Biol 45: 63-73 (2001)

2372


1 2 3 4 5 6 7 8 9

Position

0

0.5

1

1.5

2

Info

rmation c

onte

nt

−500 −400 −300 −200 −100 100 200 300 400 500

0.5

1.0

1.5

2.0

Flower footprinting

Leaf footprinting

−500 −400 −300 −200 −100 100 200 300 400 500

0.5

1.0

1.5

2.0

Leaf: 818 Leaf: 282


Homeodomain protein ATHB6 is a target of the protein phosphatase ABI1 and regulates hormone responses in Arabidopsis

EMBO J. 21:3029-3038 (2002)

1369


1 2 3 4 5 6 7 8 9

Position

0

0.5

1

1.5

2

Info

rmation c

onte

nt

−500 −400 −300 −200 −100 100 200 300 400 500

0.4

0.8

1.2

1.6

Flower footprinting

Leaf footprinting

−500 −400 −300 −200 −100 100 200 300 400 500

0.4

0.8

1.2

1.6

Leaf: 392 Leaf: 117

CArG promoter motif

Antagonistic regulation of flowering-time gene SOC1 by CONSTANS and FLC via separate promoter motifs

EMBO J. 21: 4327-4337 (2002)

4959


1 2 3 4 5 6 7 8 9 10

Position

0

0.5

1

1.5

2

Info

rmation c

onte

nt

−500 −400 −300 −200 −100 100 200 300 400 500

0.6

1.0

1.4

1.8

Flower footprinting

Leaf footprinting

−500 −400 −300 −200 −100 100 200 300 400 500

0.6

1.0

1.4

Leaf: 1672 Leaf: 460

CCA1 binding site motif

A myb-related transcription factor is involved in the phytochrome regulation of an Arabidopsis Lhcb gene

Plant cell 9:491-507 (1997)

11141


1 2 3 4 5 6 7 8

Position

0

0.5

1

1.5

2

Info

rmation c

onte

nt

−500 −400 −300 −200 −100 100 200 300 400 500

0.2

0.6

1.0

1.4

Flower footprinting

Leaf footprinting

−500 −400 −300 −200 −100 100 200 300 400 500

0.2

0.6

1.0


CCA1 motif1 BS in CAB1

A myb-related transcription factor is involved in the phytochrome regulation of an Arabidopsis Lhcb gene.

Plant cell 9:491-507 (1997)

268


1 2 3 4 5 6 7 8 9 10

Position

0

0.5

1

1.5

2

Info

rmation c

onte

nt

−500 −400 −300 −200 −100 100 200 300 400 500

0.5

1.0

1.5

2.0

Flower footprinting

Leaf footprinting

−500 −400 −300 −200 −100 100 200 300 400 500

0.5

1.0

1.5

Leaf: 57 Leaf: 27

DRE-like promoter motif

The Expression Profile Matrix of Arabidopsis Transcription Factor Genes Suggests Their Putative Functions in Response to Environmental Stresses

Plant Cell (2002) 14:559-574

4423


1 2 3 4 5 6 7 8 9

Position

0

0.5

1

1.5

2

Info

rmation c

onte

nt

−500 −400 −300 −200 −100 100 200 300 400 500

0.5

1.5

2.5

Flower footprinting

Leaf footprinting

−500 −400 −300 −200 −100 100 200 300 400 500

0.5

1.0

1.5

2.0



E2F binding site motif

Cell cycle regulation of the tobacco ribonucleotide reductase small subunit gene is mediated by E2F-like elements

Plant Cell 12: 1987-2000 (2000)

1098


1 2 3 4 5 6 7 8

Position

0

0.5

1

1.5

2

Info

rmation

conte

nt

−500 −400 −300 −200 −100 100 200 300 400 500

0.5

1.0

1.5

2.0

Flower footprinting

Leaf footprinting

−500 −400 −300 −200 −100 100 200 300 400 500

0.2

0.6

1.0

1.4

Leaf: 207 Leaf: 80

EveningElement promoter motif

Orchestrated transcription of key pathways in Arabidopsis by the circadian clock

Science 290: 2110-3 (2000)

2539


1 2 3 4 5 6 7 8 9

Position

0

0.5

1

1.5

2

Info

rmation c

onte

nt

−500 −400 −300 −200 −100 100 200 300 400 500

0.5

1.0

1.5

Flower footprinting

Leaf footprinting

−500 −400 −300 −200 −100 100 200 300 400 500

0.2

0.6

1.0

1.4

Leaf: 695 Leaf: 227

GATA promoter motif

Arabidopsis thaliana GATA factors: organisation, expression and DNA-binding characteristics

Plant Mol Biol. 2002 Sep;50(1):43-57.

108341


1 2 3 4 5 6

Position

0

0.5

1

1.5

2

Info

rmation

conte

nt

−500 −400 −300 −200 −100 100 200 300 400 500

0.5

1.0

1.5

2.0

Flower footprinting

Leaf footprinting

−500 −400 −300 −200 −100 100 200 300 400 500

0.6

1.0

1.4

1.8

Leaf: 24195 Leaf: 6384

GCC-box promoter motif Molecular responses to dehydration and low temperature

Curr. Opin. Plant Biol. 3:217-223

2667


1 2 3 4 5 6

Position

0

0.5

1

1.5

2

Info

rmation c

onte

nt

−500 −400 −300 −200 −100 100 200 300 400 500

0.5

1.0

1.5

2.0

Flower footprinting

Leaf footprinting

−500 −400 −300 −200 −100 100 200 300 400 500

0.4

0.8

1.2

1.6

Leaf: 779 Leaf: 204

Hexamer promoter motif Identification of cis-elements regulating the expression of an Arabidopsis histone H4 gene

Plant J 10:425-435 (1996)

3717


1 2 3 4 5 6

Position

0

0.5

1

1.5

2

Info

rmation c

onte

nt

−500 −400 −300 −200 −100 100 200 300 400 500

0.5

1.5

2.5

Flower footprinting

Leaf footprinting

−500 −400 −300 −200 −100 100 200 300 400 500

0.5

1.0

1.5

2.0


HSEs binding site motif

Arabidopsis and the heat stress transcription factor world: how many heat stress transcription factors do we need?

Cell Stress Chaperones. 2001 Jul;6(3):177-89. Review.

3232


1 2 3 4 5 6 7 8 9 10

Position

0

0.5

1

1.5

2

Info

rmation c

onte

nt

−500 −400 −300 −200 −100 100 200 300 400 500

0.4

0.8

1.2

1.6

Flower footprinting

Leaf footprinting

−500 −400 −300 −200 −100 100 200 300 400 500

0.4

0.8

1.2

Leaf: 610 Leaf: 196

L1-box promoter motif

Identification of a cis-regulatory element for L1 layer-specific gene expression, which is targeted by an L1-specific homeodomain protein

Plant J 26: 487-494 (2001)

6011


1 2 3 4 5 6 7 8

Position

0

0.5

1

1.5

2

Info

rmation c

onte

nt

−500 −400 −300 −200 −100 100 200 300 400 500

0.6

1.0

1.4

Flower footprinting

Leaf footprinting

−500 −400 −300 −200 −100 100 200 300 400 500

0.4

0.8

1.2


Leaf: 667 Leaf: 333

MYB binding site promoter

A flower-specific Myb protein activates transcription of phenylpropanoid biosynthetic genes

EMBO J 13:128-137 (1994)

12040


1 2 3 4 5 6 7 8

Position

0

0.5

1

1.5

2

Info

rmation c

onte

nt

−500 −400 −300 −200 −100 100 200 300 400 500

0.5

1.0

1.5

2.0

Flower footprinting

Leaf footprinting

−500 −400 −300 −200 −100 100 200 300 400 500

0.5

1.0

1.5

Leaf: 3503 Leaf: 1079

MYB2 binding site motif MYB transcription factors in plants

Trends Genet. 13:67-73 (1997)

589


1 2 3 4 5 6 7 8 9

Position

0

0.5

1

1.5

2

Info

rmation c

onte

nt

−500 −400 −300 −200 −100 100 200 300 400 500

0.5

1.5

2.5

Flower footprinting

Leaf footprinting

−500 −400 −300 −200 −100 100 200 300 400 500

0.5

1.0

1.5

2.0

Leaf: 150 Leaf: 70

MYB4 binding site motif

Expression profile matrix of Arabidopsis transcription factor genes suggests their putative functions in response to environmental stresses.

Plant Cell. 2002 Mar;14(3):559-74.

47919 Flower: 12731 Flower: 3561

1 2 3 4 5 6 7

Position

0

0.5

1

1.5

2

Info

rmation c

onte

nt

−500 −400 −300 −200 −100 100 200 300 400 500

0.6

1.0

1.4

1.8

Flower footprinting

Leaf footprinting

−500 −400 −300 −200 −100 100 200 300 400 500

0.4

0.8

1.2

1.6


Leaf: 12156 Leaf: 3628

Nonamer promoter motif Identification of cis-elements regulating the expression of an Arabidopsis histone H4 gene

Plant J 10:425-435 (1996)

129


1 2 3 4 5 6 7 8 9

Position

0

0.5

1

1.5

2

Info

rmation

conte

nt

−500 −400 −300 −200 −100 100 200 300 400 500

0.5

1.5

2.5

Flower footprinting

Leaf footprinting

−500 −400 −300 −200 −100 100 200 300 400 500

0.5

1.5

2.5

Leaf: 40 Leaf: 13

T-box promoter motif

Promoter analysis of the nuclear gene encoding the chloroplast glyceraldehyde-3-phosphate dehydrogenase B subunit of Arabidopsis thaliana

Plant Mol Biol 46: 131-141 (2001).

27941


1 2 3 4 5 6

Position

0

0.5

1

1.5

2

Info

rmation c

onte

nt

−500 −400 −300 −200 −100 100 200 300 400 500

0.4

0.8

1.2

1.6

Flower footprinting

Leaf footprinting

−500 −400 −300 −200 −100 100 200 300 400 500

0.4

0.8

1.2

Leaf: 6382 Leaf: 1641

Bellringer/replumless/pennywise BS1 IN AG

Repression of AGAMOUS by BELLRINGER in Floral and Inflorescence Meristems

Plant Cell 16: 1478-1489 (2004)

16470


1 2 3 4 5 6 7 8

Position

0

0.5

1

1.5

2

Info

rmation

conte

nt

−500 −400 −300 −200 −100 100 200 300 400 500

0.2

0.6

1.0

1.4

Flower footprinting

Leaf footprinting

−500 −400 −300 −200 −100 100 200 300 400 500

0.2

0.6

1.0

Leaf: 3579 Leaf: 1824



Plant Cell 16: 1478-1489 (2004)

5202


1 2 3 4 5 6 7 8

Position

0

0.5

1

1.5

2

Info

rmation c

onte

nt

−500 −400 −300 −200 −100 100 200 300 400 500

0.5

1.0

1.5

Flower footprinting

Leaf footprinting

−500 −400 −300 −200 −100 100 200 300 400 500

0.5

1.0

1.5




Plant Cell 16: 1478-1489 (2004)

5202


1 2 3 4 5 6 7 8

Position

0

0.5

1

1.5

2

Info

rmation c

onte

nt

−500 −400 −300 −200 −100 100 200 300 400 500

0.5

1.0

1.5

Flower footprinting

Leaf footprinting

−500 −400 −300 −200 −100 100 200 300 400 500

0.5

1.0

1.5


Leaf: 75 Leaf: 38

SORLREP2

Identification of key promoter motifs involved in the network of light-regulated gene expression by combined analysis of genomic sequence and microarray data.

Plant Physiology.133. 1605–1616. (2003)

573


1 2 3 4 5 6 7 8 9

Position

0

0.5

1

1.5

2

Info

rmation c

onte

nt

−500 −400 −300 −200 −100 100 200 300 400 500

0.5

1.0

1.5

2.0

Flower footprinting

Leaf footprinting

−500 −400 −300 −200 −100 100 200 300 400 500

0.5

1.0

1.5

2.0

Leaf: 158 Leaf: 69

SORLREP4

Identification of key promoter motifs involved in the network of light-regulated gene expression by combined analysis of genomic sequence and microarray data.

Plant Physiology.133. 1605–1616. (2003)

432


1 2 3 4 5 6 7 8 9

Position

0

0.5

1

1.5

2

Info

rmation c

onte

nt

−500 −400 −300 −200 −100 100 200 300 400 500

0.5

1.0

1.5

Flower footprinting

Leaf footprinting

−500 −400 −300 −200 −100 100 200 300 400 500

0.5

1.0

1.5

Leaf: 104 Leaf: 42


dnase-seq data correlation among different biological genome … · 2012-06-19 · supplemental...

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