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Primers on chromatin
Author: Sabbi Lall
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"T o accompany the Focus on Chromatin appearing in this issue of Nature Structural & Molecular Biology, a series of primers has been specially prepared that covers the wealth of knowledge in four areas of chromatin research. These areas include functions associated with covalent histone modifications, the enzymes that mediate these modifications, modules that recognize chromatin, and the ATP-dependent chromatin-remodeling complexes. In such a complex field, the information has inevitably been somewhat simplified. As an example, the correlation between modifications and functions are often context dependent. For instance, H3K9 methylation has been associated with transcriptional activation when present in the coding region of the gene, but has also been associated with repression. The reference list provides further reading and details, as do the Reviews and Perspective in this issue. Although there are many informative structures in this field, space constraints allowed only representative structures to be shown, followed by reference citations for related structures (?3D REF? column). The primers can be used as a stand-alone resource ? feel free to tear them out of the issue or print out the PDF versions and modify or add to them yourself as new data emerge. The online versions of the primers contain hyperlinks to the Protein Data Bank as well as 3D view links that allow structural visualization. Sabbi Lall is an Associate Editor at Nature Structural & Molecular Biology, 75 Varick Street, New York, New York, 10013, USA. e-mail: s.lall@natureny.com PRIMERS ON CHROMATIN SABBI LALL. DESIGN BY KATIE RIS-VICARI. NATURE STRUCTURAL & MOLECULAR BIOLOGY VOLUME 14 NUMBER 11 NOVEMBER 2007 1110 C S S S Me1 Me2 Me3 Ub1Ac Me2Me1 Cit PhosSuH2A H2B H2AX H2A.Z H3 1AOI 3D View (ref.1) H4 CENP-A Symbols indicate processes associated or correlated with modification (effects will be context dependent) C S Lys Arg Ser Thr Cell divisionChromatin condensation Replication/histone depositionDNA repairDomain-limited functional chromatin changes Active transcription Symbols in purple indicate data from yeastApoptosisRepressed transcription/ silent regions R2 R8 R17 R26 S7/17/ 19/27 S139 T3 S10 T11 S28 Other modifications include ADP ribosylation, such as that at H2BE2, proline isomerization, such as that at H3P38 and biotinylation. ?3D ref? columns list structure citations (in some cases including homologs from other species). Further reading can be found in refs. 106?139 and references cited therein. Additional histone variants have been identified and are modified. These include macroH2A and histone H3.3 (ref. 106). Residues not shown are also modified 106 , and the Reviews in this issue cover in detail the functions associated with modifications and cross-talk between modifications 107?112 . Structure figures used PyMOL (http://pymol.sourceforge.net/), domain assignments used PubMed and/or SMART (http://smart.embl-heidelberg.de/). Me, methylation; Ub1, monoubiquitination; Ac, acetylation; Cit, citrullination; Phos, phosphorylation; Su, sumoylation. 1111 VOLUME 14 NUMBER 11 NOVEMBER 2007 NATURE STRUCTURAL & MOLECULAR BIOLOGY FUNCTIONS ASSOCIATED WITH COVALENT HISTONE MODIFICATIONS (x8) (x4) (x7) Prolyl Isomerases PROTEIN TARGETPROTEIN TARGET 3D REF 3D REF Kinases 67,68 60,61 62 Non?SET domain lysine HMTs SET domain lysine HMTs Histone deacetylases (HDACs) MYST family GNAT family Histone methyltransferases (HMTs) Histone demethylases Arginine HMTs LSD1/BHC110 (x4) (x7) (x6) (x3) JmjC family demethylases Histone acetyltransferases (HATs) Ubiquitin ligases Deiminases Other 44,45 (x8) ATM/ATR/DNA-PK (Sc Mec1/Tel1) MST1 (Sc Ste20) Haspin MSK1&2 Sc Aurora B & Sc Snf1 Dm NHK1 ZIP Sc CK II & Sps1 H3S10 Dm H2T119 H3T11 H4S1 H2AXS139 (Sc H2AS129) H2BS14 (Sc H2BS10) H3T3 H3S10 63 64?66 PROTEIN REPRESENTATIVE STRUCTURE TARGET 3D REFDOMAIN 3D REFPROTEIN TARGET DOMAIN 5GCN 3D View 1FY7 3D View 1W22 3D View 1O9S 3D View 1ORI 3D View Tt Gcn5 HDAC8 Sc Esa1 SET7/9 PRMT1 LSD1 2CKL 3D View 2DEY 3D View Protein database codes in red For other modifying enzymes see further reading. BMI?RING1B PADI4 2H94 3D View 2Q8E 3D View JMJD2A (x6) Gcn5 PCAF &GCN5L Sc Rpd3 HDAC8 b Sc Hos1 & Hos2 Sc Hos3 Sc Hda1 Sc Esa1 (TIP60) MOZ & MORF/ Sc Sas3 Sc Set1 a , SET1A & 1B MLL1-4 a Ash1 a SUV39H1 & H2 ESET/SETDB1 Nc DIM-5 RIZ1 G9a EuHMTase1 CARM1 PRMT1/Sc Hmt1 Sc Dot-1 & DOT1L LSD1/BHC110 Sc Fpr4 PADI4 BMI?RING1B RNF20/40 Cul4-DDB-Roc1 Sc Rad6/Bre1 Dm Lid/JARID1A,B,C,D JHDM2a & b JMJD2D JMJD2B Sc Rtt109 H3K9/14/18/23/27, H2B H3K9/14/18 H2A, H2B, H3, H4K5/8/12ac H3ac, H4ac H3ac, H4ac H2BK11/16ac, H4K12ac H3, H2BK11/16ac H2A, H4 H3K14/23 H3K4 H3K4 H3K4 H3K9 H3K9 H3K9 H3K9 H3K9 H3K9 H3R2/17/26 H4R3 H3K79 H3K4me1/2, H3K9me1/2 H3P30/38 H3R2/8/17/26, H4R3 H2AK119 H2B H3/H4 H2BK123 H3K4me2/3 H3K9me1/2 H3K9me2/3 H3K9me3 H3K56 19?21 2?9 10,11 14,15 16 29 30 31,32 46,47 48,49 50?54 Sc Hpa2 Sc Hat1 Hst3 & 4 SIRT1 b Sc SIRT2 Sc Hst2 Sc Sir2 HBO1 MOF/Dm Mof/ Sc Sas2 Sp Clr4 Dm E(z) & EZH2 SET2 NSD1 SMYD2 SUV420H1 & H2 SET7/9 SET8/PR-SET7 PRMT5 PRMT6 UTX JMJD2A & C JHDM1a & b JMJD6 CBP/p300 H3K14 H2AK5/7, H4K5/12 H3K56ac H3K9ac, H4K16ac, H1ac H3K9ac, H4K16ac H4K16ac H3K56ac, H4K16ac H4K5/8/12 H4K16 H3K9 H3K27(EZH2, H1bK26) a H3K36 H3K36 H3K36 H4K20 H3K4 H4K20 H3R8/H4R3 H3R2 H3K27me2/3 H3K9/36me2/3 H3K36me1/2 H3R2me2, H4R3me2 H2AK5, H2BK12/15 H3K14/18, H4K5/8/12 55?59 17 12 13 See note 23 27 22?26 28 33,34 35,36 37?41 42,43 PROTEIN TARGET 3D REF (Sas3) a In complexes, COMPASS for Set1, EZH2 in PRC complexes. b Please see further reading for the full set of mammalian HDACs. Proteins mammalian except Sc, S. cerevisiae; Sp, S. pombe; Nc, N. crassa; Tt, T. thermophila; Dm, D. melanogaster Enzyme may have different in vitro, in vivo or context-dependent targets, and may have higher efficiency for one residue over others. Additional structures both awaiting publication and published (e.g. CBP/p300) are available in the protein databank. The human HDACs and other structures in this family are discussed in ref. 28 and references therein. PRMT SWIRM PWWP Ankyrin WW JmjC JmjN KIX BAH HDAC PHD TPR Sir2-like Tudor SANT RRM SET Post-SET Pre-SET (any type) Fbox Zinc finger (any type) AT hooks Bright/ARID Bromodomain Chromodomain MYST acetyltransferase Acetyltransferase Methyl-binding (MBD) Other conserved domain Amino oxidase domain NATURE STRUCTURAL & MOLECULAR BIOLOGY VOLUME 14 NUMBER 11 NOVEMBER 2007 1112 HISTONE-MODIFYING ENZYMES CBP/p300 Sc Bdf1/BRD8/dBrd8 Polybromo/BAF180 Sc Rsc1,2,4 Dm NURF301/BPTF hACF1/dACF ? H4ac H3ac H3K14ac (Rsc4) ? ? 140 71 (Rsc4) 81 (BPTF) Sc Gcn5 PCAF TAF1 hBRG1 Sc Snf2 Sc Sth1 H4K16ac H4K16ac H4ac H3K14ac H3ac/H4ac ? HP1/Swi6 PC1/PC2/Polycomb/LHP1 CHD1 Sc Chd1 dTip60/hTIP60, MOF, Esa1 Sp Clr4, SUV39H1 dMi-2/CHD3/CHD4/CHD5 CHD6/CHD7/CHD8/CHD9 hBAF155 dMrg15/hMRG15, Sc Eaf3 a CDY1 ? ? ? H3K36me, H3K4me H3K9me2/3 H3K9me2/3 H3K27me3, H3K9me3 H3K4me1/3 ? ? H3K9me BHC80 Yng1 ING2 BPTF/Dm NURF301 NSD1 MLL hACF1/dACF Ash1 JMJD2A/2B/2C JHDM1a/b JARID1C dMi-2/CHD3/CHD4 Core histones ? ? ? H3K9me3 ? H3K4me0 H3K4me2/3 H3K4me2/3 H3K4me2/3 ? ? JMJD2A 53BP1 Sp Crb2 H3K4me3/H4K20me3 H4K20me1/2 H4K20me2 5,6 10 18 69,70 77 72,73 74,75 76 101,102 17 (Dm MOF) 33 (Clr4) 78 79 80 81 55 82 82 Chromodomain PHD Tudor Bromodomain PROTEIN REPRESENTATIVE STRUCTURE TARGET 3D REF ESET/SETDB1 JMJD2B/2C PHF20 H3K9 ? H4K20me2 GCN5 HP1 Yng1 53BP1 1E6I 3D View 1KNE 3D View 2JMJ 3D View 2IG0 3D View PROTEIN TARGET 3D REF WDR5 RbAp46/48 p55 H3R2*/H3K4me2* ? ? MDC1 Sp Crb2 53BP1 MCPH1 H2AXPh H2APh ? H2AXPh 14-3-3 H3S10Ph/H3S28Ph 83?85, 141 86,87 88 WD40 BRCT 14-3-3 L(3)MBTL1 SCML2 SFMBT PHF20L1 H1bK26me1/2, H4K20me1/2 ? H3K9me1/2, H4K20me1/2 H3K4me1, H4K20me1 89 90 MBT (*WDR5 can bind unmodified H3 tail) PROTEIN TARGET 3D REF WDR5 MDC1 14-3-3 L(3)MBT L1 PROTEIN TARGET 3D REF See ref. 108 for further information and examples. Question mark indicates that the exact histone binding specificity is unknown. a Chromo barrel-like motif. List is mostly limited to proteins on these pages. 2H6N 3D View 2AZM 3D View 2C1N 3D View 1OZ2 3D View 1113 VOLUME 14 NUMBER 11 NOVEMBER 2007 NATURE STRUCTURAL & MOLECULAR BIOLOGY HISTONE RECOGNITION DOMAINS The SWI/SNF family Rsc1,2,4 Snf6 Swp82 Taf14/ Swp29 Swi3 Swp73 Snf11 Arp7 Swi2/Snf2 Swi1/Adr6 Snf5 Arp9 Rtt102 Rsc9 Rsc5 Rsc10 Rsc30 Rsc3 2R0S 3D View (ref. 71) (See note A) Rsc7 Htl1 Rsc8/Swh3 Ldb7/ Rsc14 Rsc6 Sth1 Sfh1 SWI/SNF RSC 2FQ3 3D View (ref. 96) 1Z63 3D View (Ss Swi2/Snf2, ref. 97) Arp7 Arp9 Rtt102 Bap55 BAP PBAP Mor/ BAP155 Brahma Osa/Eyelid BAP170 Polybromo PBAF BAF180 BAF200 Snr1/BAP47 Actin BAP/PBAP BAF BAF250/ OSA1 BAF (hSWI/SNF)/PBAF BAP111BAP60 BAF57 BAF155 BAF53a,b BAF45a, b,c,d BAF170 BAF60a, b or c BRG1 or hBRM (BRG1 in PBAF) BAF47/ INI1/ hSNF5 ? Actin The INO80 family The CHD/Mi-2 family The ISWI family Sub-family specific Actin-like Complex name Remodeling catalytic ATPase For EM structures see refs. 91?95. (See note B) NURF 301 BPTF Ioc4 Ioc3 p55 RbAp46,48 ISWI hSNF2L Dls1 dCHRAC16 hCHRAC15 Dpb4 dCHRAC14 hCHRAC17 Isw1 Ioc2 NURF 38 Itc1 Acf1 hACF1 (WCRF 180) NURF, NURF Isw2, ACF, ACF NoRC Isw1a Isw1b Isw2 ISWI hSNF2h RSF1 RSF WICH CHRAC dCHRAC huCHRACWSTF TIP5 Brd8 Ies2 hIES2 Ies6 hIES6 Taf14 Pleiohomeotic Ies4 Nhp10 Ies5 NFRKB CCDC95 MCRS1 AmidaYY1 FLJ20309 Arp5 dArp5 hARP5 Ino80 dIno80 hINO80 Actin1 dActin1 Arp4 BAF53a Arp8 dArp8 hARP8 Ies3 Ies1 Eaf6 dEaf6 EAF6 Bdf1 Swr1, SRCAP dINO80 INO80 hINO80 Tip60 Rvb1,Rvb2 Reptin, Pontin RUVBL1,2 Swc5 Htz1 H2AZ H2B H2B Swc6/ Vps71 ZnF-HIT1 Swc2/ Vps72 hYL-1 Rvb1 Rvb2 RUVBL1,2 Swc3 Swc7 Swc4 DMAP1 Yaf9 GAS41 Swr1 SRCAP Actin1 Arp6 ARP6Arp4 BAF53a RUVBL1,2 hYL-1 p400 (hDomino) BAF53a TIP60 Swc4 Eaf5 Eaf1 Yaf9 Actin1 Arp4 NuA4 dTra1 TRRAP Tra1 dTip60 TIP60 Esa1 dMrgBP MRGBP Eaf7 dMRG15 MRG15/X Eaf3Yng2 dIng3 ING3 Epl1 E(Pc) EPC1 GAS41 ? Actin Note A: The BAF complex is combinatorially assembled with interchangeable subunits 138 . The situation is further complicated by the presence of 29 swi2 homologs in the human genome, and the presence of actin-like subunits in BAF, that differ from yeast SWI/SNF or RSC. Note B: The INO80 family name used is based on the remodeling catalytic ATPase, though the NuA4 acetyltransferase complex was identified earlier. YEAST HOMOLOG FLY HOMOLOG HUMAN HOMOLOG Ss, S. solfataricus (Similar color sphere denotes similar subunits, i.e. Swi3 and Swh3 are related) DMAP1 dBrd8 Reptin, Pontin dYL-1 H2Av H2B Domino Bap55 dGAS41 Actin87E dDMAP1 dMBD2/3 MBD3 p66/68 p66?,? dMTA MTA1-3 p55 RbAp46,48chd1 dCHD1 CHD1 dMi-2 CHD3 CHD4 dRPD3 HDAC1,2 CHD1 dMi-2/ NuRD, NuRD 2B2W 3D View (ref. 76, chd1 refs. 101,102) 2F6J 3D View (ref. 81) 1OFC 3D View (ref. 103,104) 2BYK 3D View (ref. 105) 2C9O 3D View (ref. 100) 2F5J 3D View (ref. 98,99) NATURE STRUCTURAL & MOLECULAR BIOLOGY VOLUME 14 NUMBER 11 NOVEMBER 2007 1114 CHROMATIN REMODELING COMPLEXES NATURE STRUCTURAL & MOLECULAR BIOLOGY VOLUME 14 NUMBER 11 NOVEMBER 2007 1115 ACKNOWLEDGEMENTS Thank you to the people that gave us feedback at different stages, including Francisco J. Asturias, Genevi�ve Almouzni, Peter B. Becker, Mark T. Bedford, Dan Bochar, Karim Bouazoune, Bradley R. Cairns, Joan A. Conaway, Jacques C�t�, Gerald R. 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Dhirendra K Pandey
04/12/2011
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