UPF1

Smbb’

SMG6

Smbb’

KD - SMG6 SMG6 100% 33% 11% shRNA1 shRNA2

0

20

40

60

80

100UPF1 mRNA

0

20

40

60

80

100SMG6 mRNA

020406080

100

SMG7 mRNA

no KD shRNA1 shRNA2

KD - UPF1 UPF1 100% 33% 11% shRNA1 shRNA2

Supplementary Figure 1

UPF1 protein

SMG6 protein

rela

tive

mR

NA

leve

lsre

lativ

e m

RN

A le

vels

rela

tive

mR

NA

leve

ls

no KD shRNA1 shRNA2

no KD shRNA1 shRNA2

DNAJB6

tv1

DNAJB6

tv2

LETM

D1

POFUT2

tv1

POFUT2

tv2

POFUT2

tv3

RCP9

RP9P

TMEM

-183

A

0

1

2

3

4

5

6

7

8

9

10

11

12

13

14

mRNA expression levels in NMD factors' knockdown

no KD

UPF1 KD microarray

UPF1 KD RT-qPCR

SMG6 KD microarray

SMG6 KD RT-qPCR

SMG7 KD microarray

SMG7 KD RT-qPCR

rela

tive

mR

NA

leve

lsSupplementary Figure 2

Supplementary Figure 3

KD - UPF1 SMG6 SMG70

0.2

0.4

0.6

0.8

1

1.2

1.4

1.6

1.8

2

Histone transcripts in several NMD factors' knockdowns

HIST1H1

HIST1H2ab

HIST1H3

Rel

ativ

e e

xpre

ssio

n o

f hi

sto

ne

tra

nsc

rip

ts