Supplementary Text ——— Environmental Perturbations Lead to Extensive Directional Shifts in RNA Processing

Supplementary text ——— Environmental perturbations lead to extensive directional shifts in RNA processing

A. L. Richards1,†, D. Watza1, A. Findley1, A. Alazizi1, X. Wen2, A. A. Pai3,†, R. Pique-Regi1,4,†, F. Luca1,4,†

1Center for Molecular Medicine and Genetics, Wayne State University 2Department of Biostatistics, University of Michigan 3Department of Biology, Massachusetts Institute of Technology 4Department of Obstetrics and Gynecology, Wayne State University

†To whom correspondence should be addressed: ﬂ[email protected], [email protected], [email protected], [email protected] April 26, 2017

1 1 Supplementary Figures and Tables

Treatment Code Full Treatment Name Treatment Name HUVEC LCL Mel PBMC SMC CO1 Media (Water) CO1 X X X X X CO2 Ethanol CO2 X X X X X CO3 DMSO CO3 X T2C1 Biotin Vitamin H X T3C1 Niacin (Nicotinic acid) Vitamin B3 X T4C1 Panthothenic acid Vitamin B5 X X T5C1 Vitamin B6 Vitamin B6 X X T6C1 Retinoic Acid Vitamin A X X X X X T7C1 Vitamin E Vitamin E X X T9C1 Aldosterone Aldosterone X T12C1 Dexamethasone Dexamethasone X X X X X T13C1 Caffeine Caffeine X X X X X T14C1 Nicotine Nicotine X T15C1 Copper (Copper (II) Chloride) Copper X X T16C1 Iron (Iron (III) Chloride)(5mM) Iron (C1) X T18C1 Molybdenum (Molybdenum (V) Chloride) Molybdenum X X X T19C1 Selenium (Sodium Selenite) Selenium X X X X T20C1 Zinc (Zinc Chloride) Zinc X T21C1 Tunicamycin Tunicamycin X T23C1 Vitamin D Vitamin D X X X X T24C1 Acrylamide Acrylamide X X X T25C1 Benzophenone-3 (BP-3) BP-3 X X T26C1 Bisphenol A (BPA) BPA X X T27C1 Cadmium Cadmium X X T29C1 Perfluorooctanoic Acid (Nonstick Cookware) PFOA X X T30C1 Triclosan (Disinfectant) Triclosan X X X T33C1 Insulin Insulin X X X T37C1 Acetylcholine Acetylcholine X T40C1 Butylated HydroxyAnisole BHA X X X T41C1 Ibuprofen (NSAID) Ibuprofen X T42C1 Acetaminophen (NSAID) Acetaminophen X X X T43C1 Aspirin (NSAID) Aspirin X X X X X T44C1 Loratadine (Allergy) Loratadine X X T45C1 Cetirizine (Allergy) Cetirizine X T47C1 Mono-n-butyl Phthalate Phthalate X X X X

Table S1: List of 89 Environments Analyzed for RNA Processing Events. Cellular environments are deﬁned by combinations of 5 cell types, 32 treatments and 3 controls.

2 Figure S1: Color legend for treatments. This is a ﬁgure depicting the colors that are used to denote each of the 32 treatments throughout the manuscript.

3 Alternative p-value Subcategory Subcategory Expected Observed Enrichment (FDR) Name intracellular GO:0005622 2288.25 2442 9.60E-12 up nucleus GO:0005634 1082.89 1244 1.26E-10 up intracellular part GO:0044424 2224.95 2373 1.40E-10 up organelle GO:0043226 1905.38 2061 5.47E-10 up intracellular organelle GO:0043229 1902.97 2059 5.47E-10 up RNA binding GO:0003723 175.093 246 1.20E-08 up protein binding GO:0005515 1686.26 1834 1.33E-08 up nucleobase, nucleoside, nucleotide GO:0006139 875.12 1006 4.37E-08 up and nucleic acid metabolic process membrane-bounded organelle GO:0043227 1738.54 1877 1.39E-07 up intracellular membrane-bounded GO:0043231 1737.17 1875 1.53E-07 up organelle organelle organization GO:0006996 339.866 428 1.63E-07 up cellular metabolic process GO:0044237 1518.39 1657 1.63E-07 up cellular nitrogen compound GO:0034641 929.127 1054 3.35E-07 up metabolic process cellular macromolecule metabolic GO:0044260 1191.59 1324 3.35E-07 up process cellular process GO:0009987 2252.47 2371 3.88E-07 up gene expression GO:0010467 764.01 880 4.85E-07 up cellular component organization GO:0016043 603.709 706 2.06E-06 up nitrogen compound metabolic GO:0006807 947.703 1064 3.35E-06 up process intracellular organelle part GO:0044446 1079.8 1200 3.35E-06 up organelle part GO:0044422 1092.18 1212 3.72E-06 up nucleic acid binding GO:0003676 624.693 723 8.76E-06 up binding GO:0005488 2363.58 2465 9.86E-06 up nucleic acid metabolic process GO:0090304 761.946 863 2.62E-05 up regulation of cellular metabolic GO:0031323 715.163 812 4.49E-05 up process regulation of primary metabolic GO:0080090 680.764 775 5.46E-05 up process regulation of metabolic process GO:0019222 753.002 850 6.06E-05 up nucleotide binding GO:0000166 497.071 580 6.66E-05 up nuclear part GO:0044428 473.335 554 7.94E-05 up cytoplasm GO:0005737 1629.84 1740 8.22E-05 up regulation of macromolecule GO:0060255 661.5 752 9.97E-05 up metabolic process macromolecule metabolic process GO:0043170 1283.1 1390 0.000125 up non-membrane-bounded organelle GO:0043228 565.87 650 0.000134 up intracellular non-membrane- GO:0043232 565.87 650 0.000134 up bounded organelle primary metabolic process GO:0044238 1537.65 1645 0.000141 up cellular biosynthetic process GO:0044249 851.041 946 0.000198 up

4 Alternative p-value Subcategory Subcategory Expected Observed Enrichment (FDR) Name cellular macromolecule GO:0034645 697.619 784 0.000377 up biosynthetic process regulation of cellular protein GO:0032268 132.438 175 0.000379 up metabolic process biosynthetic process GO:0009058 869.616 961 0.000478 up cellular protein metabolic process GO:0044267 563.806 642 0.000535 up posttranscriptional regulation of GO:0010608 55.383 83 0.000547 up gene expression metabolic process GO:0008152 1674.22 1773 0.000639 up histone deacetylation GO:0016575 5.84789 15 0.000751 up chromatin organization GO:0006325 90.8144 125 0.000767 up macromolecule biosynthetic GO:0009059 710.347 793 0.000846 up process regulation of gene expression GO:0010468 560.71 636 0.000961 up transcription factor binding GO:0008134 123.494 162 0.001161 up translation GO:0006412 97.0062 131 0.001395 up chromosome organization GO:0051276 122.118 160 0.001395 up response to stress GO:0006950 364.977 426 0.001729 up regulation of protein metabolic GO:0051246 149.981 191 0.001729 up process regulation of protein ubiquitination GO:0031396 33.7114 54 0.001759 up regulation of organic acid transport GO:0032890 3.43994 10 0.002049 up cell death GO:0008219 270.723 323 0.002405 up negative regulation of metabolic GO:0009892 184.037 228 0.002405 up process death GO:0016265 270.723 323 0.002405 up chromatin modification GO:0016568 81.8705 112 0.002433 up cell cycle GO:0007049 238.732 288 0.002436 up negative regulation of GO:0010605 173.373 216 0.002436 up macromolecule metabolic process regulation of nitrogen compound GO:0051171 568.278 639 0.002482 up metabolic process regulation of cellular process GO:0050794 1204.67 1293 0.002509 up negative regulation of protein GO:0031397 22.7036 39 0.002558 up ubiquitination regulation of nucleobase, nucleoside, nucleotide and nucleic GO:0019219 563.806 633 0.003159 up acid metabolic process regulation of biological process GO:0050789 1263.49 1351 0.003159 up protein amino acid deacetylation GO:0006476 7.56786 17 0.003473 up nuclear lumen GO:0031981 371.169 429 0.003671 up transcription regulator activity GO:0030528 281.731 333 0.003717 up regulation of macromolecule GO:0010556 543.854 611 0.003888 up biosynthetic process cytosol GO:0005829 315.442 369 0.003956 up 5 Alternative p-value Subcategory Subcategory Expected Observed Enrichment (FDR) Name heterogeneous nuclear GO:0030530 4.12793 11 0.004376 up ribonucleoprotein complex molecular_function GO:0003674 2764.68 2817 0.00461 up chromosome GO:0005694 112.83 146 0.00461 up translational elongation GO:0006414 24.7676 41 0.00461 up lysine N-methyltransferase activity GO:0016278 11.0078 22 0.00473 up protein-lysine N-methyltransferase GO:0016279 11.0078 22 0.00473 up activity histone-lysine N-methyltransferase GO:0018024 11.0078 22 0.00473 up activity regulation of biosynthetic process GO:0009889 563.462 630 0.004935 up RNA processing GO:0006396 145.165 182 0.005224 up regulation of cellular biosynthetic GO:0031326 560.022 626 0.005288 up process biological regulation GO:0065007 1328.16 1411 0.006572 up regulation of translation GO:0006417 33.0234 51 0.006864 up cell cycle process GO:0022402 160.301 198 0.006872 up transcription cofactor activity GO:0003712 84.9665 113 0.006881 up programmed cell death GO:0012501 249.051 295 0.006889 up mRNA binding GO:0003729 14.7917 27 0.007265 up double-stranded RNA binding GO:0003725 8.59984 18 0.007548 up apoptosis GO:0006915 246.644 292 0.007548 up histone methyltransferase activity GO:0042054 12.7278 24 0.00798 up positive regulation of cellular GO:0048522 417.952 474 0.009184 up process nucleobase, nucleoside and GO:0055086 113.862 145 0.009987 up nucleotide metabolic process protein methyltransferase activity GO:0008276 16.5117 29 0.010365 up negative regulation of cellular GO:0048523 378.049 431 0.010921 up process covalent chromatin modification GO:0016569 45.0632 65 0.011098 up negative regulation of cellular GO:0031324 168.213 205 0.011541 up metabolic process regulation of cell cycle GO:0051726 106.294 136 0.011616 up histone modification GO:0016570 44.3752 64 0.012068 up biological_process GO:0008150 2579.95 2638 0.012605 up cellular response to stimulus GO:0051716 235.636 278 0.012917 up response to protein stimulus GO:0051789 25.1115 40 0.012917 up cytoskeleton organization GO:0007010 117.302 148 0.013022 up proteolysis involved in cellular GO:0051603 85.6544 112 0.013917 up protein catabolic process nucleoside phosphate metabolic GO:0006753 108.702 138 0.014617 up process nucleotide metabolic process GO:0009117 108.702 138 0.014617 up protein metabolic process GO:0019538 638.108 701 0.015009 up 6 Alternative p-value Subcategory Subcategory Expected Observed Enrichment (FDR) Name protein metabolic process GO:0019538 638.108 701 0.015009 up regulation of cellular catabolic GO:0031329 52.2871 73 0.015009 up process cellular response to stress GO:0033554 166.493 202 0.015062 up negative regulation of biological GO:0048519 407.289 460 0.015062 up process positive regulation of biological GO:0048518 453.04 508 0.015159 up process ubiquitin-dependent protein GO:0006511 74.6466 99 0.015353 up catabolic process membrane organization GO:0061024 95.6303 123 0.015353 up cellular protein catabolic process GO:0044257 85.9984 112 0.015415 up transcription activator activity GO:0016563 96.6622 124 0.016192 up proteasomal ubiquitin-dependent GO:0043161 43.3432 62 0.016858 up protein catabolic process methyltransferase complex GO:0034708 14.7917 26 0.01719 up histone methyltransferase complex GO:0035097 14.7917 26 0.01719 up chromatin remodeling GO:0006338 14.1037 25 0.018331 up cellular membrane organization GO:0016044 95.2863 122 0.01881 up proteasomal protein catabolic GO:0010498 44.3752 63 0.018917 up process mRNA processing GO:0006397 80.4945 105 0.020165 up transcription GO:0006350 518.055 574 0.020779 up ribonucleotide binding GO:0032553 407.289 458 0.020779 up purine ribonucleotide binding GO:0032555 407.289 458 0.020779 up cytoskeletal part GO:0044430 187.821 224 0.020779 up response to biotic stimulus GO:0009607 78.0866 102 0.021864 up purine nucleotide binding GO:0017076 423.8 475 0.021992 up chromosomal part GO:0044427 92.1903 118 0.021992 up RNA metabolic process GO:0016070 516.679 572 0.02208 up transcription repressor activity GO:0016564 71.2067 94 0.02208 up ribonucleoprotein complex GO:0030529 123.494 153 0.02208 up cytoplasmic part GO:0044444 1116.26 1187 0.02208 up modification-dependent protein GO:0019941 75.6786 99 0.022912 up catabolic process protein catabolic process GO:0030163 97.6942 124 0.022912 up modification-dependent GO:0043632 75.6786 99 0.022912 up macromolecule catabolic process protein modification by small GO:0070647 91.5023 117 0.022912 up protein conjugation or removal negative regulation of ligase GO:0051352 18.9197 31 0.023935 up activity negative regulation of ubiquitin- GO:0051444 18.9197 31 0.023935 up protein ligase activity organelle lumen GO:0043233 452.352 504 0.024747 up 7 Alternative p-value Subcategory Subcategory Expected Observed Enrichment (FDR) Name histone deacetylase activity GO:0004407 4.12793 10 0.02505 up protein deacetylase activity GO:0033558 4.12793 10 0.02505 up response to unfolded protein GO:0006986 14.4477 25 0.02556 up nucleoplasm GO:0005654 237.356 276 0.027426 up regulation of transcription GO:0045449 493.287 546 0.027426 up negative regulation of ubiquitin- protein ligase activity involved in GO:0051436 17.5437 29 0.027426 up mitotic cell cycle regulation of catabolic process GO:0009894 60.5429 81 0.027878 up regulation of intracellular protein GO:0010627 73.6147 96 0.028092 up kinase cascade protein ubiquitination GO:0016567 73.6147 96 0.028092 up M phase of mitotic cell cycle GO:0000087 71.8947 94 0.028269 up macromolecular complex GO:0032991 672.164 731 0.028269 up N-methyltransferase activity GO:0008170 16.8557 28 0.02864 up organelle fission GO:0048285 72.9267 95 0.030187 up macromolecule modification GO:0043412 425.176 474 0.030826 up mRNA metabolic process GO:0016071 95.9743 121 0.030859 up Golgi apparatus GO:0005794 191.605 226 0.031185 up post-translational protein GO:0043687 351.218 396 0.032351 up modification positive regulation of cellular GO:0031325 199.172 234 0.032496 up metabolic process nuclear division GO:0000280 70.5187 92 0.032634 up mitosis GO:0007067 70.5187 92 0.032634 up RNA splicing GO:0008380 76.7106 99 0.033302 up nucleoside-triphosphatase GO:0060589 106.982 133 0.033302 up regulator activity intracellular organelle lumen GO:0070013 445.816 495 0.033302 up polysome GO:0005844 3.09594 8 0.036019 up regulation of ligase activity GO:0051340 23.3916 36 0.036302 up mitotic cell cycle GO:0000278 123.494 151 0.036472 up membrane-enclosed lumen GO:0031974 458.888 508 0.036817 up ATP binding GO:0005524 338.834 382 0.037558 up melanosome GO:0042470 27.5195 41 0.038419 up pigment granule GO:0048770 27.5195 41 0.038419 up regulation of molecular function GO:0065009 223.252 259 0.038419 up M phase GO:0000279 95.9743 120 0.040551 up GTPase regulator activity GO:0030695 104.918 130 0.040551 up regulation of catalytic activity GO:0050790 185.413 218 0.040551 up

8 Alternative p-value Subcategory Subcategory Expected Observed Enrichment (FDR) Name response to stimulus GO:0050896 606.117 660 0.040551 up adenyl ribonucleotide binding GO:0032559 343.306 386 0.041464 up microtubule organizing center GO:0005815 71.2067 92 0.041957 up muscle tissue development GO:0060537 32.6794 47 0.04449 up striated muscle tissue development GO:0014706 30.2715 44 0.046665 up adenyl nucleotide binding GO:0030554 359.129 402 0.046665 up nuclear speck GO:0016607 31.9914 46 0.048643 up

Table S2: Gene Ontology of Events that Signiﬁcantly Shift Following Environmental Perturbation. Genes that contained events that shifted in at least one environment were compared to genes that were tested but had no signiﬁcant event shift. Analysis was performed using GeneTrail [1].

9 A B ρ = 0.59, p < 0.001

ρ = 0.15, p = 0.02

Number Significant RNAProcessing of Shifts Number Significant RNAProcessing of Shifts

Library Coverage Number of Differentially Expressed Genes

Figure S2: Correlation of the Number of Significant Shifts in Events with Sequencing Coverage and Number of DEG. This is a two panel figure depicting the following: A) This plot indicates the read coverage for each library assessed for change in RNA processing events. The y-axis is the number of significant shifts for each library. Each point is a library and the color indicates the treatment for each sample. Spearman’s correlation and significance is indicated. B) Each point depicts the number of differentially expressed genes (x-axis) and the number of significant RNA processing event changes (y-axis). Each point is colored by the treatment.

10 A ALE in Iron B ALE in Selenium

● ● ● ρ = 0.27 ρ = -0.18 22 p < 0.01 p < 0.01

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0 ● ● ● ● ● ● ● ● ● ● Change in Gene in Change Change in Gene in Change ●● ● ● ● ● ● ● ● ● ● ● ● ●● ● ●● ● ● ● −1 ● ● ● ● ● ● ● ● ●

● ●● ● ● ● ● Expression ( Expression ( -1 ● ● ● ●● ● ●● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ●● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●●● ● ● ● ● ● ● ● ● ●●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● −2 ● -2 ● ● ●

● ●

● -1−1 ●●

−0.2 0.0 0.2 −0.50 −0.25 0.00 0.25 -0.2 0.00aveNewDPsi 0.2 -0.50 -0.25 aveNewDPsi0.00 0.25 Average ΔΨ Average ΔΨ

C SE in Vitamin D D AFE in Copper 0.80.8 ● ● ● ● ●● ρ = 0.21 ● ρ = -0.26

22 p < 0.01 p < 0.01 ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● 0.4 ● ● ● ● ● ● ● ● ● ● ● ●● ● ●●● ● 0.4 ● ●

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● ● ● ● ● ● g g ● ● ● ● ● ● ●● ● ● 0.0 ● ● ● ● ● ● ● ● ● ● 0.0 ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ●● ● ● ● ● ● ● ●● ● ● ●● ● ● ● ● ● ● ● ● ● Change in Gene in Change ● ● ● ● ● ● Gene in Change ● ● ● ● ● ● ● ● ●

Expression ( ● ● ● ● ● Expression ( ● ● ● ● ● ● ● −2 ● ● ● ● -2 ● ● ● ● ●● ● ●

● ●● ● ● ● ● ● ●● ●● ● ● ● ● ● ● ● −0.4 ● -0.4 ● ● ● ● ● ● ● ● ● ● ● ● ● ●

● ●

−0.50 −0.25 0.00 0.25 0.50 −0.2 0.0 0.2 -0.50 -0.25 aveNe0.0wDPsi 0.25 -0.50 -0.2 aveNe0.00wDPsi 0.2 Average ΔΨ Average ΔΨ

Figure S3: Examples of Correlation between Differential Gene Expression and Differential RNA Processing. These graphs show the correlation of gene expression changes and significant RNA processing shifts (using ∆Ψ) following various treatments. Each point represents one RNA processing shift in a given cell type, with treatment indicated above the graph. Specifically, A is a graph for genes with shifts in AFE usage following vitamin B6, B) shows genes with shifts in AFE following tunicamycin, C) shows genes with shifts in RI following caffeine exposure and D) shows genes with shifts in ALE usage following treatment with cadmium.

11 Treatment Spearman’s ρ p-value Type Vitamin D 0.146 0.0069 RI Loratadine 0.2513 0.0308 RI Aspirin -0.1883 0.0421 AFE Copper -0.2606 5.00E-04 AFE Caffeine -0.22 3.00E-04 AFE Selenium -0.0861 0.0336 AFE Cadmium -0.206 0.0187 AFE Iron -0.3228 1.00E-04 AFE Vitamin B3 -0.4707 0.0029 AFE Vitamin H -0.3888 0.0144 AFE Selenium -0.1817 1.00E-04 ALE Loratadine 0.1781 0.0469 ALE Iron 0.2711 0.0022 ALE Vitamin D 0.2114 < 0.001 SE Selenium -0.3211 0.0149 TandemUTR

Table S3: Table of Correlation between Differential Gene Expression and Differential RNA Processing. Spearman’s correlations were calculated between log-fold change in gene expression and ∆Ψ for genes containing significant shifts in RNA processing. Only treatments with p-value < 0.05 are reported here.

12 A B HUVEC Mel 1 1

v 0.10 D = 0.05 D = 0.09 Fn(x)

n p < 0.01 p < 0.01

f 0 0

n 0.05 -0.4 0.4 -0.4 0.4

i Proportion of of Proportion

o PBMC SMC Significant Events Significant

o 1 1

0.00

l C e C C E V ;M M M D = 0.34 D = 0.02 D B ;S Fn(x) U ;P D ;H in D D m in a in m p < 0.01 p = 0.59 in it m a m V a it a it V it V V Environments 0 0 -0.4 0.4 -0.4 0.4 Environments Δψ C D HUVEC Mel 1 1 0.008

n 0.006

e D = 0.02 D = 0.1 Fn(x)

p = 0.02 p < 0.01

g 0.004

S 0 0

o -0.4 0.4 -0.4 0.4

r Proportion of of Proportion

o 0.002 SMC

p Significant Events Significant

o 1

0.000

l C e C E ;M M D = 0.06 V S Fn(x) U lin ; H u lin ; s u lin In s p < 0.01 u n s I In Environments

0 Environments -0.4 0.4 Δψ

Figure S4: Examples of Different and Shared Directional Changes in RI Following Treatments. A) This plot indicates the direction of shifts for RI in the different cell types following exposure to vitamin D. The height of each bar shows the proportion of significant event shifts. A binomial test compares the proportion of significant events to the average across all environments. Each bar is then broken in two with the shaded region showing the proportion of the significant changes that shifted towards a positive ∆Ψ (inclusion of intron) while the white region of each bar is the proportion of sites with a negative ∆Ψ. If there is a significant departure from the expected 50:50 for positive to negative ∆Ψ (tested using a binomial test), the row of boxes shows this (red denotes enrichment for positive ∆Ψ, blue for negative ∆Ψ). B) These plots correspond to those in A and show the ECDF of the ∆Ψ across all event shifts, not just the significant event shifts. C) This plot is similar to A) but it shows the direction of shifts for AFE in various cell types responding to treatment with insulin (with positive ∆Ψ equating to inclusion of the upstream AFE). D) Corresponding ECDF plots to C) that show the ∆Ψ across all event shifts. Alternative Last Tandem UTR Aldosterone;SMC Aldosterone;SMC Dexamethasone;SMC Exon Dexamethasone;SMC Dexamethasone;PBMC Dexamethasone;PBMC Dexamethasone;Mel Dexamethasone;Mel Dexamethasone;LCL Dexamethasone;LCL Dexamethasone;HUVEC Dexamethasone;HUVEC Acetylcholine;PBMC Acetylcholine;PBMC Insulin;SMC Insulin;SMC Insulin;Mel Insulin;Mel Insulin;HUVEC Insulin;HUVEC Cadmium;PBMC Cadmium;PBMC Cadmium;LCL Cadmium;LCL Zinc;PBMC Zinc;PBMC Selenium;SMC Selenium;SMC Selenium;Mel Selenium;Mel Selenium;LCL Selenium;LCL Selenium;HUVEC Selenium;HUVEC Molybdenum;SMC Molybdenum;SMC Molybdenum;PBMC Molybdenum;PBMC Molybdenum;HUVEC Molybdenum;HUVEC Iron (C1);PBMC Iron (C1);PBMC Copper;PBMC Copper;PBMC Copper;LCL Copper;LCL Phthalate;PBMC Phthalate;PBMC Phthalate;Mel Phthalate;Mel Phthalate;LCL Phthalate;LCL Phthalate;HUVEC Phthalate;HUVEC BHA;PBMC BHA;PBMC BHA;Mel BHA;Mel BHA;HUVEC BHA;HUVEC Triclosan;SMC Triclosan;SMC Triclosan;Mel Triclosan;Mel Triclosan;HUVEC Triclosan;HUVEC PFOA;SMC PFOA;SMC

s PFOA;LCL

t BPA;SMC t

n BPA;SMC BPA;LCL n e BPA;LCL BP−3;SMC e BP−3;SMC

m BP−3;HUVEC m

n BP−3;HUVEC Acrylamide;SMC n o Acrylamide;SMC

Acrylamide;LCL r i Acrylamide;LCL

v Acrylamide;HUVEC

n Nicotine;PBMC n Nicotine;PBMC

E Vitamin E;PBMC E Vitamin E;PBMC Vitamin E;Mel Vitamin E;Mel Vitamin A;SMC Vitamin A;SMC Vitamin A;PBMC Vitamin A;PBMC Vitamin A;Mel Vitamin A;Mel Vitamin A;LCL Vitamin A;LCL Vitamin A;HUVEC Vitamin A;HUVEC Vitamin B6;SMC Vitamin B6;SMC Vitamin B6;PBMC Vitamin B6;PBMC Vitamin B5;SMC Vitamin B5;SMC Vitamin B5;PBMC Vitamin B5;PBMC Vitamin B3;PBMC Vitamin B3;PBMC Vitamin H;PBMC Vitamin H;PBMC Vitamin D;SMC Vitamin D;SMC Vitamin D;PBMC Vitamin D;PBMC Vitamin D;Mel Vitamin D;Mel Vitamin D;HUVEC Vitamin D;HUVEC Caffeine;SMC Caffeine;SMC Caffeine;PBMC Caffeine;Mel Caffeine;PBMC Caffeine;LCL Caffeine;Mel Caffeine;HUVEC Caffeine;LCL Cetirizine;LCL Caffeine;HUVEC Loratadine;Mel Cetirizine;LCL Loratadine;LCL Loratadine;Mel Aspirin;SMC Loratadine;LCL Aspirin;PBMC Aspirin;SMC Aspirin;Mel Aspirin;PBMC Aspirin;LCL Aspirin;Mel Aspirin;HUVEC Aspirin;LCL Acetaminophen;SMC Aspirin;HUVEC Acetaminophen;PBMC Acetaminophen;SMC Acetaminophen;Mel Acetaminophen;PBMC Ibuprofen;Mel Acetaminophen;Mel Tunicamycin;Mel Ibuprofen;Mel Tunicamycin;Mel 0 5 0 5 0 0 2 5 7 0 0 1 2 3 .0 .0 .0 .0 .1 .0 .0 .0 .0 0 0 0 0 0 0 0 0 0 ProportionPropor oftion Significant of Signficant Events Events ProportionPropor oftion Significant of Signficant Events Events

Figure S5: Additional Direction of Shift in Events Following Treatment. These plots indicate the direction of shift for 2 event types: ALE (left) and TandemUTR (Right). Each plot shows environments for which these events were tested and more than 10 significant events were identified. The height of each bar shows the proportion of significant event shifts for each environment. Each bar is then broken in two with the shaded region showing the proportion of the significant changes that shifted towards a positive ∆Ψ (inclusion longer UTR or downstream ALE) while the white region of each bar is the proportion of sites with a negative ∆Ψ. The column of boxes shows if there is a departure from the expected 50:50 for positive to negative ∆Ψ (tested using a binomial test). Red denotes enrichment for ∆Ψ > 0 and blue for ∆Ψ < 0).

14 Splicing Factor Gene Symbol BH FDR Spearman's ρ Splice Type ENSG00000075292 ZNF638 0.03507 0.390828 RI ENSG00000080802 CNOT4 0.028018 0.423203 RI ENSG00000092199 HNRNPC 0.037872 -0.38591 RI ENSG00000099995 SF3A1 0.028018 -0.44176 RI ENSG00000119314 PTBP3 0.033171 0.40685 RI ENSG00000122566 HNRNPA2B1 0.041666 0.379815 RI ENSG00000125970 RALY 0.026872 -0.46183 RI ENSG00000127054 CPSF3L 0.028018 -0.4304 RI ENSG00000136709 WDR33 0.041643 0.380642 RI ENSG00000147274 RBMX 0.037199 0.388232 RI ENSG00000149016 TUT1 0.041643 -0.44476 RI ENSG00000153914 SREK1 0.026238 0.479294 RI ENSG00000174720 LARP7 0.028018 0.441012 RI ENSG00000197111 PCBP2 0.03349 -0.39598 RI

Table S4: Correlation of Changes in Gene Expression of Splicing Factors and Proportion of RNA Processing Events. Log-fold changes in gene expression of 14 splicing factors is correlated to average ∆Ψ across three individuals for RI events.

15 Transcription Factor Gene Symbol BH FDR Spearman's ρ Splice Type ENSG00000005513 SOX8 0.030831 0.501961 AFE ENSG00000005801 ZNF195 0.007605 -0.40907 AFE ENSG00000005889 ZFX 0.003345 -0.44432 AFE ENSG00000007080 CCDC124 0.002938 0.448996 AFE ENSG00000009307 CSDE1 0.008942 -0.40056 AFE ENSG00000010818 HIVEP2 0.038052 -0.34782 AFE ENSG00000012504 NR1H4 0.042849 0.809091 AFE ENSG00000012817 KDM5D 0.045894 0.38035 AFE ENSG00000018869 ZNF582 0.045494 -0.32619 AFE ENSG00000029153 ARNTL2 0.013796 -0.477 AFE ENSG00000029363 BCLAF1 0.008431 -0.41378 AFE ENSG00000049618 ARID1B 0.002465 -0.51535 AFE ENSG00000050344 NFE2L3 0.015417 -0.37475 AFE ENSG00000055609 KMT2C 0.023405 -0.35314 AFE ENSG00000059728 MXD1 0.007176 -0.41184 AFE ENSG00000064933 PMS1 0.015919 -0.39857 AFE ENSG00000064961 HMG20B 0.00087 0.529545 AFE ENSG00000066827 ZFAT 0.011722 -0.4347 AFE ENSG00000067066 SP100 0.029784 -0.34067 AFE ENSG00000067646 ZFY 0.038455 -0.388 AFE ENSG00000068305 MEF2A 0.028748 -0.34245 AFE ENSG00000070444 MNT 0.024099 0.352026 AFE ENSG00000071564 TCF3 0.001062 0.529317 AFE ENSG00000071655 MBD3 0.000249 0.556077 AFE ENSG00000072310 SREBF1 0.003345 0.519896 AFE ENSG00000073614 KDM5A 0.049141 -0.31083 AFE ENSG00000074657 ZNF532 0.032216 -0.3384 AFE ENSG00000075407 ZNF37A 0.028599 0.420698 AFE ENSG00000077463 SIRT6 0.015729 0.378564 AFE ENSG00000077809 GTF2I 0.001436 -0.52524 AFE ENSG00000078900 TP73 0.00713 0.717391 AFE ENSG00000079432 CIC 0.001905 0.520348 AFE ENSG00000080298 RFX3 0.020701 -0.42354 AFE ENSG00000082258 CCNT2 0.002938 -0.44965 AFE ENSG00000083838 ZNF446 0.015997 0.443737 AFE ENSG00000085274 MYNN 0.026408 -0.34757 AFE ENSG00000085276 MECOM 0.010629 0.40234 AFE ENSG00000085644 ZNF213 0.01477 0.444893 AFE ENSG00000086065 CHMP5 0.01942 -0.3628 AFE ENSG00000087510 TFAP2C 0.035417 0.797203 AFE ENSG00000089902 RCOR1 0.011211 -0.38909 AFE ENSG00000090612 ZNF268 0.028292 -0.34611 AFE ENSG00000092203 TOX4 0.036846 0.336626 AFE ENSG00000095794 CREM 0.025756 -0.38082 AFE ENSG00000095951 HIVEP1 0.038052 -0.34524 AFE ENSG00000096401 CDC5L 0.003245 -0.44549 AFE ENSG00000099326 MZF1 0.011668 0.419113 AFE ENSG00000099364 FBXL19 0.001586 0.534916 AFE ENSG00000100219 XBP1 0.033326 0.33436 AFE ENSG00000100281 HMGXB4 0.046967 0.405822 AFE ENSG00000100644 HIF1A 0.043907 -0.31786 AFE 16 Transcription Factor Gene Symbol BH FDR Spearman's ρ Splice Type ENSG00000100811 YY1 0.001279 0.531399 AFE ENSG00000100968 NFATC4 0.002465 0.552615 AFE ENSG00000101126 ADNP 0.010482 -0.39345 AFE ENSG00000101412 E2F1 0.022173 0.38517 AFE ENSG00000102034 ELF4 0.024559 -0.36986 AFE ENSG00000103199 ZNF500 0.020424 0.392277 AFE ENSG00000103495 MAZ 0.002932 0.451107 AFE ENSG00000104064 GABPB1 0.037314 -0.34949 AFE ENSG00000104447 TRPS1 0.048605 -0.38015 AFE ENSG00000105663 KMT2B 0.033912 0.36624 AFE ENSG00000105698 USF2 0.008328 0.451146 AFE ENSG00000105722 ERF 0.001351 0.486706 AFE ENSG00000105732 ZNF574 0.001585 0.511275 AFE ENSG00000105750 ZNF85 0.041996 -0.37022 AFE ENSG00000105866 SP4 0.042677 -0.363 AFE ENSG00000105967 TFEC 0.023025 -0.47418 AFE ENSG00000108264 TADA2A 0.002091 -0.49579 AFE ENSG00000108509 CAMTA2 0.027316 0.370037 AFE ENSG00000109381 ELF2 0.038149 -0.33796 AFE ENSG00000109685 WHSC1 0.03288 0.3582 AFE ENSG00000110693 SOX6 0.028338 0.343604 AFE ENSG00000112242 E2F3 0.046827 -0.31401 AFE ENSG00000113658 SMAD5 0.031282 -0.35604 AFE ENSG00000114853 ZBTB47 0.008976 0.423476 AFE ENSG00000115568 ZNF142 0.001062 0.582849 AFE ENSG00000115816 CEBPZ 0.037385 -0.32671 AFE ENSG00000115966 ATF2 0.034645 -0.33134 AFE ENSG00000116044 NFE2L2 0.012098 -0.3854 AFE ENSG00000116731 PRDM2 0.025096 -0.39709 AFE ENSG00000116809 ZBTB17 0.020715 0.394011 AFE ENSG00000117010 ZNF684 0.048712 -0.36344 AFE ENSG00000117625 RCOR3 0.020481 -0.39479 AFE ENSG00000117713 ARID1A 0.036708 -0.37914 AFE ENSG00000118217 ATF6 0.009424 -0.39774 AFE ENSG00000118260 CREB1 0.027948 -0.37966 AFE ENSG00000118412 CASP8AP2 0.014896 -0.37656 AFE ENSG00000118620 ZNF430 0.019058 -0.40625 AFE ENSG00000119574 ZBTB45 0.001614 0.48575 AFE ENSG00000119725 ZNF410 0.004994 -0.42625 AFE ENSG00000120690 ELF1 0.012098 -0.38553 AFE ENSG00000120784 ZFP30 0.04937 0.457595 AFE ENSG00000121413 ZSCAN18 0.031219 0.386984 AFE ENSG00000122034 GTF3A 0.044177 -0.31736 AFE ENSG00000123636 BAZ2B 0.003556 -0.48811 AFE ENSG00000123933 MXD4 0.001108 0.500937 AFE ENSG00000124459 ZNF45 0.002938 -0.46008 AFE ENSG00000125520 SLC2A4RG 0.002938 0.460202 AFE ENSG00000125817 CENPB 0.008958 0.399904 AFE ENSG00000125846 ZNF133 0.015074 -0.37571 AFE ENSG00000125850 OVOL2 0.020629 -0.35873 AFE

17 Transcription Factor Gene Symbol BH FDR Spearman's ρ Splice Type ENSG00000125901 MRPS26 0.013655 0.387351 AFE ENSG00000126012 KDM5C 0.002938 0.461902 AFE ENSG00000126456 IRF3 0.002276 0.466144 AFE ENSG00000126561 STAT5A 0.011964 0.462959 AFE ENSG00000126603 GLIS2 0.005944 0.429916 AFE ENSG00000126767 ELK1 0.046827 0.31807 AFE ENSG00000127081 ZNF484 0.037864 -0.34586 AFE ENSG00000127528 KLF2 0.028055 0.38489 AFE ENSG00000129071 MBD4 0.004486 -0.43106 AFE ENSG00000129535 NRL 0.003556 0.537348 AFE ENSG00000129911 KLF16 0.003488 0.440371 AFE ENSG00000130522 JUND 0.007744 0.407972 AFE ENSG00000130726 TRIM28 0.033792 0.332969 AFE ENSG00000130816 DNMT1 0.049141 0.339824 AFE ENSG00000130856 ZNF236 0.025606 -0.41286 AFE ENSG00000131196 NFATC1 0.04893 0.515599 AFE ENSG00000131408 NR1H2 0.001585 0.480712 AFE ENSG00000132005 RFX1 0.020458 0.59768 AFE ENSG00000132010 ZNF20 0.04937 -0.33436 AFE ENSG00000132749 MTL5 0.037385 0.854545 AFE ENSG00000133250 ZNF414 0.013137 0.435869 AFE ENSG00000133794 ARNTL 0.027553 -0.35239 AFE ENSG00000134852 CLOCK 0.034472 -0.33174 AFE ENSG00000135164 DMTF1 0.012622 -0.38856 AFE ENSG00000135457 TFCP2 0.015161 -0.40642 AFE ENSG00000135747 ZNF670 0.020458 -0.40101 AFE ENSG00000136169 SETDB2 0.046392 -0.34139 AFE ENSG00000136997 MYC 0.003345 0.442837 AFE ENSG00000137309 HMGA1 0.047689 0.312937 AFE ENSG00000137492 PRKRIR 0.045689 -0.31535 AFE ENSG00000138336 TET1 0.038052 -0.36374 AFE ENSG00000139154 AEBP2 0.012984 -0.38249 AFE ENSG00000139624 CERS5 0.021556 -0.39228 AFE ENSG00000140262 TCF12 0.035417 -0.3301 AFE ENSG00000141510 TP53 0.020028 0.360803 AFE ENSG00000141644 MBD1 0.007176 0.436023 AFE ENSG00000141646 SMAD4 0.007176 -0.45472 AFE ENSG00000142409 ZNF787 0.000582 0.523847 AFE ENSG00000143178 TBX19 0.048029 -0.36123 AFE ENSG00000143373 ZNF687 0.004013 0.483531 AFE ENSG00000143799 PARP1 0.019722 0.36883 AFE ENSG00000144366 GULP1 0.022509 0.572875 AFE ENSG00000144485 HES6 0.005076 0.603841 AFE ENSG00000146587 RBAK 0.00713 -0.4124 AFE ENSG00000147124 ZNF41 0.020285 -0.36673 AFE ENSG00000148200 NR6A1 0.019666 -0.46485 AFE ENSG00000149050 ZNF214 0.038835 -0.61299 AFE ENSG00000149922 TBX6 0.013655 0.525516 AFE ENSG00000151612 ZNF827 0.027955 0.407987 AFE ENSG00000151702 FLI1 0.020772 0.423312 AFE ENSG00000152443 ZNF776 0.033792 -0.3537 AFE 18 Transcription Factor Gene Symbol BH FDR Spearman's ρ Splice Type ENSG00000152926 ZNF117 0.044177 -0.33692 AFE ENSG00000154655 L3MBTL4 0.013827 -0.48647 AFE ENSG00000154832 CXXC1 0.007605 0.451504 AFE ENSG00000156469 MTERFD1 0.048712 -0.34076 AFE ENSG00000156853 ZNF689 0.019386 0.399277 AFE ENSG00000158805 ZNF276 0.019976 0.426639 AFE ENSG00000159588 CCDC17 0.033792 0.463227 AFE ENSG00000159905 ZNF221 0.045894 -0.38753 AFE ENSG00000159917 ZNF235 0.011509 -0.4293 AFE ENSG00000160113 NR2F6 0.000353 0.58217 AFE ENSG00000160199 PKNOX1 0.027948 -0.3451 AFE ENSG00000160336 ZNF761 0.003952 -0.43562 AFE ENSG00000160352 ZNF714 0.036936 -0.37815 AFE ENSG00000160908 ZNF394 0.002465 0.497584 AFE ENSG00000161298 ZNF382 0.033326 0.454339 AFE ENSG00000162086 ZNF75A 0.028642 -0.38295 AFE ENSG00000162613 FUBP1 0.028835 -0.36831 AFE ENSG00000162714 ZNF496 0.028918 0.391245 AFE ENSG00000162924 REL 0.004263 -0.47423 AFE ENSG00000163795 ZNF513 0.001279 0.534307 AFE ENSG00000163939 PBRM1 0.010997 -0.39117 AFE ENSG00000165156 ZHX1 0.042849 -0.35141 AFE ENSG00000165259 HDX 0.043361 -0.39527 AFE ENSG00000165462 PHOX2A 0.036729 0.721429 AFE ENSG00000165655 ZNF503 0.046491 0.354646 AFE ENSG00000166188 ZNF319 0.028437 0.377692 AFE ENSG00000166478 ZNF143 0.028055 -0.34891 AFE ENSG00000166704 ZNF606 0.007604 0.550024 AFE ENSG00000166888 STAT6 0.02597 0.348397 AFE ENSG00000167232 ZNF91 0.007145 -0.41727 AFE ENSG00000167380 ZNF226 0.036154 -0.329 AFE ENSG00000167384 ZNF180 0.002465 -0.48598 AFE ENSG00000167394 ZNF668 0.001614 0.491488 AFE ENSG00000167491 GATAD2A 0.008942 0.400448 AFE ENSG00000167548 KMT2D 0.009982 0.450831 AFE ENSG00000167625 ZNF526 0.011895 0.388664 AFE ENSG00000167685 ZNF444 0.00387 0.481224 AFE ENSG00000167967 E4F1 0.000206 0.566237 AFE ENSG00000168036 CTNNB1 0.036708 -0.32837 AFE ENSG00000168286 THAP11 0.043381 0.33564 AFE ENSG00000168813 ZNF507 0.048712 -0.31175 AFE ENSG00000169155 ZBTB43 0.019644 -0.37402 AFE ENSG00000169375 SIN3A 0.028642 -0.36119 AFE ENSG00000169554 ZEB2 0.044629 -0.4052 AFE ENSG00000169951 ZNF764 0.032907 0.415242 AFE ENSG00000169957 ZNF768 0.001092 0.534257 AFE ENSG00000170265 ZNF282 0.001278 0.544019 AFE ENSG00000170653 ATF7 0.021904 -0.35606 AFE ENSG00000170949 ZNF160 0.024244 -0.35157 AFE ENSG00000171163 ZNF692 0.000742 0.601395 AFE ENSG00000171169 NAIF1 0.007605 0.480789 AFE ENSG00000171223 JUNB 0.008431 0.413755 AFE Transcription Factor Gene Symbol BH FDR Spearman's ρ Splice Type ENSG00000171425 ZNF581 0.000106 0.569626 AFE ENSG00000171466 ZNF562 0.005361 -0.44815 AFE ENSG00000171574 ZNF584 0.028642 0.356417 AFE ENSG00000171735 CAMTA1 0.001959 -0.52587 AFE ENSG00000172262 ZNF131 0.031168 -0.34473 AFE ENSG00000172845 SP3 0.001339 -0.4873 AFE ENSG00000173041 ZNF680 0.00957 -0.46382 AFE ENSG00000173120 KDM2A 0.013717 -0.39467 AFE ENSG00000173153 ESRRA 0.000467 0.554279 AFE ENSG00000173451 THAP2 0.033424 0.334221 AFE ENSG00000173917 HOXB2 0.007604 0.477639 AFE ENSG00000174197 MGA 0.003245 -0.51799 AFE ENSG00000174282 ZBTB4 0.020028 0.360866 AFE ENSG00000174586 ZNF497 0.027463 0.399133 AFE ENSG00000174652 ZNF266 0.038052 0.388961 AFE ENSG00000174796 THAP6 0.011665 0.449003 AFE ENSG00000175105 ZNF654 0.027553 -0.34574 AFE ENSG00000175213 ZNF408 0.019817 0.394703 AFE ENSG00000175387 SMAD2 0.031158 -0.33836 AFE ENSG00000175467 SART1 9.68E-05 0.584687 AFE ENSG00000175787 ZNF169 0.011211 -0.43706 AFE ENSG00000176371 ZSCAN2 0.018119 0.497082 AFE ENSG00000176946 THAP4 0.020028 0.360752 AFE ENSG00000177030 DEAF1 0.005978 0.443874 AFE ENSG00000177045 SIX5 0.013796 0.43331 AFE ENSG00000177426 TGIF1 0.044484 0.427941 AFE ENSG00000177732 SOX12 0.000742 0.535866 AFE ENSG00000178338 ZNF354B 0.04959 -0.3614 AFE ENSG00000178951 ZBTB7A 0.000106 0.566907 AFE ENSG00000179111 HES7 0.015074 0.584274 AFE ENSG00000179195 ZNF664 0.04937 0.385469 AFE ENSG00000179588 ZFPM1 0.033326 0.334423 AFE ENSG00000179627 ZBTB42 0.017455 0.455676 AFE ENSG00000179922 ZNF784 0.024667 0.429929 AFE ENSG00000179965 ZNF771 0.046814 0.346097 AFE ENSG00000181135 ZNF707 0.018867 0.472824 AFE ENSG00000181315 ZNF322 0.033431 -0.36782 AFE ENSG00000181666 HKR1 0.008782 -0.45726 AFE ENSG00000181827 RFX7 0.030573 -0.33935 AFE ENSG00000182141 ZNF708 0.040885 -0.3281 AFE ENSG00000182158 CREB3L2 0.01974 0.371136 AFE ENSG00000182979 MTA1 0.000992 0.516757 AFE ENSG00000184436 THAP7 0.00484 0.472122 AFE ENSG00000184517 ZFP1 0.002276 -0.52085 AFE ENSG00000184635 ZNF93 0.04893 -0.35667 AFE ENSG00000184677 ZBTB40 0.041162 -0.32996 AFE ENSG00000185024 BRF1 2.72E-05 0.673735 AFE ENSG00000185122 HSF1 0.000306 0.538807 AFE ENSG00000185129 PURA 0.018421 0.519353 AFE ENSG00000185252 ZNF74 0.014909 0.440241 AFE

20 Transcription Factor Gene Symbol BH FDR Spearman's ρ Splice Type ENSG00000185513 L3MBTL1 0.010482 0.636563 AFE ENSG00000185668 POU3F1 0.004044 0.623681 AFE ENSG00000185730 ZNF696 0.009369 0.453965 AFE ENSG00000185947 ZNF267 0.011479 -0.40328 AFE ENSG00000186017 ZNF566 0.047551 -0.3531 AFE ENSG00000187098 MITF 0.025567 -0.44955 AFE ENSG00000188290 HES4 0.006995 0.486093 AFE ENSG00000188994 ZNF292 0.012281 -0.44974 AFE ENSG00000189042 ZNF567 0.033877 -0.39072 AFE ENSG00000189079 ARID2 0.042296 -0.31998 AFE ENSG00000189144 ZNF573 0.016848 -0.42669 AFE ENSG00000196150 ZNF250 0.047422 0.317441 AFE ENSG00000196233 LCOR 0.044066 -0.33264 AFE ENSG00000196247 ZNF107 0.012259 -0.39209 AFE ENSG00000196268 ZNF493 0.025606 -0.38993 AFE ENSG00000196378 ZNF34 0.029598 0.458571 AFE ENSG00000196417 ZNF765 0.039728 0.640351 AFE ENSG00000196418 ZNF124 0.04225 -0.34481 AFE ENSG00000196453 ZNF777 0.011211 0.396415 AFE ENSG00000196456 ZNF775 0.016112 0.372399 AFE ENSG00000196498 NCOR2 0.01005 0.440091 AFE ENSG00000196591 HDAC2 0.020028 -0.36074 AFE ENSG00000196646 ZNF136 0.037508 -0.36802 AFE ENSG00000196705 ZNF431 0.02772 -0.35915 AFE ENSG00000196757 ZNF700 0.047422 -0.31347 AFE ENSG00000196826 ZNF709 0.046827 -0.31804 AFE ENSG00000196843 ARID5A 0.034828 0.358989 AFE ENSG00000197008 ZNF138 0.031158 -0.37807 AFE ENSG00000197020 ZNF100 0.006398 -0.47779 AFE ENSG00000197050 ZNF420 0.038052 -0.36109 AFE ENSG00000197054 ZNF763 0.048148 -0.31232 AFE ENSG00000197362 ZNF786 0.026047 0.369447 AFE ENSG00000197372 ZNF675 0.002298 -0.50532 AFE ENSG00000197483 ZNF628 0.040307 0.382229 AFE ENSG00000197497 ZNF665 0.036863 0.488196 AFE ENSG00000197608 ZNF841 0.03285 -0.33522 AFE ENSG00000197779 ZNF81 0.008616 -0.44462 AFE ENSG00000197782 ZNF780A 0.004557 -0.43504 AFE ENSG00000198026 ZNF335 0.016382 0.371754 AFE ENSG00000198160 MIER1 0.00812 -0.40613 AFE ENSG00000198169 ZNF251 0.042695 0.381947 AFE ENSG00000198176 TFDP1 0.00433 0.480609 AFE ENSG00000198182 ZNF607 0.002817 -0.54309 AFE ENSG00000198466 ZNF587 0.033675 -0.33383 AFE ENSG00000198517 MAFK 0.006398 0.432469 AFE ENSG00000198521 ZNF43 0.010482 -0.41954 AFE ENSG00000198554 WDHD1 0.049141 -0.3168 AFE ENSG00000198815 FOXJ3 0.037839 -0.38613 AFE ENSG00000198816 ZNF358 0.028748 0.391835 AFE ENSG00000198911 SREBF2 0.03358 0.349606 AFE

21 Transcription Factor Gene Symbol BH FDR Spearman's ρ Splice Type ENSG00000204231 RXRB 0.044904 0.336019 AFE ENSG00000204304 PBX2 0.033729 0.356597 AFE ENSG00000204514 ZNF814 0.017669 -0.37064 AFE ENSG00000204519 ZNF551 0.018119 0.425798 AFE ENSG00000204859 ZBTB48 0.001331 0.540091 AFE ENSG00000204946 ZNF783 0.037629 0.380009 AFE ENSG00000205903 ZNF316 0.001279 0.497756 AFE ENSG00000213015 ZNF580 0.000249 0.558377 AFE ENSG00000213297 ZNF625-ZNF20 0.049141 -0.32323 AFE ENSG00000213347 MXD3 0.029827 0.340544 AFE ENSG00000214022 REPIN1 0.002427 0.486217 AFE ENSG00000215421 ZNF407 0.0298 0.613636 AFE ENSG00000218891 ZNF579 0.006529 0.44006 AFE ENSG00000225614 ZNF469 0.022173 0.403079 AFE ENSG00000229809 ZNF688 0.011085 0.539212 AFE ENSG00000234444 ZNF736 0.013363 -0.38812 AFE ENSG00000236609 ZNF853 0.018577 0.578889 AFE ENSG00000242802 AP5Z1 0.014896 0.399207 AFE ENSG00000243943 ZNF512 0.001139 -0.49642 AFE ENSG00000244405 ETV5 0.035739 -0.3975 AFE ENSG00000249459 ZNF286B 0.018236 0.526675 AFE ENSG00000249709 ZNF564 0.042849 -0.33646 AFE ENSG00000250571 GLI4 0.00386 0.543777 AFE ENSG00000251369 ZNF550 0.036936 0.431869 AFE

Table S5: Correlation of Changes in Gene Expression of Transcription Factors and Proportion of RNA Processing Events. Log-fold changes in gene expression of 328 transcription factors is correlated to average ∆Ψ across three individuals for AFE events.

22 References

[1] Backes, C., Keller, A., Kuentzer, J., Kneissl, B., Comtesse, N., Elnakady, Y.A., Muller, R., Meese, E., Lenhof, H.P.: GeneTrail–advanced gene set enrichment analysis. Nucleic Acids Res. 35(Web Server issue), 186–192 (2007)