1. Chromatin remodeling
ATPases
non-covalent change

2. Lecture outline Types of chromatin remodelers complexes
protein domains
Activities of chromatin remodelers
on chromatin
in the organism

3. Chromatin remodeling ATPases
txn
assembly
DNA methylation
txn
exchange
txn repression
repair
DNA
methylation
heterochromation
recombination
archeal
TBP

4. ISWI
CHD
SWI2/SNF2
INO80/SWR1

5. ATPase domain Clapier and Cairns Ann. Rev. Biochem. 2009
Bromodomian: binds acetylated Lys on Histone tails
Chromodomain: binds methylated lysines on histone tails
SANT: interaction with N-termini of Histones
Clapier and Cairns Ann. Rev. Biochem. 2009

6. Activities of chromatin
remodeling ATPases

7. Clapier and Cairns, Annu. Rev. Biochem. 2009
Chromatin assembly
Clapier and Cairns, Annu. Rev. Biochem. 2009

8. Dynamic Range of Chromatin Structure Created by ATP-Dependent Chromatin Remodeling
Slide courtesy of Dr. Hua-Ying Fan

9. Shared characteristics of chromatin remodeling complexes
bind nucleosomes
are DNA-dependent ATPases
recognize histone modifications
ATPase activity can be regulated
interact with other proteins
From Clapier and Cairns, Annu. Rev. Biochem. 2009

10. Assays for chromatin remodeling
Non-covalent alteration!

11. sliding
Domains of SNF2-like ATPase

12. Assays for chromatin remodeling
Also MNAse qPCR or MNAse seq or MNAse H3 ChIP seq

13. Persistence

14. Perturbation of nucleosome core structure by the SWI/SNF
Proc. Natl. Acad. Sci. USA
Vol. 95, pp. 4947–4952, April 1998
Perturbation of nucleosome core structure by the SWI/SNF
complex persists after its detachment, enhancing subsequent
transcription factor binding
JACQUES COˆTE ,CRAIG L. PETERSON, AND JERRY L. WORKMAN
cold competitor
oligonucleosomes

15. Chromatin remodeling one remodeler per nucleosome
multiple enzymatic reactions destabilize 1 nucleosome
14 histone-DNA contacts
use ATP hydrolysis to break (ca. 1kcal/mol for each contact)
ATPases bind near center of nucleosomes (2 turns from dyad)
translocate along DNA 3’ to 5’
generate DNA loops, reposition nucleosome or destabilize

16. ISWI
(SNF2H)

17. SMALL COMPLEXES (generally)
Yadon and Tsukiyama Cell Snapshot 2011

18. SMALL COMPLEXES (generally)
MANY COMPLEXES
Yadon and Tsukiyama

19. nucleosome array formation chromatin assembly, replication
Roles of ISWI
nucleosome array formation
chromatin assembly, replication
heterochromatin formation
reprogramming (nuclear transfer)
transcriptional regulation
some PolII, PolI
Transcription: homeotic genes in Drosophila
Male X condensation defect (fly), also position effect variegation and polycomb repression defects( need regularly spaced chromatin)
ACF, WICH enriched at replication fork during heterochromatin replication, WSTF binds PCNA

20. ISWI can position nucleosomes onto unfavorable DNA

21. ISWI role in transcription
ISWI: green
PolII: red
Deuring et al., Molecular Cell, Vol. 5, 355–365, February, 2000The ISWI Chromatin-Remodeling Protein Is Required for Gene Expression and the Maintenance of Higher Order Chromatin Structure In Vivo.

22. ISWI: required for condensation of male X
Female iswi mut. Male iswi mut.
Deuring et al., Molecular Cell, Vol. 5, 355–365, February, 2000The ISWI Chromatin-Remodeling Protein Is Required for Gene Expression and the Maintenance of Higher Order Chromatin Structure In Vivo.

23. Role of the domains

24. Role of the domains Blue + charge Red - charge
Positive charge: contact DNA, negative charge contact histones

25. Role of the domains
Yamada et al., Nature 2011

26. ROLE of ISWI domains SANT/HAND domain contacts histone tails
- charge: histone tail interaction
+ charge: DNA interaction
Slide domain
linker DNA contact, ’measures’ distance
equal spacing of nucleosomes
ATPase domain
near dyad, motor, translocation

27. Loop propagation models
Eitehr dynaimc linker DNA or hinge region ratchets in right chromosome to close location
Yamada et al., Nature 2011

28. SWI/SNF

29. chromatin-remodeling ATPases
SWI2/SNF2 subfamily of
chromatin-remodeling ATPases
Isolated as sucrose-non-fermenting mutants in yeast
snf2, snf5, snf6
Isolated as mating type switch deficient mutants in yeast
swi1, swi2, swi3
SNF2=SWI2

30. LARGE COMPLEXES (generally)
Ca. 11 subunits, 2 MD in size
Casten et al., Cell snapshot 2011

31. SWI2/SNF2 complexes Core complex ATPase Snf2 (BRM/BRG1) Snf5 (BAF47)
Swi3 (BAF155/BAF170)
Function of some subunits not yet understood
ATPase and core: sufficient in vitro,
other subunits required in vivo
other subunits
Swp73 or BAF60
actin related proteins (ARP)
BAF 57

32. Two types of complexes in most organisms
a,b
a,b
Trends in Genetics 2007

33. Clapier and Cairns, Annu. Rev. Biochem. 2009

34. Ho and Crabtree Nature 2010

35. ROLE of SNF2/BRM domains
BROMO domain
binds acetylated lysines on histone tails
HSA domain
protein interactions
actin/ARP
transcription factors
ATPase domain
near dyad, motor, translocation

36. ROLE of SNF2/BRM domains
Hopfner et al. COSB 2012
Sen et al., NAR 2011
New SnAC domain required for remodeling activity

37. SNF2 ATPase activity change nucleosome position
increased regulatory protein access!
change nucleosome conformation
eject histone octamer
displace H2A/H2B dimer

38. Inducible gene expression: transcription initiation
Roles of SWI2/SNF2
Inducible gene expression:
transcription initiation
transcription elongation
Splicing
Repair
Roles in development and stress responses

39. Chromatin Remodeling Complex
Activation or repression!
sliding
ATP-dependent
Chromatin Remodeling Complex
Cis-regulatory element

40. Chromatin Remodeling Complex
Activation or repression!
sliding
ATP-dependent
Chromatin Remodeling Complex
Cis-regulatory element

41. Only a subset of genes depends on SWI2/SNF2
Whole genome expression analysis in S. cerevisiae
Holstege et al. (1998) Cell 95

42. Role in activation and repression of transcription
SWI2/SNF2 activities
Role in activation and repression of transcription
Regulation of select genes

43. Perturbation of nucleosome core structure by the SWI/SNF
Proc. Natl. Acad. Sci. USA
Vol. 95, pp. 4947–4952, April 1998
Perturbation of nucleosome core structure by the SWI/SNF
complex persists after its detachment, enhancing subsequent
transcription factor binding
JACQUES COˆTE ,CRAIG L. PETERSON, AND JERRY L. WORKMAN
cold competitor
oligonucleosomes

44. The 2MD SWI/SNF complex fits around the entire nucleosome
Zhang et al.

45. Nature Structural & Molecular Biology 15, 1272 - 1277 (2008) Published online: 23 November 2008

46. RSC docks onto nucleosome
RSC docks onto nucleosome
1 = ATPase

47. Casten et al., Cell snapshot 2011

48. Liu et al., MCB2011

49. CHD ATPases CHD1: role in chromatin assembly; open chromatin
in pluripotent cells
CHD3, 4
HDAC complex subunits!
NuRD complex
also contains Me-DNA binding protein (MBD2)
complex connects deacetylation, chromatin remodeling
and DNA methylation; repressive function
CHD7: together with PBAF; CHARGE syndrome
Together with SNF2: role in transcriptional elongation

50. Sims and Wade, Cell Snapshot 2011

52. New insight into domains from crystal structure
Hopfner et al. COSB 2012
Sharma et al. JBC 2011

53. ROLE of CHD ATPase domains
CHROMO and PHD domains
bind methylated lysines on histone tails
modulate activity of remodelers
ATPase domain
near dyad, motor, translocation

54. Chromodomains gate CHD1 activity
Hauk et al. Molec. Cell 2010

55. Role in chromatin assemblyHC
Lusser et al., Nature Struc Mol Biol 2005

56. INO80 SWR1 chromatin assembly DNA repair
interacts with phosphorylated H2A.X (gammaH2A.X)
transcription
exchange H2A.Z with H2A
SWR1
H2A exchange with H2A.Z
Boundary to heterochromatin spreading
transcriptionally poised promoters (together with H3.3)

57. INO80/ SWR1
ATPase domain
Bao and Shen Cell Snapshot 2011

58. Role of INO80
complex
Morrison and Shen, Nature reviews Mol Cell Biol, 2009

59. Role of SWR
complex
Biochem. Cell Biol vol

60. Instability of H2AZ allows high temperature to turn on genes in plants

61. Role of SWI2/SNF2 ATPases in the organism

62. Role of chromatin remodeling ATPases in cancer
SWI2/SNF2 subgroup
*mouse BRG1 mutants develop tumors at high
frequency (non-small lung carcinoma)
Biallelic loss observed in prostrate, lung, breast and pancreatic
cancer cell lines
*subunit hSNF5 (INI1) is tumor suppressor
LOH in nearly all cases of pediatric rhabdoid sarcoma
recapitulated in mouse models (conditional inactivation
leas to lymphomas with 100% penentrance)
Other subunits also involved

63. Role of chromatin remodeling ATPases in cancer
Others
*dNURF: ISWI and p301 involved in neoplastic
transformation
*NURD: CHD1/MI2 linked to certain breast cancers

64. Role in other diseases * X-linked mental retardation *William syndrome
*Cockayne syndrome
*Schimke immuno-osseous dysplasia

65. Why are they so important?
Maintenance and alteration of nucleosome
occupancy and positioning

66. Useful terminology

67. Specificity of chromatin remodelers
a. recruitment

68. CRM; chromatin remodeler
Transcription factor
Nuclear hormone receptors-Brg1
H3K4me-ISWI
Methyl -lysine
H3K16 non ac - ISWI
Polymerase
Gal1promoter SNF2
Histone H3 globular domain-SNF2 (hht2-11 mutant)
Acetyl-Lysine
H3K14ac-RSC
ATP-DEPENDENT NUCLEOSOME REMODELING
Peter B. Becker and Wolfram Hörz
Annu. Rev. Biochem :247–73

69. Targeting of SWI/SNF
no DNA binding specificity
recruited by transcription factors in many organisms
yeast: SWI5, GCN4, GAL4, VP16
Drosophila: Ikaros, hunchback, tramtrack
human: EKLF, C/EBPB, GR, MyoD
plants: LFY, TCP, MP

70. Regulation of SWI2/SNF2 activity 1. Post-translational modifications
phosphorylation, acetylation, de-ubiquitylation
2. Complex composition
regulatory subunits (SWI5, Drososphila)
tissue specific subunits (BAF60)
3. Interaction with small molecules
phosphatidyl inositol
Hogan and Weisz
Mutation Research 618 (2007) 41-51

71. Regulation by phosphorylation, acetylation
Binding platform figure

72. Clapier and Cairns, Ann. Rev.
Biochem. 2009

73. Regulation of SWI2/SNF2 activity
1. Post-translational modifications
phosphorylation, acetylation, de-ubiquitylation
2. Complex composition
regulatory subunits (SWI5, Drososphila)
tissue specific subunits (BAF60)
3. Allosteric regulation by ATPase domains (CHD1)
4. Interaction with small molecules
(phosphatidyl inositol)

74. Regulation by complex composition
Yoo and Crabtree, Nature 2010

75. Yoo et al., Nature 2009

76. Yoo et al., Nature 2009

77. Can have instructive roles!
Takeuchi and Bruneau Nature 2009

78. Role in many aspects of development
Ho and Crabtree Nature 2010

79. Ensure packaging of genome Enable differential accessibility
Nucleosome me
DNA
methylation
H3K27me3
from Horn and Peterson Science, 2002

80. Lecture summary Types of chromatin remodelers complexes
protein domains
Activities of chromatin remodelers
on chromatin
in the organism

81. Glossary and Summary I Chromatin remodeler Families:
ISWI; SWI/SNF; CHD; SWR1; INO80
Others involved in repair and recombination
Remodeling Complexes
ISWI: ACF, NURF, CHRAC
SWI/SNF: BAF, pBAF
CHD: Mi2/NURD
Important domains:
Bromodomain (SWI/SNF)
SANT, Slide (ISWI; CHD)
PHD, Chromodomain (CHD)
ATPase domain (all)

82. Glossary and Summary II
Activities of chromatin remodelers
properly space nucleosomes on chromatin
after replication, transcription, repair
alter nucleosome position or occupancy
in response to exogenous or endogenous cues
In the organism
prevent loss of cell identity (cancer)
role in pluripotency (ESC) and differentiation
survival under stress