Transcription Regulation And Gene Expression in Eukaryotes Cycle G2 (lecture 13709) FS 2014 P Matthias & RG Clerc

Transcription

1 Transcription Regulation And Gene Expression in Eukaryotes Cycle G2 (lecture 13709) FS 2014 P Matthias & RG Clerc P. Matthias, 16 April 2014 DNA methylation basics Acetylation Acetyltransferases/Deacetylases

2 The Players in Transcription Regulation DNA-binding transcription factors (upstream factors) Chromatin regulators Coactivators and corepressors: Mediator, etc.. Basal Machinery: RNA PolII, GTFs Chromatin regulators Mediator Co-activator Basal Machinery TFIIH TFIIE TFIID RNAPII TFIIA TFIIB TFIIF DNA-binding TFs Gene

3 DNA methylation basics Wikipedia DNA methylation is usually associated with gene inactivity

4 Methyl-C, the 5 th base

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7 Maintenance of DNA methylation

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10 Distribution of methyl groups in the genome: CpG islands

11 Distribution of methyl groups in the genome: CpG islands

12 CpG islands are not methylated

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15 DNA methylation and demethylation TET: Ten eleven translocation

16 7 th and 8 th base 5-carboxylcytosine 5-formylcytosine

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18 Chromatin structure and histone modifications in eukaryotes HDAC HAT Sparmann A et al., 2006

19 23. April 2014

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23 H3, H4 mononucleosomes can be acetylated NaButyrate-treated Control

24 H3, H4 mononucleosomes NaButyrate-treated +DNAseI Ratio H4-3/H4-0 = 0.9 NaButyrate-treated Ratio H4-3/H4-0 = 1.9

25 TJ Richmond, Nature 1997 vol. 389 (6648) pp

26 Reversible Lysine acetylation

27 The effects of Histone lysine acetylation P. Jenö, Lecture 4610

28 In-gel assay Tetrahymena crude Macronuclear activity Histones BSA

29 Some of the chromatin-binding domains present in HAT complexes in yeast

30 HATs: Complexes and single proteins More HATs: CIITA, TFIIB, CLOCK,

31 Histone Acetyltransferases (HATs): GNAT family

32 Histone Acetyltransferases (HATs): MYST family Some HAT inhibitors: anacardic acid, curcumin, garcinol

33 Elp3: HAT of GNAT family

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35 P. Jenö, Lecture 4610

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37 Some HDAC inhibitors TSA SAHA/Vorinostat Zolinza Romidepsin Istodax

38 HDAC inhibitors as drugs HDAC inhibitors: TSA, SAHA, VPA, LBH Cancer, Leukemia, PolyQ disorders (neurodegeneration), Autoimmune and inflammatory diseases, HDACs Deacetylation of histones and various kinds of transcriptional regulators >300 clinical trials (completed or planned) 23. April 2014 Cell cycle arrest Apoptosis Differentiation,

39 (H)DAC inhibitors approved as drugs Zolinza (Vorinostat): FDA-approved on 6 Oct for cutaneous T cell leukemia (CTCL) MOA: The mechanism of the antineoplastic effect of Vorinostat has not been fully characterized Istodax (Romidepsin): FDA-approved on 6 Nov for cutaneous T cell leukemia (CTCL) MOA: The mechanism of the antineoplastic effect of Romidepsin observed in nonclinical and clinical studies has not been fully characterized 23. April 2014

40 We used high-resolution mass spectrometry to identify 3600 lysine acetylation sites on 1750 proteins and quantified acetylation changes in response to the deacetylase inhibitors suberoylanilide hydroxamic acid and MS-275.

41 Widespread lysine acetylation

42 HDACis in the food: broccoli sprouts Dietary compounds: Na-butyrate, diallyl disulphide, sulphoraphane Found at high levels in cruciferous (Brassicaceae) vegetables Human colon cells Human healthy volunteers

43 Classical Zn-dependent HDACs

44 NAD-dependent HDACs: Sirtuins Rajundran et al., JBB 2011, doi: /2011/368276

45 NuRD and Sin3 Complexes NuRD Sin3 Ahringer (2000). NuRD and SIN3. Trends Genet. 16,

46 HDAC recruitment: core complex Gene-specific Transcription Factors Other Gene-specific Transcription Factors Modiefied from: Knoepfler and Eisenman (1999). Sin meets NuRD and other tails of repression. Cell 99,

47 HDAC1 and 2 complexes

48 Sin3 schematic structure The PAH domains are suggested to be organized into two α-helices separated by a flexible spacer region They are among the most evolutionarily conserved regions of the large SIN3 proteins ( kda) These domains are important for Sin3 function through their independent associations with various repressors and other associated proteins PAH2 is both necessary and sufficient for interaction with the Mad proteins HDAC Interaction Domain Paired Amphipathic Helix (PAH)Domains

49 Sin3 schematic structure

50 Comprehensive HDAC interaction network. Joshi P et al. Mol Syst Biol 2013;9: by European Molecular Biology Organization

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52 Phenotypes of class I HDACs mouse knockouts

53 Phenotypes of class I HDACs mouse knockouts Reichert, Choukrallah and Matthias, CMLS, 2012 DOI /s

54 Sin3 schematic structure

55 ClassII HDACs as signal transducers

56 ClassII HDACs as cytoplasmic regulator : HDAC6