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Histone Acetyl Transferases

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1 Histone Acetyl Transferases
HAT Histone Acetyl Transferases 3 HAT Families Piu’ importanti sono GCN5 e omologo di PCAF H3-H4 istoni piu acetilati Acetilano anche altre proteine oltre istoni 3 famiglie in base alla loro struttura Solitamente correlate a attivazione genica Attività anomale da parte degli enzimi HDACs sono state evidenziate in molti diversi tipi di cancro, come la leucemia promielocitica, la leucemia mielogena acuta, il linfoma di non-Hodgkin, e altri tipi di carcinomi colorettali e gastrici. Quando questi enzimi agiscono in modo "scorretto," possono impedire la trascrizione di geni fondamentali.

2 KAT3 Family: p300 (E1Abinding protein) and CBP(CREB binding protein)
Cbp e p300 sono identiche Scoperta prima cbp Interagisce con gli attori principali del macchinario di trascrizione tra cui RNA pol2 Dominio HAT responsabile della sua attivita’ Principali domini della proteina permettono di interagire con diversi TF Infatti non lega direttamente il DNA ma fa da cofattore e attivatore Creb binding domain, bromo domain (readers), glutamine rich domain attivazione FAT factor acetyl transferase

3 P300/CBP in cancer Rubinstein–Taybi syndrome (RTS) is a developmental disorder caused by heterozygous germline mutations (point mutations, translocations or deletions) of the CBP gene. RTS is characterized by broad thumbs, cranio-facial and cardiac abnormalities, as well as mental retardation. Patients with RTS have an increased predisposition to cancer M4/M5 subtype of acute myeloid leukemia (AML) This translocation fuses the gene encoding the monocytic leukemia zinc- finger protein (MOZ) with the amino terminus of CBP. aberrant acetylation MLL-CBP and MLL-p300 translocations (MLL-mixed lineage leukemia) have also been described.(AML) aberrant acetylation and methylation Mutations in CBP or P300 are correlated with different type of tumors Chromosomal rearrangements involve CBP more commonly than p300.

4 HDAC- Histone Deacetylase Classe1: omologo yRPD3
Deacetilano il gruppo acetile Classificati in base omologia con yeast Classe1: omologo yRPD3 (dominio HDAC,nucleari) Classe2: omologo yHDA1 (dominio HDAC, nucleari/citoplasmatiche(P)) Classe 3: ySIRT2 Classe 4:classificato per omologia di sequenza

5 HDAC- Histone Deacetylase
Classe 2a: residui forforilati conservati molto importanti per il shuttling tra nucleo e cyt Classe 2b : ha due domini HDAC consecutivi Secondo gruppo sta nel cytoplasma (acetila proteine ) e fa shuttling HDAC4 This protein does not bind DNA directly, but throughtranscription factors MEF2C and MEF2D Importante nello sviluppo muscolare Dopo differenziamento in miotubi hdac4 diventa nucleare quindi ha un ruolo attivo

6 HDAC classe3 : Sir In general, sirtuins do not act autonomously but as components of large multiprotein complexes, such as pRb-E2F and mSin3A, that mediate important transcription regulatory pathways. Sirtuins have a role in regulation of transcription and apoptosis leading to substantial interest in inhibitors of these enzymes as possible antineoplastic agents. In addition, Sir2-like family deacteylases are involved in the normal ageing process through their role in resistance to cellular stress. Sirtuin-mediated deacetylation reaction couples lysine deacetylation to NAD hydrolysis Sir2 family deacetylation target consensus sequences. The amino acid sequence of the Sir2 targets are shown: histone H3 lysine 9; histone H3 lysine 14; histone H4 lysine 16; p53 lysine 382; Tubulin, alba.

7 PRMT and KMT: Methyl Transferases
Attivazione o repressione MLL importante nell leucemie infantili Interagisce con : WDR5, RBBP5, MEN1 e ASH2L

8 KMT: Lysin Methyl Transferases
leukemia KMT1 set domain preset post set domain 1a 1 b contengono oltre al set domain un cromodomain 1c e 1e un ankyrin domain fanno si di riconoscere histoni metilati Segnale repressorio KMT2 family proteins are H3K4 methyltransferases, and they share a distinct SET domain with an essential post-SET region at the C-terminus The H3K4 trimethylation activity of KDM2A requires compo- nents of its core complex, including WDR5, RbBP5, and Ash2L KMT3 histone H3K36, but their KMT activities are not restricted to H3K36 modifica nel corpo del gene KMT4 H3K79 methylation activity is essential for MLL-AF4 and MLL-AF9 fusion-induced leukemiastarget terapeutico KMT5 segnale repressorio K20 KMT6 Polycomb repressive complex2 repressione No Set domain PRC2

9 KMT: SET domain ((Su(var)3-9, Enhancer of Zeste, Trithorax))

10 PRMT:Protein arginine methyltransferases
Domini altamente conservati Motif I: VLD/EVGXGXG; Post I: V/IXG/AXD/E; Motif II: F/I/VDI/L/K; Double E Loop Motif III: LR/KXXG; THW loop

11 PRMT Altamente omologa a RMT1 del lievito S-adenosilmetionina
adenosilomocisteina Altamente omologa a RMT1 del lievito

12 KDM:Lysine Demethylase
KDM1 non rimuove trimetil H3K4 e non solo ha altri substrati agiscono in un complesso CoREST and BHC80 alter its substrates’ specificity toward H3K9 methylation when associated with nuclear receptors, thereby acting as a transcriptional coactivator H3K9 KDM2 first JmjC domain-containing histone demethylase identified [99]. KDM2A and KDM2B demethylate mono- and di-methylation from H3K36, while KDM2B is also implicated in demethylation of H3K4 The F-Box present in KDM2 family members suggests that KDM2 proteins might also be involved in additional mechanisms of chromatin regulation, such as ubiquitylation KDM3 funzionano come coattivatori KDM4 Besides the JmjC domain, they share a highly conserved JmjN domain, and three of them (all except KDM4D) contain tandem PHD fingers and Tudor domains that read distinct histone methy- lation sono I primi che tolgono una trimetilazione Kdm5 KDM5 family members KDM5A – 5D/JARID1A – 1D specif- ically remove di- and tri-methylation from H3K4 [135 – 141]. They are multi domain-containing proteins characterized by a combination of JmjC and JmjN catalytic domains with an ARID DNA-binding domain, a C5HC2 zinc finger, and two to three PHD fingers. Distinct PHD fingers of KDM5A and KDM5C were shown to bind methylated H3K4 or H3K9, re- spectively. This family of proteins shows oncogen- ic activity, as KDM5A is overexpressed in gastric cancer and KDM5B is highly induced in breast cancer KDM6 H3K27-specific histone demethy- lases, KDM7 This family of proteins possesses strong demethylation activity toward H3K9 and H3K27 mono- and di-methylation [151–157]. Furthermore, PHF8 is able to remove mono-methylation from H4K20 [154,155,158]. All three KDM7 family proteins contain a PHD finger that binds to histone H3K4me3,

13 KDM H3K9me3 H3K4me3 H3K27me3 HnHanno in comune il JMJC domain Alcune hanno anche un Tudor domain che le rende in grado di riconoscee gli istoni metilati H3K36me1,2

14  The Methylation of Histone Lysines Is Reversible and Regulates Gene Expression(A) Methylation of H3 K4 is often associated with active genes, and conversely, its demethylation accompanies gene repression.(B) In contrast, methylation of H3 K9 is often associated with silenced genes, hence removal of H3 K9 methyl marks coincides with gene activation.

15 Figure 2. Regulation of LSD1 Specificity by Association with Protein Cofactors(Upper panel) Recombinant LSD1 specifically demethylates H3 K4 of core histones (A), but not H3 K9 (B) (Shi et al., 2004). (C) LSD1 demethylates H3 K9 when affinity purified in the presence of the androgen receptor (AR; Metzger et al., 2005).(Middle panel) (A) Recombinant LSD1 alone does not bind to or act upon nucleosomal substrates. (B) Association of LSD1 with CoREST endows LSD1 with the ability to demethylate H3 K4 on nucleosomal substrates (Lee et al., 2005; Shi et al., 2005). (C) BHC80 inhibits the demethylation of nucleosomes mediated by the LSD1-CoREST complex (Shi et al., 2005).(Lower panel) (A) LSD1, as part of the CoREST corepressor complex, is recruited to genes containing the REST-responsive repressor element 1 (RE1) and participates in gene silencing through demethylation of H3 K4 (Shi et al., 2004). (B) Ligand-induced recruitment of androgen receptor (AR) to the androgen receptor element (ARE) is accompanied by demethylation of H3 K9 by LSD1, leading to transcriptional activation (Metzger et al., 2005). However, LSD1 is already tethered to the ARE through an unknown mechanism (indicated by factor X) prior to the induction of gene expression by the androgen ligand.

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23 ASH2L: important for trymetilation of H3 K4
MEN1 MEN1 MEN1 Molecular regulation of H3K4 trimethylation by ASH2L, a shared subunit of MLL complexes Melissa M Steward1, Jung-Shin Lee1, Aisling O’Donovan2,Matt Wyatt1, Bradley E Bernstein2 & Ali Shilatifard1,3 SEPTEMBER 2006 NATURE STRUCTURAL & MOLECULAR BIOLOGY

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27 Mistargeting of chromatin modifications occur as epigenetic lesions at MLL-AF4 target regions
Mistargeting of chromatin modifications occur as epigenetic lesions at MLL-AF4 target regions. (A) Binding of H3K79me2 (green) and H3K4me3 (blue) in SEM cells as determined by ChIP-seq. Binding profiles are shown across an 800-kb portion of the genome surrounding the PROM1 gene. Gene models shown in black below the graph; a black arrow indicates transcription start sites. MLL-AF4 fusion protein-binding regions are indicated by red bars. (B) Binding of H3K79me2 ChIPs (green) and H3K4me3 ChIPs (blue) in SEM cells as determined by ChIP-seq. Binding profiles are shown across 15- to 150-kb portions of the genome surrounding the HOXA9, TWIST1, HMGA2, and RUNX2 genes. Gene models are shown in black (below graph). A black arrow indicates transcription start sites. MLL-AF4 fusion protein binding is indicated by a red bar. (C) H3K79me2 (green) and H3K4me3 (blue) binding profiles for all MLL- AF4 target genes in SEM cells. Genes are ordered as in Figure 2C. (D) Composite H3K79me2 ChIP enrichments (green) and H3K4me3 ChIP enrichments (blue) for all genes (left) and all MLL-AF4 target genes (right). The start site and direction of transcription of the average gene are indicated by an arrow. Guenther M. G. et.al. Genes Dev. 2008;22: ©2008 by Cold Spring Harbor Laboratory Press

28 Model of MLL-AF4-mediated gene activation in leukemia
Model of MLL-AF4-mediated gene activation in leukemia. Schematic diagram of transcriptional misregulation in MLL-AF4-induced leukemia. MLL-AF4 associates with elongation proteins (pTEFb, ENL, and DOT1) at sites of epigenetic lesions. Phosphorylated and elongating RNA Pol II shown in yellow. Blue (H3K4me3) and green (H3K79me2) circles represent histone modifications at aberrant chromatin domains. Genes annotated as bound by MLL-AF4 and playing a role in hematopoietic stem cell function are shown to the right and subdivided into functional categories. Guenther M. G. et.al. Genes Dev. 2008;22: ©2008 by Cold Spring Harbor Laboratory Press

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30 Colon SUZ12 Colon Prostate EZH2 Breast Breast Skin Liver Lymphoma Liver Myeloma Endometrial Bladder Lung Gastric

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33 Proteins Protein domains Functions Drosophila melanogaster Human Mouse PRC2 initiation complex ESC EED WD40 repeats* E(Z) EZH1 EZH1/ENX2 SET domain‡ Histone methyltransferase EZH2 EZH2/ENX1 SU(Z)12 SUZ12 Zinc-finger domain PRC1 maintenance complex PC CBX2/HPC1 CBX2/M33 Chromodomain Methyl-lysine binding CBX4/HPC2 CBX4/MPC2 CBX8/HPC3 CBX8/PC3 PH EDR1/HPH1 EDR1/MPH1/RAE28 Zinc-finger SPM domain§ EDR2/HPH2 EDR2/MPH2 EDR3/HPH3 EDR3 RING RING1/RNF1/RING1A RING1/RING1A RING-finger domain|| Ubiquitin ligase RNF2/RING1B PSC BMI1 RNF110/ZFP144/ PCGF2 RNF110/ZFP144/MEL18 ZNF134 PHO YY1 Sequence-specific DNA binding PHO-like DNA binding SCM SCML1 SCMH1 PCL PHF1 PHF1/PCL1 PHD-finger domain

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36 Global perturbations of histones PTMs in human cancers.
H3K20me3 Lymphoma Fraga et al. Nat Genet mouse SCC H3K16ac (MOF) Lymphoma Fraga et al. Nat Genet Breast, Medulloblastoma Pfister ey al. Int J Cancer 2008. H3K4me2 (MLL) Prostate Seligson et al. Nature H3K18ac Prostate Seligson et al. Nature H3K9me2 Prostate, Kidney Seligson et al. Am J Pathol Ellinger et al. Prostate 2010. H3K18ac Lung, Kidney Seligson et al. Am J Pathol Ellinger et al. Prostate 2010. H3K27me3 (Pg) Prostate Yu et al. Caner Res

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38 p300/CBP and cancer Narayanan Gopalakrishna Iyer1, Hilal Özdag1 and Carlos Caldas1 Lysine methylation: beyond histones Xi Zhang, Hong Wen, and Xiaobing Shi


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