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Chromatin remodeling ATPases non-covalent change.

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Presentation on theme: "Chromatin remodeling ATPases non-covalent change."— Presentation transcript:

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 repression txn assembly DNA methylation exchange repair DNA methylation heterochromation recombinationarcheal TBP

4 ISWI CHD SWI2/SNF2 INO80/SWR1

5 ATPase domain Clapier and Cairns Ann. Rev. Biochem. 2009

6 Activities of chromatin remodeling ATPases

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

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

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

13 Persistence

14 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 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 Chromatin remodeling

16 ISWI (SNF2H)

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

18 SMALL COMPLEXES (generally) MANY COMPLEXES Yadon and Tsukiyama

19 Roles of ISWI nucleosome array formation chromatin assembly, replication heterochromatin formation reprogramming (nuclear transfer) transcriptional regulation some PolII, PolI

20 ISWI can position nucleosomes onto unfavorable DNA

21 ISWI: green PolII: red ISWI role in transcription 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 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. ISWI: required for condensation of male X

23 Role of the domains

24 Blue + charge Red - charge Role of the domains

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

26 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 ROLE of ISWI domains

27 Loop propagation models Yamada et al., Nature 2011

28 SWI/SNF

29 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 SWI2/SNF2 subfamily of chromatin-remodeling ATPases

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

31 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 SWI2/SNF2 complexes

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

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

34 Ho and Crabtree Nature 2010

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

36 New SnAC domain required for remodeling activity Sen et al., NAR 2011 Hopfner et al. COSB 2012

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

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

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

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

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

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

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

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

46 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

51

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

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

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

55 Role in chromatin assembly Lusser et al., Nature Struc Mol Biol 2005 CHR HC

56 INO80 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 Bao and Shen Cell Snapshot 2011 INO80/ SWR1 ATPase domain

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

59 Biochem. Cell Biol vol Role of SWR complex

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)

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

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

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

77 Takeuchi and Bruneau Nature 2009 Can have instructive roles!

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

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

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


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