SCIENCEsciencemag.org 16 JULY 2021•VOL 373 ISSUE 6552 307
-3 -2 -1 (^01) H4K79acH4Kpolyac
H4K16ac
H4K20ac
H4K5ac
H4K12ac
H4K77ac
H4K91ac
H4K8ac
H3S10ph
H3Y41ph
H3K4ac
H3K64acH3K27cr
H3K27acH3K122ac
H3K36acH3K23ac
H3K18acH3K18acK23ac
H3K37ac(H2A+H2B+H3)KpolyacH3K18cr
H3K14acH3KpolyacH3K14crH3K9acH3K56acH3K9crH3K115ac
H
3K4me3K27me3
H
(^3) R2me
H3R2me2a
H3K4me2H3K4me3
H3K4me
1
H3K27mH3K9me3
e 3
H3R
H3K36me42me2a
3
H4Kpolyac
-H
3K4me3
H4K1
2ac-H3
K4
me
3
H4Kp
olyac-H
(^3) K27m
e 3
H4Kpolyac-H4K5ac-H3K4me3
H3K9m
e3
H4K16ac-H3K4me3
H4K5ac-H3K27me3
H4K2
0ac-H3
H4K8ac-H3K4mK (^2) 7me3
e3
H4K8ac-H3K9me3
H4K20ac-H3K9me3
H4K20ac-H3K4me3
H4K12ac-H3K27me3
H4K8ac-H3K27me3
H4K12ac-H3K9me3
H4K16ac-H3K27me3
H4K5ac-H3K9me3
H4K16ac-H3K9me3
H3K4me3-H2BK120ub
H2AK119ub-H4R3me2a
H2BK120ub-H4R3me2a
H3K27me3-H2BK120ub
H2A
K119ub
H3K9m
e3-H2BK120u
b
H2B
K120ub
H3Kpo
lyac-H2BK120ub
(H2A+H2B+H3+H4)Kpolyac
(H3+H4)Kpolyac
H4R17A,R19A-H3T118H
Acidic patch
H4R17A,R19A-H3R42A
H4R17A,R19A
H3R42A
H4R45A-H3T118H
H3T118H
H3.3G34VH3.3K36MH3.3K27M
H4R45A-H3R42A
H3.3G34W
H4R45A
H3.3G34R
H2BK
108ac
H2BKpolya
c
H2
AK9ac
H2AK13acH2AKpolyacH2BK11ac
H 2
AK118
ac
H2
BK12a
c
H2AK15acH2BK15ac
H2BK12
0a
c
H2
BK
(^2) 0a
c
H2AK5acH2BK
5ac
H 2
BK
(^1) 25a
c
H 2
BK1
16ac
H (^2) A.Z
H2A.Z H3.3
H2A.
X
H3.3
H2BS112GlcNAc
5-meCpG
H4R3me2s
H4R3me2a
H4R3me
H4 acetylation &
H3 acetylation
H4 acetylation &
H3 methylation
H4
acetylation
H3 acylation
H2A/H2B acetylation
Ubiquitination
Histone core &
tail mutations
H4
methylation
Other
Histone
Variants
H3
phosphorylation
H3 methylation
ncBAF Activity
PBAF Activity
cBAF Activity
Positive No Change
A
SMARCC1
HA-DPF2
(cBAF)
SMARCC2
ARARID1BID1A/B
SMARCA4/2
SMARCB1
SMARCD2
BCL7A/C
SMARCE1
ACTL6A
HA-DPF2
SMARCD1
HA-BRD7
(PBAF)
Silver Stain
BCL7A/C
ACTL6A
SMARCD1/PHF10
HA-BRD7
SMARCA4/2
ARID2/PBRM1
SMARCC1
SMARCE 1
SMARCC2
SMARCB1
SS18
cBAF PBAF ncBAF
1.04 MDa 1.41 MDa 0.87 MDa
Nucleosome acidic patch
PHF10
ARID2
ACTL6
ACTB
SMARCE1
SMARCD1/2
SMARCC1/SMARCC2
BCL7
SMARCA4/2ATPase subunits
SMARCB1
PBRM1
BRD7
Nucleosome
acidic patch
DPF2 ARID1A/B
ACTL6
ACTB
SMARCE1
SMARCD1/2
SMARCC1/SMARCC2
BCL7
SMARCA4/2
ATPase subunits
SMARCB1
Silver Stain
HA-GLTSCR1L
(ncBAF)
BCL7A/C
β-actin
β-actin
β-actin
ACTL6A
SMARCD1
BRD9
HA-GLTSCR1L
SMARCA4/2
SMARCC1
SS18
Silver Stain
A
B
D E
C
Endogenously-purified
mSWI/SNF complexes and subcomplexes
HA-pulldown
Incubation
REAA
Nucleosome
remodeling
(rates)
Complex-NCP binding
(enrichment)
Restriction
site
109-member barcoded NCP library
Multiplexing,
pooling samples,
sequencing
core PTMs
tail PTMs
variants
core mutants tail mutants
Nucleosome acidic patch
BRD9
ACTL6
ACTB SMARCD1
SMARCC1
BCL7
SMARCA4/2ATPase subunits
SS18
GLTSCR1/1L
?
cBAF
Bindi
ng
cBAF Acti
vity
PBAF B
indin
g
PBAF
Activ
ity
ncBA
F Bind
ing
ncBA
F Ac
tivity
Complex
0.0
0.2
0.4
0.6
0.8
1.0
% of significant marks relativeto unmodified nucleosomes (n=107)
cBAF PBAF ncBAF Negative
(^01020) Time (min) 30 40 50 60
0.0
0.2
0.4
0.6
0.8
1.0
Percent Histone Substrate Remaining
(^01020) Time (min) 30 40 50 60
0.0
0.2
0.4
0.6
0.8
1.0
Percent Histone Substrate Remaining
(^01020) Time (min) 30 40 50 60
0.0
0.2
0.4
0.6
0.8
1.0
Percent Histone Substrate Remaining
Fig. 1. Comprehensive profiling of nucleosome binding and remodeling
activities of mSWI/SNF family complexes using DNA-barcoded nucleosome
libraries.(A) Schematics and representative SDS–polyacrylamide gel electro-
phoresis silver stain gel analyses of endogenous human mSWI/SNF family
complexes from HEK-293T cells using HA-tagged DPF2, BRD7, and GLTSCR1L as
baits for cBAF, PBAF, and ncBAF, respectively. (B) Strategy for high-throughput
sequencing–based nucleosome binding and remodeling activity analyses of
endogenous human mSWI/SNF complexes incubated with a DNA-barcoded
mononucleosome library (n= 109 mononucleosomes). (C) Radar plots mapping the
activity measurements of all three mSWI/SNF family complexes across the entire
mononucleosome library, normalized to activity on unmodified substrates. Marks and
variants are distinguished by color. A positive score indicates increased activity,
and a negative score decreased activity, relative to complex activity on unmodified
nucleosome substrates. Marks are sorted by cBAF remodeling activity within each
mononucleosome subtype. (D) Activity curves for cBAF, PBAF, and ncBAF complexes
across the 109 mononucleosomes in the library using one-phase decay. Average of
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