DNase l-hypersensitive sites inthe chromatin of rat growth hormone ...
DNase-seq data correlation among different biological genome … · 2012-06-19 · Supplemental...
Transcript of 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 Data. Zhang et al. (2012). Plant Cell 10.1105/tpc.111.098061
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 Data. Zhang et al. (2012). Plant Cell 10.1105/tpc.111.098061
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 Data. Zhang et al. (2012). Plant Cell 10.1105/tpc.111.098061
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 Data. Zhang et al. (2012). Plant Cell 10.1105/tpc.111.098061
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).
Supplemental Data. Zhang et al. (2012). Plant Cell 10.1105/tpc.111.098061
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.
Supplemental Data. Zhang et al. (2012). Plant Cell 10.1105/tpc.111.098061
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
Flower: 544 Flower: 132
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
ATHB2 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)
4388
Flower: 802 Flower: 230
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
ATHB5 binding site motif
DNA-binding and dimerization preferences of Arabidopsis homeodomain-leucine zipper transcription factors in vitro
Plant Mol Biol 45: 63-73 (2001)
2372
Flower: 720 Flower: 188
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
ATHB6 binding site motif
Homeodomain protein ATHB6 is a target of the protein phosphatase ABI1 and regulates hormone responses in Arabidopsis
EMBO J. 21:3029-3038 (2002)
1369
Flower: 330 Flower: 88
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
Flower: 1819 Flower: 460
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
Flower: 2237 Flower: 653
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
Leaf: 2194 Leaf: 680
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
Flower: 52 Flower: 24
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
Flower: 1648 Flower: 535
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: 1599 Leaf: 587
Supplemental Data. Zhang et al. (2012). Plant Cell 10.1105/tpc.111.098061
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
Flower: 229 Flower: 90
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
Flower: 701 Flower: 205
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
Flower: 23362 Flower: 5974
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
Flower: 835 Flower: 273
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
Flower: 1332 Flower: 444
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
Leaf: 1267 Leaf: 399
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
Flower: 588 Flower: 200
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
Flower: 1286 Flower: 327
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: 1208 Leaf: 319
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
Flower: 3780 Flower: 1130
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
Flower: 145 Flower: 65
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
Supplemental Data. Zhang et al. (2012). Plant Cell 10.1105/tpc.111.098061
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
Flower: 45 Flower: 19
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
Flower: 6452 Flower: 1696
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
Flower: 3430 Flower: 1072
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
Bellringer/replumless/pennywise BS2 IN AG
Repression of AGAMOUS by BELLRINGER in Floral and Inflorescence Meristems
Plant Cell 16: 1478-1489 (2004)
5202
Flower: 962 Flower: 243
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: 1069 Leaf: 279
Bellringer/replumless/pennywise BS3 IN AG
Repression of AGAMOUS by BELLRINGER in Floral and Inflorescence Meristems
Plant Cell 16: 1478-1489 (2004)
5202
Flower: 962 Flower: 243
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: 1069 Leaf: 279
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
Flower: 137 Flower: 57
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
Flower: 95 Flower: 30
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
Supplemental Data. Zhang et al. (2012). Plant Cell 10.1105/tpc.111.098061