DNA methylation variation of

human-specific Alu repeats

Bakshi_Figure 1

A) B)

C)

Number of Alu elements

Stan

dard

Dev

iatio

n

D)

(Med) (High)

% A

lu e

lem

ents

(Low methylation)

% methylation

Upstream (kb) Downstream (kb)

TSS

% A

lu e

lem

ents

Low Med High Low Med High

Bakshi_Figure 2

  Br-mat-N Br-mat-T Br-C Lu-N Lu-CBstUI: CpG #3 66.3% 83.7% 74.1% 81.6% 27.9%BstUI: CpG #4 64.3% 84.2% 72.6% 77.2% 29.3%A-box: CpG #5 70.1% 90.9% 77.5% 82.1% 39.5%B-box: CpG #10 70.2% 83.8% 72.8% 82.9% 30.3%HpyCH4III: CpG #12 70.5% 83.9% 69.9% 82.3% 27.2%

A)

B)

Br-mat-TBr-mat-N Br-C Lu-N Lu-C

Bakshi_Figure 3

Bakshi_Figure 4

TumorA)CEBPG-Alu

DHODH-Alu

1 2 3 4 5 6 7 8Normal 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48

B) C) D)

% m

ethy

latio

n

E)

% in

stan

ces F) G)

Bakshi_Figure 5

E)

D)

Matched Breast Normal

Mat

ched

Bre

ast T

umor

B) Normal Tumor

AluYb8 (+)chr18:14785792-14786070

Normal Tumor

AluYb8 (-)chr6:15756638-15756944

CpG: UnknownMethylated Unmethylated

Methylation Level

Stan

dard

Dev

iatio

n

Nearest gene

(within 1000 kb)

Alu methylation in primary

breast tumor

Distance to nearest gene (bp)

BRCA PANCANABCC11 2663AJAP1 -443760

ANKRD30B 37692BMP2 112122

C9orf123 -491001DHX30 127394

DTNBP1 -93518HTR1A 184729

IBTK 605939LTBP2 4264MKI67 -193520NPAP1 -81056NR1H4 30681NRG1 -601035NTRK3 162085PACRG -254508PCSK5 206705

PMFBP1 -151457RPS6KA3 -239401

RYR2 81584SRRM4 -156786

N/A N/A N/A N/A

Gene Regulation

% A

lu e

lem

ents

(Methylation ≤ 85%)A) C)

% methylation

Gene expression

BRCA LUSC LUAD Lung PANCANRABEPK          

UBE2T          

EIF2B1        

DHODH      

INTS5          

MAP3K7        

EDAR    

UGGT2        

HIGD1B  

CEBPG          

HTR3E      

OR10Q1      

OSBPL10      

AASDH      

TMSB4Y      

ADAD1          

IDNK          

HENMT1          

Bakshi_Supplemental Figure 1

CEBPG DHODH UBE2T

HpyCH4IV

Br-m

at-T

Br-C

Lu-N

Lu-C

Br-m

at-N

U HpyCH4IVU

Br-m

at-T

Br-C

Lu-N

Lu-C

Br-m

at-N

HphIUM

Br-m

at-T

Br-C

Lu-N

Lu-C

Br-m

at-N

U HpyCH4IV

BstUIU

EDAR

HpyCH4IV

Br-m

at-T

Br-C

Lu-N

Lu-C

Br-m

at-N

U

HphIMU

TaqαIU

MAP3K7

Br-m

at-T

Br-C

Lu-N

Lu-C

Br-m

at-N

U BstUI

U HpyCH4IV

A) B) C)

D) E)

Bakshi_Supplemental Figure 2

Bakshi_Supplemental Figure 3

A)

B)

DHODH:

MAP3K7:

Br-mat-TBr-mat-N Br-C Lu-N

Lu-CBr-mat-N Br-mat-T Br-C Lu-N

Bakshi_Supplemental Figure 4

A) B)