SUPPLEMENTAL DATA

EPIGENETIC MODULATION OF β-CELLS BY INTERFERON-α VIA PNPT1-miR26a-TET2 TRIGGERS

AUTOIMMUNE DIABETES

Mihaela Stefan-Lifshitz1, Esra Karakose2, Lingguang Cui1, Abora Ettela1, Zhengzi Yi3, Weijia Zhang3, and Yaron Tomer1

1Division of Endocrinology and the Fleischer Institute for Diabetes and Metabolism, Albert Einstein College of

Medicine, Bronx, NY, 10461; 2Diabetes, Obesity, and Metabolism Institute and 3Department of Medicine

Bioinformatics Core, Icahn School of Medicine at Mount Sinai, New York, NY 10029

To whom correspondence should be addressed:

Mihaela Stefan-Lifshitz, PhD,

Albert Einstein College of Medicine, Forchheimer 702 1300 Morris Park Ave, Bronx, NY, 10461 Tel: 718-430-8530 E-mail: [email protected]

KEYWORDS DNA methylation, beta cells, interferon alpha, type 1 diabetes SUPPLEMENTAL RESULTS

SI Results: Confirmation of the DNAm array results

To confirm the DNAm array results we preformed bisulfite DNA sequencing of four selected genes: the top ranked hypo- and hyper-methylated genes, GGA3 and SLC25A31 respectively, and two genes associated with T1D pathogenesis: IRF7(1) and ERAP1(2). Nine CpG sites from the GGA3 promoter and 45 CpG sites form the SLC25A31 5’UTR region overlapping the oligonucleotide probes cg19184818 and cg09796800 respectively, were analyzed in islet samples treated with IFNα for 24h and 120h and compared with CpG methylation status of untreated samples. The direction of methylation-change at analyzed CpGs was in agreement with the DNAm array analysis: 6.6% more CpG sites in the GGA3 promoter were methylated and

6.2% more CpG sites in the SLC25A31 5’UTR region were un-methylated after 24h of IFNα treatment while

10.8% more sites were methylated in GGA2 and 9.1% sites were un-methylated in SLC25A31 after 120h of

IFNα treatment (Fig. S1A). Similarly, confirming the array results, 6.4% more of the 17 CpG sites analyzed in the IRF7 5’UTR region (cg09703963) and 3.1% more of the nine CpGs analyzed in the ERAP1 gene

(cg16492584) were un-methylated after 24h of IFNα treatment (Fig. S1B).

Genomic distribution of hyper- and hypo-methylation CpG sites

We analyzed genomic functional distribution of the hyper- and hypo-methylated CpG sites relative to six gene regions annotated on the 450k array: regions located 1.5kb and 0.2kb from the TSS (TSS1500 and

TSS200 respectively), regions within the gene 5’UTR (5’UTR), 1st exon, gene body, and regions within the gene 3’ UTR (3’UTR) (Fig. S2A). There were no significant differences between the distributions of the hyper- and hypo-methylated sites across these regions. Both hypo- and hyper-methylated sites were more prevalent

(62%) in the gene body regions followed by regions up-stream to the TSS (14% hypo- and 18% hyper- methylated CpGs) in IFNα treated vs. untreated islets (Fig. S2A). We also assessed the distribution of differentially methylated CpG sites relative to CpG islands, shelfs and shores (3). Both hyper- and hypo- methylated sites were equally distributed relative to the CpG islands and genomic neighborhood regions: shores and shelfs (Fig. S2B).

1 miR-22, miR-29b miR-101 and miR-125 expression in human islets treated with IFNα

We measured the expression levels of miR-22, miR-29b, miR-101 and miR-125b in 10 - 22 human islets treated with IFNα and compared with untreated islets. miR-22 and miR-29b expression was significantly downregulated in IFNα treated islets relative to untreated islets: miR-22 expression level was reduced 0.8-fold

(P ≤ 0.02), and miR-29b expression was reduced 0.8-fold (P ≤ 0.05) (Fig. S9A). In contrast, miR-101 and miR-

125b expression remained unchanged or slightly increased upon IFNα treatment: miR-101 expression was 1.08- fold (P ≤ 0.3) and miR-125b expression was 1.3-fold (P ≤ 0.2) in IFNα treated compared to untreated islets (Fig.

S9A). Because miR-29b and miR-22 levels showed modest but significant downregulation in islets treated with

IFNα, we assessed the expression of their primary miRNA transcripts. miR-29b has two primary transcripts, miR-

29-b1 and miR-29b-2 that are encoded by different genes located in chromosome 7q32.3 and 1q32.2, respectively (4). The expression level of miR-29b-1 increased 1.6-fold (P ≤ 0.03) and that of miR-29b-2 increased

1.5-fold (P ≤ 0.005) (Fig. S9B). miR-22 is encoded by an exon of a long non-coding RNA gene, the miR-22 host gene (MIR-22HG) (5). A similar analysis for pri-miR-22 showed that its expression level in IFNα treated relative to untreated islets was non-significantly increased at 1.5-fold (P = 0.1) (Fig. S9B).

2 REFERENCES

1. Heinig M, et al. (2010) A trans-acting locus regulates an anti-viral expression network and type 1 diabetes risk. Nature 467(7314):460-464.

2. Fung EY, et al. (2009) Analysis of 17 autoimmune disease-associated variants in type 1 diabetes identifies 6q23/TNFAIP3 as a susceptibility locus. Genes Immun 10(2):188-191.

3. Portela A & Esteller M (2010) Epigenetic modifications and human disease. Nat Biotechnol 28(10):1057- 1068.

4. Kriegel AJ, Liu Y, Fang Y, Ding X, & Liang M (2012) The miR-29 family: genomics, cell biology, and relevance to renal and cardiovascular injury. Physiol Genomics 44(4):237-244.

5. Huang ZP & Wang DZ (2014) miR-22 in cardiac remodeling and disease. Trends Cardiovasc Med 24(7):267-272.

3 SUPPLEMENTAL FIGURE LEGENDS

Figure S1: Confirmation of CpG methylation status for individual genes in human islets treated and

untreated with IFNα. (A) CpG methylation status of top ranked hypo- and hyper-methylated genes in IFNα treated vs. un-treated samples. DNAm of the GGA3 gene (Golgi-Localized, Gamma Ear-Containing, ARF-

Binding Protein 3) that showed increased DNAm (Log2Rat 1.5) in the promoter region (Illumina ID: cg19184818) and of the SLC25A31 gene (Solute Carrier Family 25 Member 31) that showed decreased DNAm (Log2Rat -

0.9) in regions 0.2 Kb to the TSS (Illumina ID: cg09796800) was analyzed by direct sequencing of bisulfite DNA.

Nine CpG sites in the GGA2 promoter and 45 CpG sites in the SLC25A31 5’UTR region were analyzed in islets treated with IFNα for 24h and 120h and compared with CpG methylation status of untreated samples. (B) CpG methylation status of genes showing IFNα induced mRNA expression and hypo-methylated CpG sites: IRF7

(Interferon regulatory factor 7) and ERAP1 (Endoplasmic reticulum aminopeptidase 1). 17 CpG sites from the

IRF7 5’ UTR region (Illumina ID: cg09703963) and nine CpGs from the ERAP1 gene (Illumina ID: cg16492584) were analyzed by direct sequencing of bisulfite DNA in islets treated with IFNα for 24h and compared with untreated samples.

Figure S2: Genomic distribution and classification of the hypo- and hyper-methylated CpG sites in IFNα

treated compared with un-treated islets. (A) Distribution of the hyper- and hypo-methylated CpG sites across

six annotation gene sets relative to TSS: first exon, 5’ UTR, 3’ UTR, gene body, 1500 kb and 200 kb downstream

the TSS; (B) Distribution of hyper- and hypo-methylated CpG sites according to the CpG content of the DNA

region and genomic neighborhood context: regions annotated as islands (regions with at least 500 bp, and >

55% GC content), shores (regions 2 kb either side of an island), shelfs (regions 2 kb outside the shores). N

represents North, indicating the region upstream from a CpG island; S represents South indicating, the region

downstream from a CpG island.

Figure S3: Gene interaction networks of differentially-expressed genes in human islets treated with

IFNα. Functional gene interaction networks were identified by Ingenuity Pathway Analysis (IPA). Red color

indicates up-regulated gene expression; color intensity is indicative of fold-change level with deep red indicating

4 the highest detected level of expression for genes in the network. Legend insert: each gene was assigned a

shape and function by IPA.

Figure S4: Confirmation of RNA-seq data by qRT-PCR. Up-regulation of mRNA gene expression was

confirmed in islet samples after 24h of IFNα treatment and compared with untreated samples for OAS1, SP100,

IFIH1, CD40, TLR3 and IRS1 genes. Results are presented as fold change of expression level in IFNα treated

samples relative to untreated samples.

Figure S5: IFNα induces up-regulation of Tet1/2/3 mRNA expression in NIT-1 cells. qRT-PCR analysis of

Tet1/2/3 gene expression in NIT-1 cells treated with IFNα for 24h and 48h. Results represents fold change of gene expression level in IFNα treated samples relative to untreated samples and are presented as mean fold change of quadruplicated experiments ± SD; *, p<0.05.

Figure S6: DNMT3A and DNMT3B expression in human pancreatic islets treated with IFNα. mRNA levels

of DNMT3A and DNMT3B was analyzed by qRT-PCR . Results represents fold change of gene expression level in IFNα treated samples relative to untreated samples. The average fold expression level in IFNα treated vs. untreated islets for DNMT1A was 1.28 (p = 0.003) and for DNMT3B was 1.10 (p = 0.11). Each diamond represents an islet sample; dotted horizontal lines represent the median fold level.

Figure S7: Quantification of TET hydroxylase activity and 5hmC content in IFNα treated vs. untreated

human islets. (A) Quantification of TET hydroxylase activity in nuclear extracts from seven islets treated and

un-treated with IFNα. (B) Quantification of 5-hydroxymethylcytosine (5hmC) in genomic DNA from islets treated with IFNα for 24h and compared with untreated islets. (C) 5hmC quantification in islets treated with IFNα for 24h and 48h. White circles, samples untreated with IFNα, black circles, samples treated with IFNα; dotted squares individual pair samples, treated and untreated with IFNα.

Figure S8: IFNα induces down-regulation of miR-26a in NIT-1 cells. qRT-PCR analysis of miR-26a

expression in NIT-1 cells treated with IFNα for 24 h, 48 h. Results represent fold change of expression level in

5 IFNα treated samples relative to untreated samples and are presented as mean fold change of triplicate

experiments ± SD; *, p < 0.05.

Figure S9: Expression of miR-22, miR-29b, miR-101 and miR-125 in human pancreatic islets treated with

IFNα. (A) Relative expression levels of mature miRNAs in human islets treated and untreated with IFNα

assessed by qRT-PCR. (B) qRT-PCR for pri-miR29b-1 & pri-miR-29b-2 and pri-miR-22 in IFNα treated

compared with untreated islets. Results represent fold change of gene expression level in IFNα treated samples

relative to untreated samples. Statistical differences between different constructs were determined by t test for

independent samples; *, p < 0.05.

Figure S10: PNPT1 and XRN1 mRNA expression levels. (A) IFNα treatment downregulates Pnpt1 and Xrn1

mRNA expression in NIT1 cells. qRT-PCR analysis of Pnpt1 and Xrn1 expression in NIT1 cells treated with IFNα for 24h. Results represents fold change of gene expression level in IFNα treated samples relative to untreated samples and are presented as mean fold change of triplicate experiments ± SD; *, p < 0.05; (B) Relative

expression levels of PNPT1 and XRN1 measured by qRT-PCR in human pancreatic islets transduced with

lentiviruses expressing either XRN1 or PNPT1. (C) Relative expression levels of PNPT1 and XRN1 measured by qRT-PCR in NIT1 cells treated with PNTP1siRNA and XRN1siRNA respectively. Data represent the mean ±

SD of three independent experiments. Differences between different constructs were determined by t test for independent samples; *, p < 0.05.

Figure S11: Increased mRNA expression of IFNα-regulated genes in islets from IFNα-INS1CreERT2 mice.

qRT-PCR of gene expression in islets isolated from IFNα-INS1CreERT2 (n = 6-7) and WT (n = 5-7) mice after 4

weeks of IFNα induction. Gene expression data was normalized to Gapdh and the results are expressed as fold-

change gene expression relative to a gene expression of a randomly selected WT mice. Data show fold-change

for individual mice with mean (dotted horizontal line) ±SD; Differences between transgenic and WT mice were

determined by t test for independent samples; *, p < 0.05

6 Figure S12: Diabetes development in IFNα-INS1CreERT2 mice after multiple-low dose STZ induction of T1D.

IFNα-INS1CreERT2 and WT mice at 3-weeks after IFNα induction were injected via five consecutive daily STZ i.p. injections. (A) Urine glucose was measured before STZ administration and at day 6, 8 and 10 post-first STZ

injection. (B) Blood glucose levels in IFNα-INS1CreERT2 and WT mice at day 25 post-first STZ injection. (C) Percent islet area relative to section area in IFNα-INS1CreERT2 and WT mice at day 25 post-first STZ injection. (D) Body weight of IFNα-INS1CreERT2 and WT mice.

7 ABBREVIATIONS

T1D - Type 1 diabetes

TET1/2/3 - Tet Methylcytosine Dioxygenase 1/2/3

TDG - Thymine DNA Glycosylase

SP100 - SP100 Nuclear Antigen

IFIH1 - Interferon Induced With Helicase C Domain 1

TLR3 - Toll Like Receptor 3

IRS1 - Insulin Receptor Substrate 1

OAS1 - 2'-5'-Oligoadenylate Synthetase 1

XRN1 - 5'-3' Exoribonuclease 1

PNPT1 - Polyribonucleotide Nucleotidyltransferase 1

GGA2 - Golgi Associated, Gamma Adaptin Ear Containing, ARF Binding Protein 2

SLC25A31 - Solute Carrier Family 25 Member 31

ERAP1 - Endoplasmic Reticulum Aminopeptidase 1

IRF7 - Interferon Regulatory Factor 7

IFNα - Interferon alpha

GO - Gene ontology

DNAm - DNA methylation

5-hmC - 5-Hydroxymethylcytosine

ORFs - open reading frame

LIMMA - Linear Models for Microarray Data

TSS – Transcriptional start site

5-caC - 5-carboxycytosine

5-fC - 5-formylcytosine

5-hmC - 5-hydroxymethylcytosine

5-hmU - 5-hydroxymethyluracil

5-mC - 5-methylcytosine

CTDSPL - CTD Small Phosphatase Like

8 CTDSP2 - CTD Small Phosphatase 2

9 Figure S1

A GGA3 SLC25A31

100 100 Un-methylated CpG 95 Methylated CpG 90 90 85 80 80 75 70 70

% methylation 65 % methylation 60 60 55 50 50 - IFN1 α + IFN2 α - IFN3 α + IFN4 α - IFN1 α + IFN2 α - IFN3 α + IFN4 α 24 hours 120 hours 24 hours 120 hours B IRF7 ERAP1

100 100

90 90

80 80

70 70 % methylation % methylation 60 60

50 50 - IFN1 α + IFN2 α - IFN1 α + IFN2 α

24 hours 24 hours 10 Figure S2

28.6% Hypomethylated CpG sites (2,565) 71.4% Hypermethylated CpG sites (8,963)

3% 2% 4% 1% 8%8% 9% 1st Exon 11% 14% 8% Functional 10% 3'UTR A genomic distribution 5'UTR Body 68% 62% TSS 1500 TSS 200 19% 20% Island N_Shelf 16% 19% 20% Genomic neighborhood N_Shore 30% context 17% B 21% S_Shelf 15% 17% S_Shore 21% 23% 22% 17% 23%

11 Figure S3

(A) (B)

Enzyme

Peptidase

Kinase

Transcriptional regulator

Other Transporter

12 Figure S4

OAS1 SP100 IFIH1 CD40 TLR3 IRS1 2.5 7 - IFNα 30 5 400 9 + IFNα 4.5 6 8 350 25 2 4 7 300 5 3.5 20 6 1.5 250 3 4 5 200 15 2.5 3 4 1 2 150

Relative Relative fold change 3 Relative fold change 10 Relative fold change Relative fold change Relative fold change Relative Relative fold change 1.5 2 100 2 1 0.5 5 50 1 1 0.5

0 0 0 0 0 0 1 1 1 1 1 1

13 Figure S5 Tet2 Tet1 Tet3 1.6 2 1.6 * * 1.8 * 1.4 1.4 * * 1.6 * 1.2 1.2 1.4 1 1 1.2

0.8 1 0.8 0.8 0.6 0.6 0.6 Relative Relative fold change Relative Relative fold change 0.4 Relative fold change 0.4 0.4 0.2 0.2 0.2

0 0 0 - IFNα + IFNα + IFNα - IFNα + IFNα + IFNα - IFNα + IFN1 α + IFNα 1 1 48h 24h 48h 24h 48h 24h

14 Figure S6

DNMT3A DNMT3B 4 4

3 3

2 2

1 1 Relative fold change Relative fold Relative fold change Relative fold n = 12 n = 11 0 0 IFNα (-) IFNα (+) IFNα (-) IFNα (+)

15 Figure S7

A B C 0.25 0.8 + IFNα 0.7 + IFNα + IFNα - IFNα - IFNα - IFNα 0.7 0.6 0.2 0.6 0.5 0.5 0.15

OD/min/mg) 0.4 in total DNA in total

0.4 DNA in total 0.3 0.1 activity ( 0.3 5- hmC% 5- hmC%

TET 0.2 0.2 0.05

0.1 0.1 n = 7 0 0 0 24h 48h 24h 48h 24h 48h 1 2 3 4 5 6 7 8 0 1 2 3 4 5 6 7 0 2 4 6 8 010.5 11 1.5 2 2.5 3 3.5 4 4.5 5 5.5 6 6.5 7 7.5 8 Islet 1 Islet 2 Islet 3

16 Figure S8

1.2

1 * * 0.8

0.6

0.4 Relative Relative fold change

0.2

0 -IFNα +IFN1 α +IFNα CTR 24h 48h

17 Figure S9

A miR-22 miR-29b miR-101 miR-125b 4 4 4 4

3 3 3 3

2 * 2 * 2 2

1 1 1 1 Relative fold change Relative Relative fold change Relative Relative fold change Relative n = 19 fold change Relative n = 22 n = 15 n = 12 0 0 0 0 IFNα (-) IFNα (+) IFNα (-) IFNα (+) IFNα (-) IFNα (+) IFNα (-) IFNα (+)

pri-miR-29b1 pri-miR-29b2 pri-miR-22 B * 5 * 5 5 * 4 4 4 3 3 3

2 2 2

1 1 1 fold change Relative Relative fold change Relative Relative fold change Relative n = 13 n = 13 n = 10 0 0 0 IFNα (-) IFNα (+) IFNα (-) IFNα (+) IFNα (-) IFNα (+)

18 Figure S10

A B C PNPT1 1.6 XRN1 PNPT1 XRN1 PNPT1 XRN1 3.5 1.2 1.2 250 140 * 1.4 * * * 3 120 1 1 1.2 200 2.5 100 1 0.8 0.8 150 2 80 0.8 0.6 0.6 * 1.5 60 0.6 * 100 0.4 0.4

1 Relative fold change 40 Relative Relative fold change 0.4 XRN1 fold XRN1 change relative XRN1 fold XRN1 change relative

PNPT1 relative fold change fold relative PNPT1 50 0.2 fold XRN1 change relative

PNPT1 relative fold change fold relative PNPT1 0.2 0.5 0.2 20

0 0 0 0 0 0 CTR PNPT1 XRN1 1 CTR CTR 1PNPT1 CTR XRN1 - IFNα 1 +IFNα - IFNα 1 +IFNα siRNA siRNA siRNA1 siRNA 1

19 Figure S11

Oas1b Isg15 Ifit1 Mx2 10 * 60 * 25 * 15 * 8 20 40 10 6 15

4 10 20 5

2 fold change Relative Relative fold change Relative 5 Relative fold change Relative Relative fold change Relative

0 0 0 0 WT IFNα-INS1CreERT2 WT IFNα-INS1CreERT2 WT IFNα-INS1CreERT2 WT IFNα-INS1CreERT2

20 Figure S12

A B C D 0.3 100 800 30

* ) 80 2 25 600 0.2 20 60 400 15 40 0.1 10 WT n = 10 20 (mg/dl)Glucose 200

% Diabetic mice WT n = 10 IFNα-INS1CreERT2 n = 14 % islet area (µm 5 IFNα-INS1CreERT2 n = 14

0 (g) weight body Average 0 0.0 0 day11 day62 day83 day104 CreERT2 WT IFNα-INS1 WT IFNα-INS1CreERT2 day1 1 day102 day3 24

21 Table S1 Gene ontology enrichment analysis based on "Biological process" (BP) term for genes associated with hypo-methylated CpGs. GO Term Count PValue Genes Fold EnrichmBonferroni Benjamini FDR

GO:0046320~regulation of fatty acid oxidation 15 3.64915E-05 NM_003749, NM_001014431, NM_005544, NM_001626, NM_000387, NM_004958, NM_001079670, NM_005037, NM_013261, NM_001040633, NM_001995, 3.2881773 0.1531107 0.0205589 0.0687399 NM_005399, NM_001001928, NM_016203, NM_000455, NM_024429, NM_000098 GO:0006468~protein amino acid phosphorylation 147 6.46032E-05 NM_005546, NM_004783, NM_001259, NM_015000, NM_001006944, NM_000601, NM_001014431, NM_020530, NM_006482, NM_001715, NM_001135937 1.3855924 0.5473731 0.0430826 0.327458 NM_002401, NM_006343, NM_005012, NM_012152, NM_017525, NM_003137, NM_002006, NM_001006932, NM_001010938, NM_003747, NM_001040439, NM_005211, NM_003993, NM_001039538, NM_005921, NM_001080507, NM_001143784, NM_002419, NM_001135944, NM_006724, NM_003852 NM_003331, NM_001164664, NM_004850, NM_003128, NM_006504, NM_001079880, NM_001570, NM_001101401, NM_015183, NM_014602, NM_001080448, NM_004333, NM_007118, NM_021135, NM_001113239, NM_001134946, NM_001015878, NM_015076, NM_000454, NM_001012418, NM_016204, NM_006070, NM_004226,NM_001122956, NM_000455, NM_006206, NM_003010, NM_001141969, NM_018979, NM_001081640, NM_004445,NM_001004106, NM_001080395 NM_002737, NM_005906, NM_004642, NM_001203, NM_022048, NM_016395, NM_012424, NM_002350, NM_004734,NM_024652, NM_022963, NM_014916, NM_003391, NM_005255, NM_002944, NM_012395,NM_014911, NM_015905, NM_005308, NM_000124, NM_001099436, NM_004442, NM_004443, NM_001004057, NM_001005862, NM_001168238, NM_001433, NM_002958, NM_004721, NM_004720, NM_001144914, NM_001626, NM_002562, NM_001033582, NM_001130028, NM_015358, NM_001163213,NM_001033581, NM_003957, NM_003954, NM_021643, NM_004431, NM_001099691, NM_001896, NM_017593, NM_001328, NM_004755, NM_001161563, NM_000294, NM_001893, NM_002758, NM_001099660, NM_002759, NM_022740, NM_001042555, NM_001105558, NM_005526, NM_002039, NM_002753, NM_005876, NM_013254, NM_014482, NM_004383, NM_006035, NM_001128919, NM_006556, NM_006658, NM_001319, NM_005751, NM_002747, NM_015016, NM_013233, NM_002744, NM_001110, NM_016151, NM_003565, NM_002031, NM_004958, NM_013993, NM_005026, NM_002577, NM_007174, NM_000875, NM_001031801, NM_006256, NM_001114329, NM_015148, NM_014572, NM_006182 GO:0010628~positive regulation of gene expression 122 0.001926774 NM_002015, NM_001065, NM_000168, NM_020530, NM_024007, NM_018659, NM_001257, NM_017519, NM_001130823, NM_002309, NM_002585, 1.2888599 0.9998467 0.1610967 3.5689524 NM_001128164, NM_001135937, NM_006194, NM_000572, NM_001519, NM_005149, NM_001136021, NM_001160045, NM_001130102, NM_002316,, NM_001145645, NM_007249, NM_002006, NM_004904, NM_014352, NM_006325, NM_001136039, NM_016269, NM_001168278, NM_002518, NM_018717, NM_005921, NM_020920, NM_006540, NM_004571, NM_000281, NM_003852, NM_002920, NM_000461, NM_004991, NM_001113239, NM_002527, NM_001166693, NM_022845, NM_007121, NM_005466, NM_024969,NM_016204, NM_016205, NM_006206, NM_001146688, NM_001143820, NM_020338, NM_000057, NM_021975, NM_001081640, NM_001171628, NM_001098213, NM_004343, NM_000832, NM_015069, NM_004451, NM_015995, NM_001142434, NM_002131, NM_001142589, NM_001400, NM_001128846, NM_014223, NM_001128845, NM_000321, NM_001130867, NM_017617, NM_015472, NM_003181, NM_001964, NM_015905, NM_001134445, NM_000124, NM_003074, NM_001126240, NM_001430, NM_005596, NM_005597, NM_000551, NM_000333, NM_014587, NM_022362, NM_001146284, NM_001011722, NM_001146283, NM_002052, NM_001145811, NM_006060, NM_002813, NM_004396, NM_014249, NM_013261, NM_007298, NM_001001890, NM_005642, NM_001145819, NM_001001928, NM_012326, NM_006565, NM_022740, NM_001730, NM_004557, NM_007360, NM_001429, NM_024503, NM_007162, NM_005933, NM_005037, NM_012475, NM_005225, NM_014482, NM_001145841, NM_016260, NM_001005463, NM_006037, NM_012330, NM_001079846, NM_001949, NM_022114, NM_005427, NM_003213, NM_005121, NM_022898, NM_003214, NM_024665, NM_014079, NM_006942, NM_000675, NM_004959, NM_006186, NM_000875, NM_012082, NM_001166119, NM_012137, NM_001037165 GO:0043067~regulation of programmed cell death 161 0.00440263 NM_001134407, NM_001018160, NM_002015, NM_000269, NM_000601, NM_001014431, NM_000168, NM_006482, NM_001257, NM_005338, NM_015225, 1.2170036 1 0.2196964 7.9781021 NM_000572, NM_003253, NM_005343, NM_001098633, NM_002840, NM_000314, NM_020870, NM_000787, NM_002506, NM_000312, NM_006092, NM_000477, NM_009588, NM_020731, NM_001145645, NM_002006, NM_018647, NM_004881, NM_019850, NM_006024, NM_022173, NM_000617, NM_004360, NM_014350, NM_001142861, NM_002412, NM_002111, NM_001047160, NM_004666, NM_000081, NM_001134398, NM_015973, NM_004330, NM_001112706, NM_005921, NM_002419, NM_020920, NM_015318, NM_001135944, NM_001127183, NM_001042492, NM_000389, NM_016434, NM_004333, NM_001127184, NM_007118, NM_021138, NM_004666, NM_000081, NM_001134398, NM_015973, NM_001112706, NM_005921, NM_002419, NM_020920, NM_015318, NM_001135944, NM_001127183, NM_001042492, NM_000389, NM_016434, NM_004333, NM_004330, NM_001127184, NM_007118, NM_021138, NM_006324, NM_001113239, NM_001134946, NM_002527, NM_005778, NM_000595, NM_001664, NM_004849, NM_001080453, NM_001112732, NM_024969, NM_000454, NM_004226, NM_000250, NM_006005, NM_001143820, NM_006290, NM_001141969, NM_003012, NM_005793, NM_021975, NM_013371, NM_001081640, NM_001171628, NM_005658, NM_006595, NM_002128, NM_004343, NM_000832, NM_002737, NM_016009, NM_024420, NM_001143761, NM_006909, NM_001130867, NM_020631, NM_017617, NM_024110, NM_018413, NM_001775, NM_021962, NM_001170715, NM_000029, NM_000124, NM_004307, NM_004924, NM_001126240, NM_002164, NM_001005862, NM_001159740, NM_004723, NM_002959, NM_000551, NM_001135155, NM_001433, NM_004052, NM_001001389, NM_001146284, NM_003589, NM_002562, NM_001033582, NM_024310, NM_014448, NM_003883, NM_001146283, NM_001010989, NM_003592, NM_016373, NM_003591, NM_003590, NM_001033581, NM_015356, NM_004394, NM_007298, NM_013962, NM_001958, NM_002457, NM_003478, NM_001098522, NM_001166451, NM_001031680, NM_002758, NM_022740, NM_006463, NM_005882, NM_002570, NM_002226, NM_004280, NM_001030288, NM_001113511, NM_002661, NM_005427, NM_001161353, NM_022898, NM_004747,NM_003217, NM_001098517, NM_002744, NM_001130006, NM_001167618, NM_000675, NM_006186, NM_000876, NM_000875, NM_018941, NM_001103,

22 Table S2 Gene ontology enrichment analysis based on "Biological process" (PB) term for transcripts induced by IFNα. GO Term Count P Value Genes Fold Enrichmen Bonferroni Benjamini FDR GO:0006955~immune response 57 1.1E-23 TLR3, APOBEC3G, IFI44L, TNFSF13, CXCL11, APOBEC3F, CXCL10, B2M, TMEM173, MYD88, CFH, ERAP1, ERAP2, HLA-H, GTPBP1, SP100, GBP5, BST2, 4.880045567 1.59815E-20 1.59815E-20 1.824E-20 HLA-A, HLA-C, SERPING1, HLA-B, CTSS, HLA-E, IL18BP, GBP4, GBP3, GBP2, GBP1, PSMB10, IFIH1, CXCL5, IFITM2, IFITM3, OAS3, CC GO:0009615~response to virus 25 1.81E-20 IFIH1, ZC3HAV1, RSAD2, CCL8, TLR3, APOBEC3G, APOBEC3F, IFI35, ISG20, TRIM5, ISG15, MX1, MX2, BST2, SAMHD1, IFI44, IFI16, STAT1, TRIM22, STAT2, 13.54913665 2.62794E-17 1.31397E-17 2.999E-17 DDX58, IRF9, PLSCR1, IRF7, EIF2AK2 GO:0048002~antigen processing and presentation of peptide antigen 11 1.53E-11 HLA-H, TAP2, HLA-A, IFI30, ERAP1, HLA-C, ERAP2, HLA-B, HLA-E, TAPBPL, CD74, B2M 23.2077355 2.21583E-08 7.38608E-09 2.529E-08 GO:0006952~defense response 37 5.24E-11 IFIH1, NMI, TLR3, CCL8, RSAD2, APOBEC3G, C1R, C1S, CX3CL1, CXCL11, APOBEC3F, CD74, CXCL10, TMEM173, LGALS3BP, MYD88, NOD1, TAP2, TAP 3.554059715 7.59999E-08 1.9E-08 8.673E-08 ITGB6, CFH, MX1, MX2, DHX58, SP100, SAMHD1, SERPING1, HLA-C, HLA-B, IDO1, CD40, APOL2, DDX58, APOL3, APOL1, NUPR1, HIST2 GO:0002474~antigen processing and presentation of peptide antigen via MHC class I 9 1.23E-10 HLA-H, TAP2, HLA-A, ERAP1, HLA-C, ERAP2, HLA-B, HLA-E, TAPBPL, B2M 31.27459543 1.78161E-07 3.56321E-08 2.033E-07 GO:0043123~positive regulation of I-kappaB kinase/NF-kappaB cascade 13 7.94E-08 CFLAR, SECTM1, BST2, TLR3, CD40, LGALS9, APOL3, TRIM38, TNFSF10, MYD88, NOD1, SHISA5, CASP1 7.917165624 0.000115075 1.91801E-05 0.0001313 GO:0045087~innate immune response 15 8.32E-08 IFIH1, SP100, SAMHD1, TLR3, SERPING1, C1R, APOBEC3G, C1S, APOBEC3F, DDX58, TMEM173, APOL1, MYD88, CFH, DHX58 6.421112588 0.000120561 1.72239E-05 0.0001376 GO:0019882~antigen processing and presentation 12 1.36E-07 HLA-H, HLA-A, IFI30, HLA-C, HLA-B, HLA-E, CD74, B2M, PSME1, TAP2, ERAP1, ERAP2, TAPBPL 8.54085337 0.000197454 2.46838E-05 0.0002254 GO:0010740~positive regulation of protein kinase cascade 14 4.98E-06 CFLAR, SECTM1, BST2, TLR3, CD40, LGALS9, TRIM38, APOL3, TNFSF10, MYD88, NOD1, SHISA5, JAK2, CASP1 4.952331146 0.007189249 0.000721261 0.0082336 GO:0019883~antigen processing and presentation of endogenous antigen 5 5.22E-06 TAP2, ERAP1, ERAP2, TAPBPL, CD74 36.92139738 0.007536687 0.000687512 0.008633 GO:0006954~inflammatory response 18 3.67E-05 NMI, CCL8, TLR3, SERPING1, C1R, IDO1, CD40, C1S, CXCL11, CXCL10, APOL2, APOL3, NOD1, MYD88, NUPR1, IRF7, ITGB6, CFH 3.271803829 0.051815318 0.004424017 0.0606996 GO:0009967~positive regulation of signal transduction 17 4.07E-05 CFLAR, SECTM1, BST2, CSF1, TLR3, CD40, IRS1, LGALS9, CDKN1C, TRIM38, APOL3, TNFSF10, NOD1, MYD88, SHISA5, JAK2, CASP1 3.404277996 0.057271846 0.004526441 0.0672816 GO:0002230~positive regulation of defense response to virus by host 4 4.61E-05 DDX58, PML, APOBEC3G, APOBEC3F 47.25938865 0.064641492 0.004761868 0.0762313 GO:0019884~antigen processing and presentation of exogenous antigen 5 6.89E-05 PSME1, TAP2, IFI30, CD74, B2M 21.09794136 0.095064289 0.0066373 0.1139299 GO:0019885~antigen processing and presentation of endogenous peptide antigen via MHC clas 4 9.1E-05 TAP2, ERAP1, ERAP2, TAPBPL 39.38282387 0.123649207 0.008215369 0.1505107 GO:0010647~positive regulation of cell communication 17 0.000147 CFLAR, SECTM1, BST2, CSF1, TLR3, CD40, IRS1, LGALS9, CDKN1C, TRIM38, APOL3, TNFSF10, NOD1, MYD88, SHISA5, JAK2, CASP1 3.052468112 0.191502679 0.012426726 0.2422973 GO:0048584~positive regulation of response to stimulus 14 0.000186 TLR3, SERPING1, C1R, CX3CL1, C1S, IDO1, IRS1, B2M, MYD88, NOD1, TAP2, IRF7, CFH, JAK2 3.504403819 0.23610394 0.014851038 0.306877 GO:0009611~response to wounding 22 0.000247 NMI, TLR3, CCL8, SERPING1, C1R, IDO1, CD40, C1S, CXCL11, MDK, CXCL10, APOL2, APOL3, PLSCR1, NOD1, MYD88, NUPR1, FGB, IRF7, ITGB6, CFH, J 2.45213809 0.300787733 0.01865542 0.4074856 GO:0002697~regulation of immune effector process 9 0.000303 DDX58, TAP2, PML, APOBEC3G, TNFSF13, SERPING1, CD40, APOBEC3F, B2M 5.264040815 0.355488942 0.021723731 0.5000277 GO:0010627~regulation of protein kinase cascade 14 0.000312 CFLAR, SECTM1, BST2, TLR3, CD40, LGALS9, TRIM38, APOL3, TNFSF10, MYD88, NOD1, SHISA5, JAK2, CASP1 3.321442977 0.36403808 0.021322561 0.5151889 GO:0050691~regulation of defense response to virus by host 4 0.000368 DDX58, PML, APOBEC3G, APOBEC3F 26.25521591 0.413744049 0.023980461 0.60754 GO:0006508~proteolysis 34 0.000392 PSMB10, MMP9, LGMN, UBA7, C1R, C1S, MYCBP2, TRIM5, USP18, ISG15, CASP7, CFH, FBXO6, ERAP1, RBCK1, ERAP2, CASP1, LONRF2, CFLAR, 1.90562051 0.434024893 0.024444329 0.647465 HERC6, HERC5, UBE2L6,SERPING1, CTSS, TMEM27, LAP3, CASP10, RNF43, PSME1, PSME2, CAPN13, CTSO, RNF19B, NEURL3 GO:0002478~antigen processing and presentation of exogenous peptide antigen 4 0.000705 TAP2, IFI30, CD74, B2M 21.48154029 0.640564398 0.04173812 1.1608957 GO:0002684~positive regulation of immune system process 13 0.000722 TLR3, SERPING1, C1R, TNFSF13, CD40, C1S, IDO1, CD74, B2M, CD47, MYD88, TAP2, CFH 3.226743973 0.648999439 0.0410139 1.1876774 GO:0001819~positive regulation of cytokine production 8 0.000804 DDX58, NOD1, MYD88, TLR3, JAK2, IDO1, CD40, CASP1 5.251043183 0.688486826 0.043866965 1.3221647 GO:0032020~ISG15-protein conjugation 3 0.002735 ISG15, UBA7, UBE2L6 35.44454148 0.981147822 0.136774022 4.4306498 GO:0016553~base conversion or substitution editing 3 0.002735 APOBEC3G, APOBEC3F, ADAR 35.44454148 0.981147822 0.136774022 4.4306498

23 Table S3: Canonical pathways identified by Ingenuity pathway analysis of genes up-regulated by IFNα in pancreatic islets.

Ingenuity Canonical Pathways -log(p- Ratio Genes value) (identified/pa thway Genes)

Interferon Signaling 1.12E+01 0.306 IFIT3,IFIT1,OAS1,IFITM1,MX1,IFI35,STAT2,IRF9,JAK2, STAT1,TAP1

Activation of IRF by Cytosolic Pattern 8.04E+00 0.153 DHX58,IFIH1,IRF7,CD40,DDX58,STAT2,IRF9,STAT1,A Recognition Receptors DAR,IFIT2,ISG15

Antigen Presentation Pathway 8.02E+00 0.225 B2M,HLA-A,HLA-E,HLAB, NLRC5, CD74, TAP1, TAP2, HLA-C

Role of Pattern Recognition 6.11E+00 0.104 IFIH1,OAS1,IRF7,OAS2,MYD88,DDX58,CASP1,NOD1, Receptors in Recognition of Bacteria EIF2AK2,TLR3,OAS3 and Viruses

24 Table S4: Top 12 transcriptional regulators identified by IPA upstream regulator analysis.

Upstream Log p-value of Target molecules in dataset Regulator Ratio overlap

IRF7 3.6 1.31E-59 ADAR,APOBEC3G,BCL2L13,CD40,CXCL10,DDX58,DHX58,GBP1,GBP3,GBP4,GBP5,HERC5,IDO1,IFI16,IFI35,IFI44,IFI44L,IFI6,IFIH1,IFIT1,IFIT2,IFIT3,IFITM1,IFIT M2,IFITM3,IL4I1,IRF9,ISG15,ISG20,JAK2,MX1,MX2,NMI,OAS1,OAS2,OAS3,OASL,PLSCR1,PSMB10,PSME1,PSME2,RSAD2,RTP4,STAT1,STAT2,TAP1,TAP2,TNF SF10,TRIM21,TRIM22,TRIM5,UBA7,UBE2L6,USP18,XAF1,ZC3HAV1

IRF1 1.28E-38 B2M,C1R,CASP1,CASP7,CD40,CEACAM1CTSS,CXCL10,EIF2AK2,ERAP1,GBP2,IDO1,IFI35,IFI44L,IFIH1,IFIT1,IFIT2,IFIT3,IFIT5,IFITM1,IFITM3,IL18BP,IRF4,IRF7, IRF9,ISG15,JAK2,MMP9,MX1,OAS1,OAS2,PML,PSMB10,PSME1,PSME2,RARRES3,RSAD2,STAT1,STAT2,TAP1,TAP2,TLR3,TNFSF10,TRIM22

STAT1 3.7 1.28E-37 APOBEC3G,APOL6,B2M,BATF2,CASP1,CCL8,CCND3,CD274,CD40,CMPK2,CXCL10,CXCL11,EIF2AK2,GBP1,GBP2,GBP5,HERC6,IDO1,IFI27,IFI35,IFI6,IFIT1,IFI T2,IFIT3,IFITM1,IRF7,IRF9,ISG15,JAK2,LY6E,MMP9,NEURL3,PSMB10,PSME1,PSME2,RNF213,RSAD2,SAMHD1,SERPING1,SLFN5,SP110,STAT1,STAT2,TAP1, TAPBPL,TLR3,TNFSF10,TRAFD1,TRIM22,TYMP,USP18,WARS

TRIM24 1.07E-33 BST2,CMPK2,CXCL10,DDX58,DDX60,DHX58,EPSTI1,GBP2,GBP4,HERC6,IFI35,IFI44,IFIH1,IFIT2,IFIT3,IRF7,IRF9,ISG15,JAK2,LGALS3BP,MOV10,NMI,OAS1,OA SL,PARP12,PSMB10,RTP4,SAMD9L,SAMHD1,SHISA5,STAT1,STAT2,TAP1,TRAFD1,UBA7,USP18

STAT3 9.7E-29 CASP1,CASP7,CCL8,CD274,CD40,CD74,CEACAM1,CFLAR,CXCL10,EIF2AK2,FGB,GBP2,HERC5,HLAC,IFI16,IFI27,IFI30,IFI35,IFI44,IFI6,IFIH1,IFIT1,IFIT3,IFIT5,I FITM1,IFITM2,IFITM3,IRF4,IRF7,ISG15,ISG20,ITGB6,JAK2,MMP9,MX1,MX2,MYD88,OAS1,OAS2,OAS3,OASL,PLSCR1,SLFN5,SP110,STAT1,TAP1,TLR3,TNFSF1 0,TRIM14,TRIM22,TRIM5,WARS,XAF1

IRF2 2.08E-18 B2M,CASP1,CEACAM1, CTSS,CXCL10,EIF2AK2,ERAP1,GBP1,IRF7,ISG15,OAS1,PSMB10,PSME1,PSME2,TAP1,TAP2,TLR3,TNFSF10,USP18

STAT2 2.2 5.44E-17 CXCL10,GBP1,IFI27,IFI35,IFI6,IFIT1,IFIT2,IFIT3,IFITM1,IRF7,IRF9,ISG15,MX1,OAS1,TNFSF10

IRF3 2.11E-11 B2M,CXCL10,DDX58,DHX58,GBP1,IFI44,IFI6,IFIH1,IFIT1,IFIT2,IFIT3,IRF7,ISG15,ISG20,MMP9,MX1,OAS3,RSAD2,USP18

IRF9 1.9 2.61E-10 CXCL10,GBP1,IFI27,IFIT3,IFITM1,IRF7,ISG15,STAT1,STAT2,TNFSF10

ISGF3 1.46E-09 IFIH1,IFIT2,IRF7,ISG15,RSAD2,TNFSF10

IRF5 3.07E-08 CXCL11,IFI44,IFIT1,IFIT2,ISG15,OAS1,PLSCR1,RSAD2,SP110,TNFSF10

IRF8 1E-07 B2M,CD40,CTSS,GBP1,IDO1,IFI44L,IFI6,IFIT2,ISG15,MMP9,OAS1,PML,TLR3

25 Table S5: Genes showing incresed mRNA expression and decresed DNA methylation.

RNAseq DNAm - Illumina 450 BeadChip Symbol RefSeq Name log2Rat_median q.value. Chr Start End Length ILMNNA ID UCSC_REFGENE Log2Rat.x ttest.p ttest.padj Storey.et.al..2003. GROUP ETV7 (ETS) NM_016135 ets variant 7 3.437541445 2.9E-131 chr6 36441948 36463445 1634 cg01270038 Body -0.6410 0.1407 0.9946 SIDT1 NM_017699 SID1 transmembrane family, member 1 1.654155171 5.54E-24 chr3 114733907 114831112 5027 cg07074309 Body -0.5668 0.0547 0.9946 RNF43 NM_017763 ring finger protein 43 0.935103643 4.75E-09 chr17 53786036 53849930 4567 cg21644778 Body -0.4646 0.2358 0.9946 TRIM38 NM_006355 tripartite motif-containing 38 1.808889382 3.36E-63 chr6 26071049 26093331 3278 cg22262055 3'UTR -0.4337 0.0037 0.9946 INPP4B NM_001101669 inositol polyphosphate-4-phosphatase, type II, 105kDa 0.921804285 1.05E-14 chr4 143168631 143987054 4050 cg06733281 Body -0.4310 0.0721 0.9946 ERAP1 NM_001040458 endoplasmic reticulum aminopeptidase 1 0.79433666 5.2E-18 chr5 96122269 96169648 5604 cg16492584 Body -0.4078 0.0299 0.9946 PNPT1 NM_033109 polyribonucleotide nucleotidyltransferase 1 3.023699385 0 chr2 55714701 55774515 4607 cg04770593 Body -0.3992 0.1682 0.9946 FAM111A NM_198847 family with sequence similarity 111, member A 1.503129787 4.87E-24 chr11 58666893 58679085 3787 cg15474378 3'UTR -0.3882 0.1769 0.9946 NUB1 NM_016118 negative regulator of ubiquitin-like proteins 1 1.856388333 3.43E-169 chr7 150669790 150706465 3119 cg11350520 3'UTR -0.3789 0.0008 0.9946 SCARB2 NM_005506 scavenger receptor class B, member 2 0.696472895 2.13E-135 chr4 77298917 77354059 4760 cg17465343 3'UTR -0.3683 0.0630 0.9946 EPSTI1 NM_033255 epithelial stromal interaction 1 (breast) 4.252076307 0 chr13 42360121 42464377 1586 cg17116694 Body -0.3598 0.0807 0.9946 CASP7 NM_033340 caspase 7, apoptosis-related cysteine peptidase 0.687924377 2.39E-29 chr10 115428924 115480654 2425 cg10981747 TSS1500 -0.3565 0.0235 0.9946 EIF2AK2 NM_001135651 eukaryotic translation initiation factor 2-alpha kinase 2 3.075901756 0 chr2 37187202 37228469 2280 cg23820429 TSS1500 -0.3551 0.1009 0.9946 CX3CL1 NM_002996 chemokine (C-X3-C motif) ligand 1 2.545085669 1.88E-190 chr16 55963914 55976457 3276 cg00331677 Body -0.3489 0.0583 0.9946 HLA-C NM_002117 major histocompatibility complex, class I, C 1.625447312 0 chr6 31344507 31347834 1533 cg11574174 Body -0.3408 0.0031 0.9946 STAT1 NM_139266 signal transducer and activator of transcription 1, 91kDa 3.729890695 0 chr2 191548507 191587221 2821 cg22595870 3'UTR -0.3396 0.0671 0.9946 CD47 NM_198793 CD47 molecule 0.764753304 2.49E-113 chr3 109244630 109292625 5357 cg21382749 Body -0.3309 0.0934 0.9946 TRANK1 NM_014831 tetratricopeptide repeat and ankyrin repeat containing 1 2.538510242 1.17E-111 chr3 36843312 36961552 10506 cg14220170 Body -0.3301 0.0131 0.9946 SPATS2L NM_015535 spermatogenesis associated, serine-rich 2-like 1.368158298 2.47E-263 chr2 200879229 201055231 6334 cg04945753 Body -0.3049 0.1149 0.9946 GSDMD NM_024736 gasdermin D 1.307344124 4.95E-32 chr8 144711619 144716372 1770 cg22995724 TSS1500 -0.2981 0.2371 0.9946 KLHDC4 NM_017566 kelch domain containing 4 1.569105973 2.04E-41 chr16 86298918 86357043 1886 cg07503662 Body -0.2923 0.0744 0.9946 ACSL5 NM_016234 acyl-CoA synthetase long-chain family member 5 0.849817308 3.41E-16 chr10 114125012 114178128 3402 cg13849691 TSS1500 -0.2893 0.0853 0.9946 PRKD2 NM_016457 protein kinase D2 1.631891075 9.84E-44 chr19 51869412 51912224 3619 cg00340161 Body -0.2892 0.0283 0.9946 IFI44L NM_006820 interferon-induced protein 44-like 6.890835056 0 chr1 78858675 78884418 5883 cg00458211 3'UTR -0.2818 0.0111 0.9946 NMI NM_004688 N-myc (and STAT) interactor 2.627121831 4.06E-303 chr2 151835227 151854676 1487 cg21213426 Body -0.2797 0.0509 0.9946 TYMP NM_001113756 thymidine phosphorylase 1.741466905 2.03E-137 chr22 49311047 49315380 1680 cg00082897 Body -0.2746 0.0924 0.9946 PHACTR4 NM_023923 phosphatase and actin regulator 4 0.834602837 8.46E-44 chr1 28568679 28699468 6225 cg11072045 TSS1500 -0.2738 0.0364 0.9946 NT5C3 NM_016489 5'-nucleotidase, cytosolic III 3.779743466 0 chr7 33020268 33047046 1646 cg10724774 Body -0.2724 0.1166 0.9946 PML NM_033238 promyelocytic leukemia 2.645312626 7.69E-64 chr15 72074066 72115788 3089 cg07194295 Body -0.2709 0.1296 0.9946 SLC2A12 NM_145176 solute carrier family 2 , member 12 0.894995995 4.91E-17 chr6 134350411 134415482 5604 cg05888385 Body -0.2698 0.0525 0.9946 IRS1 NM_005544 insulin receptor substrate 1 0.875142519 5.43E-14 chr2 227304276 227371750 8738 cg20951650 3'UTR -0.2691 0.0572 0.9946 TTC38 NM_017931 tetratricopeptide repeat domain 38 0.584053109 0.00000116 chr22 45042524 45068569 2624 cg03068030 3'UTR -0.2647 0.0785 0.9946 RUFY1 NM_001040452 RUN and FYVE domain containing 1 0.644997335 3.51E-14 chr5 178919337 178969625 2627 cg06868132 body -0.2647 0.2256 0.9946 TAP2 NM_000544 transporter 2, ATP-binding cassette 1.391286889 0.0000427 chr6 3979239 3992602 5691 cg03438552 body -0.2643 0.0818 0.9946 ATP10A NM_024490 ATPase, class V, type 10A 1.73058121 1.87E-11 chr15 23474952 23659442 5255 cg00602502 Body -0.2635 0.1147 0.9946 NCOA7 NM_181782 nuclear receptor coactivator 7 1.12958142 0 chr6 126153693 126293959 5471 cg08432204 body -0.2566 0.1250 0.9946 RNF213 NM_020954 ring finger protein 213 2.096142852 4.11E-98 chr17 75849261 75984680 18770 cg08059361 body -0.2551 0.0576 0.9946 NLRC5 NM_032206 NLR family, CARD domain containing 5 2.522832627 1.49E-232 chr16 55580910 55674937 6871 cg04799664 5'UTR -0.2547 0.0314 0.9946 ZC3HAV1 NM_024625 zinc finger CCCH-type, antiviral 1 1.882280066 1.96E-61 chr7 138378805 138445005 7184 cg08637123 body -0.2545 0.2553 0.9946 CASP1 NM_032977 caspase 1, 1.236735886 7.73E-38 chr11 104401446 104411067 1301 cg16837206 TSS1500 -0.2493 0.1076 0.9946 KIAA0226 NM_014687 KIAA0226 0.894714519 0.0000232 chr3 198882710 198960965 6924 cg14312391 body -0.2487 0.0736 0.9946 NOD1 NM_006092 nucleotide-binding oligomerization domain containing 1 0.876980288 4.61E-08 chr7 30430667 30484918 4510 cg18789624 5'UTR -0.2360 0.1604 0.9946 OGFR NM_007346 opioid growth factor receptor 1.525406348 1.36E-43 chr20 60906621 60915797 2427 cg13887016 body -0.2348 0.0302 0.9946 EPS8L1 NM_017729 EPS8-like 1 0.723506367 0.000000396 chr19 60283571 60291103 2217 cg07608565 body -0.2315 0.0658 0.9946 NEURL3 NR_026875 neuralized homolog 3 (Drosophila) pseudogene 1.785422948 2.06E-60 chr2 96527111 96537573 1677 cg25567448 TSS1500 -0.2282 0.1776 0.9946 IRF7 NM_004029 interferon regulatory factor 7 3.627674179 0 chr11 602554 605728 2060 cg09703963 TSS1500 -0.2241 0.2080 0.9946 CLIP3 NM_015526 CAP-GLY domain containing linker protein 3 1.254038037 1.04E-22 chr19 41197402 41215615 3363 cg24329710 body -0.2167 0.0786 0.9946 EHD4 NM_139265 EH-domain containing 4 0.893060905 1.54E-60 chr15 39978932 40052047 2897 cg18601229 3'UTR -0.2141 0.2163 0.9946 N4BP1 NM_153029 NEDD4 binding protein 1 1.521135575 5.93E-105 chr16 47130137 47201621 7113 cg01701649 Body -0.2129 0.0614 0.9946 WARS NM_213645 tryptophanyl-tRNA synthetase 2.475713614 2.16E-303 chr14 99869877 99912433 2498 cg24986058 Body -0.2069 0.1257 0.9946 RBCK1 NM_006462 RanBP-type and C3HC4-type zinc finger containing 1 1.370149178 1.46E-40 chr20 336708 359610 2774 cg02185402 Body -0.1983 0.0857 0.9946 SAMD9L NM_152703 sterile alpha motif domain containing 9-like 4.17051757 0 chr7 92597303 92615616 7138 cg11214047 body -0.1983 0.0395 0.9946 SERPING1 NM_001032295 serpin peptidase inhibitor, clade G, member 1 1.345285574 3.64E-76 chr11 57122280 57138902 1821 cg14311630 TSS1500 -0.1875 0.1308 0.9946 IDO1 NM_002164 indoleamine 2,3-dioxygenase 1 2.410165006 8.75E-63 chr8 39890484 39905104 1579 cg10262052 TSS1500 -0.1844 0.0937 0.9946 COL25A1 NM_032518 collagen, type XXV, alpha 1 0.804833335 0.0000704 chr4 109964487 110443248 2701 cg06501766 body -0.1841 0.1791 0.9946 SECTM1 NM_003004 secreted and transmembrane 1 4.137816618 2.83E-136 chr17 77872188 77885210 2287 cg09340279 3'UTR -0.1737 0.1115 0.9946 C5orf56 NM_001013717 chromosome 5 open reading frame 56 2.010904505 3.85E-10 chr5 131774571 131825958 2029 cg19734164 3'UTR -0.1584 0.0869 0.9946 MOBKL2C NM_145279 MOB1, Mps One Binder kinase activator-like 2C 1.322177647 5.48E-30 chr1 46845973 46855150 2826 cg01417692 body -0.1330 0.2487 0.9946

26 Table S6: Gene ontology enrichment analysis based on “Biological processes” of genes that showed increased mRNA expression and hypo- methylation induced by IFNα.

GO term Count % Gene name p Fold Bonferroni FDR Enrichment

GO:0002376~immune 25 43.1 CX3CL1; CD47; NMI; NLRC5; RBCK1; RUBCN; CASP10; 2.24E-08 3.33 4.21E-05 3.82E-05 system process ERAP1; EIF2AK2; EIF2AK2; EIF2AK2; FAM111A; GSDMD; IDO1; IFI44L; IRF7; HLA-C; NUB1; NOD1; PML; PRKD2; SECTM1; SERPING1; STAT1; TAP2; TRIM38; ZC3HAV1

GO:0031347~regulation 14 24.1 CX3CL1; CD47; NMI; NLRC5; ERAP1; EIF2AK2; IDO1; 5.83E-08 6.81 1.10E-04 9.95E-05 of defense response IRF7; NOD1; PML; SERPING1; STAT1; TRIM38; ZC3HAV1

GO:0006952~defense 9 15.5 NLRC5; EIF2AK2; FAM111A;IFI44L;IRF7;PML;STAT1; 3.47E-07 12.94 6.53E-04 5.93E-04 response to virus TRIM38; ZC3HAV1

GO:0045087~innate 14 24.1 CX3CL1; NMI; NLRC5; EIF2AK2; GSDMD; IRF7; HLA-C; 6.72E-07 5.51 0.0012 0.0011 immune response NUB1; NOD1; PML; SERPING1; STAT1; TRIM38; ZC3HAV1 GO:0001817~regulation 12 20.6 CX3CL1; NMI; NLRC5; EIF2AK2; GSDMD; IRF7; HLA-C; 7.92E-07 6.84 0.0014 0.0013 of cytokine production NUB1; NOD1; PML; SERPING1; STAT1; TRIM38; ZC3HAV1

27 Table S7: Insulin (INS) and glucagon (Gcg) mRNA levels detected by qRT-PCR in FACS sorted cell populations stained and unstained by Newport Green DCF diacetate (NG).

Sample Condition INS relative fold change Gcg relative fold change # (IFNα – or IFNα+) NG unstained NG stained NG unstained NG stained 1 IFNα plus 1 170.67 1 0.53 IFNα minus 1 49.87 1 0.40 2 IFNα plus 1 3.31 1 0.27 IFNα minus 1 3.12 1 0.31 3 IFNα plus 1 90.47 1 0.54 IFNα minus 1 86.44 1 0.80 4 IFNα plus 1 50.47 1 0.72 IFNα minus 1 93.85 1 0.84 5 IFNα plus 1 7.80 1 0.44 IFNα minus 1 4.75 1 0.64

28 Table S8: Primers used in experiments.

Primers for bisulfate DNA amplification Gene Forward Reverse SLC25A31 5’-TTTTTTTTATTAGAAAGTTTAGGTTT-3’ 5’- CTACACCTACAACAACAACTTCACC-3’ GGA3 5’-AGGGATTTTTTGTAAAGAGTGTTTG-3’ 5’-AACTTAATAAAACCCACTACCTCCC-3’ ERAP1 5’-TTTTTTTGGTTTTGTAGGTGTTTTT-3’ 5’-CCAATTCATTATAATCTCTTAATCCATAC-3’ IRF7 5’-TGAGGTTTATTTTGATTAAGGAG-3’ 5’-CTTCCCAAACTAACTAACACAAAC-3’

Primers for qRT-PCR hOAS1 5’-CCCCATTATTATTGAAAAGTACCTGAGA-3’ 5’-GCCGGGTCCAGGATCAC-3’ hSP100 5’-TGAACCATCTTCCTGCACACA-3’ 5’-CACCCTGGTCTTCCGTGAA-3’ hTLR3 5’-GGCTAGCAGTCATCCAACAGAA-3’ 5’-GCCCCCCCAAAAGTAGATACA-3’ hCD40 5’-CTCGCCCGGCTTTGG-3’ 5’-GGCTCGCAGATGGTATCAGAA-3’ hIFIH1 5’- AACAGCAACATGGGCAGTGA-3’ 5’-GCCACATTCTCTTCATCTGAATCA-3’ hGAPDH 5’-TGGGTGTGAACCATGAGAAGTA-3’ 5’-GAGTCCTTCCACGATACCAAAG-3’ hXRN1 5’-AAGAAAACATGACCCTCACAGAAAA-3’ 5’-TTGGGACCAACACTCAGCTTT-3’ hPNPT1 5’-TCCAGCTGGCTACTTCTATGATACA-3’ 5’-TCAGGCTCATTTACACCATCTACTG-3’ mTet1 5’-ACCAAGTGTGGCTGCTGTCA-3’ 5’-GGATTGCCTTCCCCTTCTG-3’ mTet2 5’-GGCAAATGTGAAGGATGCAA-3’ 5’-CCAGCTCCTAGATGGGTATAATAAGG-3’ mTet3 5’-CTGGCCCCACAGTAGCTTC-3’ 5’-CCCTTTTCTCCATACCGATCCT-3’ mGapdh 5’-CGTGCCGCCTGGAGA-3’ 5’-GATGCCTGCTTCACCACCTT-3’ mPnpt1 5’-GATCCAGAGCGGTGACTGTAGA-3’ 5’-TTGCCAGTTTCCCAGAGGATA-3’ mXrn1 5’-AGCCGTCCCTCCTGTTTTTAC-3’ 5’-GCCAAAGAGATGAGACGATGAA-3’

Primers for RT-PCR mTet2 5’-GAGATCGAGTGAGGAGGAGAAA-3’ 5’-GATTCTCACCCTGACAACAACA-3’ mXrn1 5’-AAGATGGGCGTCGATGTAGTAT-3’ 5’-AGATAGGAAGGGTGCGTAATGA-3’ mPnpt1 5’-ACATTGTTGCAAAGGAGGTTTT-3’ 5’-CCTGTGTTTGTCCTCTCTGAAA-3’

29