Supplementary Information
Histone modifications are associated
with transcript isoform diversity in normal and cancer cells
Ondrej Podlaha1, Subhajyoti De2,3,4, Mithat Gonen5, and Franziska Michor1*
1Department
of Biostatistics and Computational Biology, Dana-Farber Cancer Institute,
and Department of Biostatistics, Harvard School of Public Health, Boston, MA 02215, USA.
2Department of Medicine, University of Colorado School of Medicine, Aurora, CO 80045, USA.
3Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO
80045, USA. 4Molecular Oncology Program, University of Colorado Cancer Center, Aurora, CO
80045, USA. 5Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer
Center, New York, NY 10065, USA. *Author for correspondence. Department of Biostatistics and
Computational Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215,
USA. Tel: 617 643 5045. Fax: 617 632 2444. Email: michor@jimmy.harvard.edu.
*Author
for correspondence.
0.19414
0.20887
0.21417
0.20439
0.22092
0.2197
0.20944
0.1689
0.18625
0.19439
0.19874
0.19932
0.19623
0.18684
0.18261
0.19586
0.19913
0.196
0.18104
0.1809
0.18183
0.06013
0.02652
-0.0103
-0.0042
0.03215
0.0492
0.06678
0.18245
0.19155
0.20042
0.1997
0.18191
0.18299
0.17865
-0.0931
-0.0849
-0.0807
-0.0637
-0.067
-0.0749
-0.077
0.18285
0.17339
0.1458
0.11141
0.17047
0.18304
0.18827
0.10298
0.13896
0.15884
0.15922
0.15337
0.14385
0.1176
Ct
az
H2
H3
0.13219
0.06034
0.01543
0.00439
0.05415
0.09123
0.13604
cf
e2
e3
k7
9m
e3
k3
6m
H3
k2
7m
H3
0.0018
-0.0333
-0.0551
-0.0508
-0.053
-0.0506
-0.0458
k2
7a
H3
-0.0936
-0.0884
-0.0834
-0.07
-0.0709
-0.0798
-0.0825
c
e1
k2
0m
e3
k9
m
e1
k9
m
H3
k9
ac
e3
H3
k4
m
e2
H3
k4
m
H3
k4
m
H3
0.17302
0.1763
0.15372
0.12824
0.1946
0.19834
0.18888
H4
Average of Fisher
Transformed Spearman
rank correlations for
normal cells
Distance
from exon
-5kb
-2kb
-1kb
0kb
+1kb
+2kb
+5kb
H3
lincRNA TSSIR
e1
Table S1. Association between the transcription start site inclusion rate (TSSIR) of
lincRNAs and histone modification enrichment in normal cell lines. We analyzed six
normal human cell lines (Gm12878, Hsmm, Huvec, H1hesc, Nhek, Nhlf) for the
associations between the transcription start site inclusion rate (TSSIR) and histone
modification enrichment for lincRNAs. Values represent the average of Fisher
transformed Spearman rank correlations to enable direct comparison. Coefficients are
color-coded, with red representing increasingly negative and green representing
increasingly positive correlation. Distance from exon categories signifies a region
relative to a given exon where histone enrichment was measured. 0kb represents a
region within given exon boundaries, and 1kb, 2kb, and 5kb signify regions from the
exon boundary either upstream (negative) or downstream (positive).
0.10297
0.11261
0.11568
0.08318
0.08444
0.07837
0.06618
Ct
cf
H2
az
e2
e3
H3
k7
9m
H3
k3
6m
e3
H3
k2
7m
H3
k2
7a
c
e1
H4
k2
0m
e3
H3
k9
m
e1
H3
k9
m
H3
k9
ac
e3
H3
k4
m
e2
k4
m
k4
m
H3
Average of Fisher
Transformed Spearman
rank correlations for
cancer cells
Distance
from exon
-5kb
-2kb
-1kb
0kb
+1kb
+2kb
+5kb
H3
Protein coding
Splicing
e1
Table S2. Association between splicing exon inclusion rate (SEIR) of protein coding
genes and histone modifications in cancer cell lines. We analyzed three cancer cell lines
(Hepg2, Helas3, K562) for associations between splicing exon inclusion rate (SEIR) and
histone modification enrichment for protein coding genes. Values represent the average
of Fisher transformed Spearman rank correlations to enable direct comparison.
Coefficients are color-coded, with red representing increasingly negative and green
representing increasingly positive correlation. Distance from exon categories signifies a
region relative to a given exon where histone enrichment was measured. 0kb represents
region within given exon boundaries, and 1kb, 2kb, and 5kb signify regions from the
exon boundary either upstream (negative) or downstream (positive).
-0.1264
-0.1204
-0.0688
-0.1399
-0.159
-0.1433
-0.0498
-0.2367
-0.2231
-0.1773
-0.2532
-0.2615
-0.2579
-0.1907
-0.2353
-0.223
-0.1839
-0.2437
-0.2501
-0.2515
-0.1958
-0.1345
-0.1065
-0.0591
-0.1475
-0.1351
-0.112
-0.174
0.15088
0.16649
0.17715
0.13425
0.13922
0.14339
0.06073
-0.0553
-0.0666
-0.0887
-0.0555
-0.0551
-0.0692
-0.0396
0.07855
0.09038
0.09863
0.01208
0.00976
0.01514
0.00168
-0.1433
-0.1157
-0.0679
-0.1531
-0.1376
-0.1094
-0.1384
-0.2172
-0.2291
-0.243
-0.2317
-0.2432
-0.2588
-0.1557
0.33112
0.32191
0.3049
0.38082
0.36847
0.33757
0.28785
0.02958
0.05967
0.10801
-0.0347
-0.0212
0.00058
-0.0229
-0.2238
-0.2192
-0.1921
-0.225
-0.2353
-0.2356
-0.2164
-0.1341
-0.117
-0.0894
-0.1223
-0.1076
-0.0802
-0.1099
lincRNA TSSIR
Average of Fisher
Transformed Spearman
rank correlations for
cancer cells
0.18236
0.18136
0.15496
0.12096
0.19572
0.20292
0.20012
0.18413
0.19889
0.20463
0.20517
0.2186
0.21546
0.21656
0.18131
0.19575
0.20116
0.20588
0.20999
0.20723
0.20768
0.19036
0.20194
0.20348
0.20127
0.20923
0.20741
0.20573
0.03933
0.03041
-0.001
-0.0046
0.00853
0.0248
0.03642
-0.0621 0.0378 0.20156
-0.0472 0.01576 0.21458
-0.0427 -0.0178 0.21322
-0.0218 -0.0172 0.20345
-0.0474 -0.0354 0.21293
-0.0656 -0.0328 0.20882
-0.0629 -0.0132 0.20996
-0.0733
-0.0479
-0.0429
-0.0293
-0.0502
-0.0676
-0.0795
0.15204
0.0921
0.02366
0.01656
0.07038
0.11181
0.15723
0.17973
0.16921
0.15336
0.12869
0.17467
0.18386
0.19777
0.10571
0.14187
0.15004
0.14774
0.15045
0.13667
0.11818
cf
Ct
H2
az
e2
e3
k7
9m
H3
k3
6m
e3
H3
k2
7m
H3
H3
k2
7a
c
e1
k2
0m
e3
H4
k9
m
e1
H3
k9
m
H3
k9
ac
e3
H3
k4
m
e2
H3
k4
m
H3
H3
Distance
from exon
-5kb
-2kb
-1kb
0kb
+1kb
+2kb
+5kb
k4
m
e1
Table S3. Association between transcription start site inclusion rate (TSSIR) of
lincRNAs and histone modification enrichment in cancer cell lines. We analyzed three
cancer cell lines (Hepg2, Helas3, K562) for associations between transcription start site
inclusion rate (TSSIR) and histone modification enrichment for lincRNAs. Values
represent the average of Fisher transformed Spearman rank correlations to enable
direct comparison. Coefficients are color-coded, with red representing increasingly
negative and green representing increasingly positive correlation. Distance from exon
categories signify region relative to a given exon where histone enrichment was
measured. 0kb represents region within given exon boundaries, and 1kb, 2kb, and 5kb
signify regions from the exon boundary either upstream (negative) or downstream
(positive).
0.1007
0.11348
0.1186
0.08401
0.08887
0.07812
0.07658
lincRNA Splicing
Average of Fisher
Transformed Spearman
rank correlations for
cancer cells
0.07083
0.05181
0.04643
0.04437
0.04117
0.05316
0.05464
0.04938
0.02422
0.01278
0.01107
0.01633
0.02978
0.02587
0.04611
0.02366
0.00786
0.00734
0.0091
0.01871
0.02135
0.0469 -0.0376
0.02734 -0.0216
0.01699 -0.0043
0.00202 -0.0154
0.01646 -0.0073
0.03418 0.00309
0.03263 -0.0077
-0.0029
0.00367
0.00968
0.00065
-0.0015
0.00943
-8E-08
-0.0234
-0.0289
-0.0146
-0.0057
-0.0134
-0.0066
-0.0058
0.06169
0.03241
0.0202
0.03141
0.02087
0.03846
0.04028
-0.0438
-0.0438
-0.0382
-0.0344
-0.0485
-0.0411
-0.0425
0.06375
0.04163
0.05165
0.06258
0.05638
0.07357
0.07824
Ct
cf
e2
az
H2
H3
k7
9m
e3
H3
k3
6m
e3
k2
7m
H3
H3
k2
7a
c
e1
k2
0m
H4
e3
H3
k9
m
e1
k9
m
H3
k9
ac
H3
e3
H3
k4
m
e2
k4
m
H3
H3
Distance
from exon
-5kb
-2kb
-1kb
0kb
+1kb
+2kb
+5kb
k4
m
e1
Table S4. Association between splicing exon inclusion rate (SEIR) of lincRNAs and
histone modifications in cancer cell lines. We analyzed three cancer cell lines (Hepg2,
Helas3, K562) for associations between splicing exon inclusion rate (SEIR) and histone
modification enrichment for protein coding genes. Values represent the average of
Fisher transformed Spearman rank correlations to enable direct comparison.
Coefficients are color-coded, with red representing increasingly negative and green
representing increasingly positive correlation. Distance from exon categories signifies a
region relative to a given exon where a histone enrichment was measured. 0kb
represents region within given exon boundaries, and 1kb, 2kb, and 5kb signify regions
from the exon boundary either upstream (negative) or downstream (positive).
0.05791 0.02593 0.01036
0.04083 0.00101 -0.0055
0.03466 -0.0096 -0.0103
0.0134 -0.0391 -0.0115
0.02072 -0.0205 -0.0056
0.04411 -0.0006 0.00556
0.0518 -0.0043 0.01127
Table S5. Association between histone modification enrichment and transcription
start site inclusion rate. Correlations between transcription start site inclusion rate or splicing
and enrichment of selected histone modifications in normal or cancer cell lines. The following
correlations and cell line categories are: (A) transcription start site switching and normal cell lines,
(B) splicing and normal cell lines, (C) transcription start site switching and cancer cell lines, and
(D) splicing and cancer cell lines. Black dots represent median Spearman rank correlations
between exon inclusion rate and given histone marks. All correlation coefficients were
transformed using a Fisher’s transformation before plotting. Notches were calculated as
æ IQR ö
±1.58´ ç
÷ where IQR stands for inter quartile range and n for sample size. Distances from
è n ø
exon represent genomic blocks of a given size from exon start (upstream regions) or exon end
(downstream regions).
A
B
C
D
Table S6. Top 20 ontology categories enriched among 840 candidate genes that
showed a significant association between splicing exon inclusion rates and histone
modification enrichment.
GO term
GO:0048583
GO:0051716
GO:0044763
GO:0009966
GO:0050794
GO:0065007
GO:0007165
GO:0044767
GO:0023051
GO:0032502
GO:0010646
GO:0050789
GO:0048522
GO:1902531
GO:0051128
GO:0019222
GO:0044699
GO:0006928
GO:0048518
GO:0009987
Description
regulation of response to stimulus
cellular response to stimulus
single-organism cellular process
regulation of signal transduction
regulation of cellular process
biological regulation
signal transduction
single-organism developmental process
regulation of signaling
developmental process
regulation of cell communication
regulation of biological process
positive regulation of cellular process
regulation of intracellular signal transduction
regulation of cellular component organization
regulation of metabolic process
single-organism process
cellular component movement
positive regulation of biological process
cellular process
P-value
1.77E-10
2.53E-10
2.66E-10
5.79E-10
1.57E-09
3.93E-09
4.47E-09
4.93E-09
9.31E-09
1.13E-08
1.34E-08
1.34E-08
2.30E-08
4.11E-08
6.87E-08
7.50E-08
1.69E-07
2.00E-07
2.37E-07
2.57E-07
FDR q-value
2.11E-06
1.51E-06
1.05E-06
1.72E-06
3.74E-06
7.79E-06
7.60E-06
7.33E-06
1.23E-05
1.35E-05
1.45E-05
1.33E-05
2.10E-05
3.49E-05
5.45E-05
5.58E-05
1.19E-04
1.33E-04
1.49E-04
1.53E-04
Table S7. Leave-one-out cross validation summary statistics.
Validation
cell line
Gm12878
H1hesc
Hsmm
Huvec
Nhek
Nhlf
Helas3
Hepg2
K562
Mono
Hmec
Total Number Of
Genes
29354
29354
29354
29354
29354
29354
29354
29354
29354
29354
29354
Number of Genes
Assigned to
Categories
2750
2745
2770
2696
2753
2786
2357
2720
2707
2519
2792
Number of
Significant Genes
686
660
665
652
667
687
455
684
672
654
669
Number of
Significant Cancer
Genes
26
23
29
25
23
27
15
21
21
22
29
Module S1. Epigenetically aberrant regions in three cancer cell lines are enriched for
oncogenes. Using the cancer gene consensus from COSMIC, we tested for oncogene
enrichment in epigenetically aberrant regions of three cancer cell lines (Helas3, Hepg2,
and K562) with regard to specific histone marks using the hypergeometric test. All p
e2
H2
az
9m
e3
H3
k7
6m
e3
H3
k3
c
7a
7m
H3
k2
e1
H3
k2
0m
m
e3
H4
k2
H3
k9
ac
e3
H3
k9
m
e2
H3
k4
m
H3
k4
CellLine
Helas3 0.06855 0.0916 0.0058 0.0231 0.0231 0.0231 0.0054 0.0684 0.8893 0.0003 3E-06 0.0054
Hepg2 0.00181 0.3192
0.61 0.0085 0.3566 NA
0.0003 0.3216 0.644 0.0018 0.0002 0.2707
K562 0.63255 0.0922 0.2228 0.0052 0.0052 0.9498 0.0922 0.0922 0.6325 0.0922 4E-05 0.6325
Ct
Hypergeometric
test p value
H3
k4
cf
m
e1
values were corrected for multiple testing (FDR). Green highlights significantly enriched
marks at the 5% FDR level.