4 male, 4 female LCLs HumanChimpanzeeRhesus Macaque Expression: RNAseq Active Gene Marks: Pol II...
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4 male, 4 female LCLs Human Chimpanzee Rhesus Macaque Expression : RNAseq Active Gene Marks: Pol II (ChIPseq) H3K4me3 (ChIPseq) Repressed Region Mark: H3K27me3 (ChIPseq) Enhancer Marks: H3K4me1 (ChIPseq) H3K27ac (ChIPseq) 5 male, 3 female LCLs 6 male, 2 female LCLs 3 Species 8 Samples per species RNAseq+ 5 ChIPseq S1. An illustration of the study design
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Transcript of 4 male, 4 female LCLs HumanChimpanzeeRhesus Macaque Expression: RNAseq Active Gene Marks: Pol II...
4 male, 4 female LCLs
Human Chimpanzee Rhesus Macaque
Expression:
RNAseq
Active Gene Marks:
Pol II (ChIPseq)
H3K4me3 (ChIPseq)
Repressed Region Mark:
H3K27me3 (ChIPseq)
Enhancer Marks:
H3K4me1 (ChIPseq)
H3K27ac (ChIPseq)
5 male, 3 female LCLs 6 male, 2 female LCLs
3 Species
8 Samplesper species
RNAseq+5 ChIPseq
Figure S1. An illustration of the study design
Figure S2. Choices of cutoffs for classifying regions as enriched
H3K4me1 H3K4me3
H3K27ac H3K27me3
PolII RNA
Figure S3. Pairwise Spearman’s rank correlations between individuals from the three primates for four histone marks, Pol II and RNA
H
C
R
H
C
R
H
C
R
Figure S4. Fold enrichment of the five marks in regions near TSSs in three primates
ChimpanzeeHuman Rhesus Macaque
ChimpanzeeHuman Rhesus Macaque
Fo
ld E
nri
ch
me
nt,
TS
S +
/- 1
0 k
bF
old
En
ric
hm
en
t, T
SS
+/-
50
kb
A
B
H3K27ac H3K27me3H3K4me1 H3K4me3 Pol II
-0.4 0.0 0.3 0.7 1.0
Chimpanzee Human Rhesus Macaque
Figure S5. Pairwise Spearman’s rank correlations between marks in each of the three primates
Figure S6. Mark enrichment levels are correlated with gene expression levels in chimpanzee
R2
Sc
ale
d E
nri
ch
me
nt
Le
ve
lE
nri
ch
me
nt
Le
ve
l
Low Expressed Medium Expressed High Expressed
Distance to TSS (kb) Distance to TSS (kb) Distance to TSS (kb)
Gene Expression Level TSS +/- 2kb TSS +/- 10kb TSS +/- 50kb
marginal marginal + interactionsH3K27ac H3K27me3H3K4me1 H3K4me3 Pol II
Figure S7. Mark enrichment levels are correlated with gene expression levels in rhesus macaque
R2
Sc
ale
d E
nri
ch
me
nt
Le
ve
lE
nri
ch
me
nt
Le
ve
l
Low Expressed Medium Expressed High Expressed
Distance to TSS (kb) Distance to TSS (kb) Distance to TSS (kb)
Gene Expression Level TSS +/- 2kb TSS +/- 10kb TSS +/- 50kb
marginal marginal + interactionsH3K27ac H3K27me3H3K4me1 H3K4me3 Pol II
ChimpanzeeHuman Rhesus Macaque
TS
S +
/- 1
0 k
bT
SS
+/-
50
kb
Sc
ale
d E
nri
ch
me
nt
Le
ve
lS
ca
led
En
ric
hm
en
t L
ev
el
Figure S8. Mark enrichment levels are plotted against gene expression levels for sliding windows of genes ordered by increasing expression levels in the three primates
Gene Expression LevelGene Expression Level Gene Expression Level
H3K27ac H3K27me3H3K4me1 H3K4me3 Pol II
Pre
dic
ted
Ge
ne
Ex
pre
ss
ion
Le
ve
l
True Gene Expression Level
Figure S9. Scatterplot of predicted gene expression levels against true gene expression levels for all analyzed genes in human
H3K27ac H3K27me3H3K4me1 H3K4me3 Pol II marginal
H3K4me1 H3K27ac Pol II
H3K4me3 H3K27me3 H C R
Posterior Inclusion Probability
0.0 0.2 0.5 0.8 1.0
Figure S10. Importance of the marginal and first-order interaction effects from the five marks for explaining gene expression levels in the three primates
Marginal and Interaction Terms
FDR < 2.5%
FDR < 7.5%
FDR < 10%
Figure S11. TSS regions associated with inter-species differences in enriched marks are enriched for differentially expressed (DE) genes
H vs C H vs R C vs R
Fo
ld E
nri
ch
me
nt
of
TS
S A
ss
oc
iate
d w
ith
In
ter-
Sp
ec
ies
Ma
rk D
iffe
ren
ce
s i
n D
E G
en
es
H3K27ac H3K27me3H3K4me1 H3K4me3 Pol II
Figure S12. An example of mark abundance and gene expression levels across three species
EENSG00000076043, REX02
Hu
ma
n
H3K27ac H3K27me3H3K4me1 H3K4me3 Pol IIRNA Input
Rh
es
us
Ma
ca
qu
eC
him
pa
nze
e
Figure S13. Differences in mark enrichment level plotted against differences in gene expression level for sliding windows of genes ordered by increasing differences in expression level
TSS +/- 50 kb
Sc
ale
d D
iffe
ren
ce
in
E
nri
ch
me
nt
Le
ve
l
Difference in Gene Expression Level
H vs R C vs R
TSS +/- 10 kb
H vs C
Sc
ale
d D
iffe
ren
ce
in
E
nri
ch
me
nt
Le
ve
l
Difference in Gene Expression Level
H3K27ac H3K27me3H3K4me1 H3K4me3 Pol II
FDR < 10%
FDR < 7.5%
FDR < 2.5%
Figure S14. R squared by mark enrichment level differences for all pairwise comparisons among the three primates
marginal marginal + interactions
R2
H vs C H vs R C vs R
H3K27ac H3K27me3H3K4me1 H3K4me3 Pol II
Figure S15. Scatterplot of predicted gene expression level differences plotted against true gene expression level differences for DE genes between human and chimpanzee
Pre
dic
ted
Ge
ne
Ex
pre
ss
ion
Dif
fere
nc
e
True Gene Expression Difference
H3K27ac H3K27me3H3K4me1 H3K4me3 Pol II marginal
Figure S16. Scatterplot of gene expression level differences plotted against sequence conservation and divergence for DE genes
Dif
fere
nc
e i
n G
en
e E
xp
res
sio
n L
ev
el
H vs R C vs RH vs C
Figure S17. R squared by four histone modifications and Pol II or by four histone modifications alone
H vs C H vs R C vs R
w/o Pol II FDR < 5%
A
C
R2
in P
ol
II
w/ Pol II
R2
in R
NA
H vs C H vs R C vs R
w/o Pol II
w/ Pol II
H C RH C R
R2
in P
ol
II
R2
in R
NA
B
D
marginal marginal + interactions
H3K27ac H3K27me3H3K4me1 H3K4me3
