EPIGENOMICS
André Goffeau
Institut Pasteur/EMBO/CNPq course
Florianopolis, July 11, 2008.
Epigenomics is any regulation (on/off) of
gene expression that is not due to DNA mutations and is heritable
Epigenetic jargon
• Paramutation• Bookmarking• Imprinting• Gene silencing• X chromosome inactivation• Position effect• Reprogramming• Transvection• Maternal effects• Carcinogenesis• Teratogen effects• Histone and chromatin modifications• Parthenogenesis • Cloning • Prions• Embryogenesis
Jean-Baptiste Lamark 1744-1829
Charles Darwin 1809-1882
According to Lamarck's theory, acquired characteristics can be passed to subsequent generations.
According to Darwin's (and Wallace's) theory of natural selection, a population of giraffes will have individuals with variations in neck length. If having a longer neck is advantageous in feeding, longer necked giraffes will be more successful and reproduce more.
Two views about the type of mechanism that promotes evolution.
RNA interference, Histone acetylation and DNA methylation
DNA METHYLATION
Cytosine methylation occurs at CpG and is mutagenic
It prevents activation of promoters
Methylation of CpG islands
and the informatician?
they try to predict which
cytosines
are methylated
in DNA
EMBRIO EPIGENETICS
Reprogramming in Germ Cells and Embryos
CHROMATIN CODE
Chromatin chemistryAcetylation or methylation
Histone modifications
Methylation Genomics
Aberrant methylation in human and mouse leukemia
DISEASES and DRUGS
Epigenetic diseases
Epigenetic drugs
Gene silencing and pharmacology
siRNA
RNA silencing
and YEAST??S.cerevisiae has no DNA methylationS.cerevisiae has no siRNAS.cerevisiae has chromatin modification S.pombe siRNA controls heterochromatinN.crasa DNA methylation depends on a histone methyl transferaseS.cerevisiae has other epigenetic systems such: Mating type silencing, FLO11 a pseudohyphal telomeric gene, Prions
RNA interference, Histone acetylation and DNA methylation
For elucidation of mechanism, use S.pombe, N.crassa or Y.lipolytica ?? but not at S.cerevisiae
Epigenetics References Pennisi E. Behind the scenes of gene expression. 2001 Science, 293:1604-1607.
Egger G, Liang G, Aparicio A & Jones PE. Epigenetics in human disease and prospects for epigenetic therapy. 2004. Nature,429:457-463.
Jenuwein T and Allis CD. Translating the Histone Code 2001 Science, 293:1074-1080.
Matzke M, Matzke AJM, Kooter JM RNA: Guiding gene silencing. 2001 Science, 293:1080-1083.
Reik W, Dean W, WalterJ. Epigenetic reprogramming in mammaliandevelopment. 2001 Science, 293:1089-1093
Hatada I et al. A genomic scanning method for higher organisms using restriction sites as landmarks. 1991. P.N.A.S.,88,9523-9527
Kimura et al. Methylation profiles of genes utilizing newly developed CpG island methylation microarray on colorectal cancer patients 2005 Nucleic Acids Research, 20, E pub
Agrawal et al. RNA interference: biology, mechanism and applications. 2003 Microb. and Molec Biology Reviews, 67, 657-685
QuickTime™ et undécompresseur Sorenson Video 3
sont requis pour visionner cette image.
http://www.nature.com/focus/rnai/animations/animation/animation.htm
PARENTAL DIFFERENTIAL METHYL TAGGING
Hinny and Dolly
EARLY EXAMPLES
• agouti mice (folic acid)
• cancer human (p16)
• diseases human (BWS)
• eye apendage fly (Hsp90)
Methyl detector
Yellow: hyper-methylated; Blue: under-methylated
Restriction Landmark Genomic Scanning
Reprogramming and Imprinting
Deoxynucleoside analogue inhibition
GENOME EVOLUTION
Genomesequencing
Deletomics(systematic)
Overexpressionics(systematic)
Transcriptomics(DNA chips)
Proteomics(2D gels/2 hybrids)
PhysiologistsPathologists
Structuralists Biologists BiochemistsREDUCTIONICS
(SPECIFIC)
NEW TOOLS(GLOBAL)
GENOMICS(GLOBAL)
Genomemapping
Genomecomparisons
Genomology
Databases
Schematic alternating signature for Whole Genome Duplication
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 2211 22 33 44 55 66 77 88 99 1010 1111 1212 1313 1414 1515 1616 1717 1818 1919 2020 2121 2222
4 5 6 7 10 11 12 13 14 15 16 20 21 224 5 6 7 10 11 12 13 14 15 16 20 21 22
1 2 3 4 8 9 10 11 16 17 18 191 2 3 4 8 9 10 11 16 17 18 19
Duplicated copy 1in S. cerevisiae
Duplicated copy 2 in S. cerevisiae
Reference blockin K. waltii
The dark grey genes are contiguous in the non-duplicated reference species (K. waltii, K. lactis or A. gossypii). Yellow genes are conserved in both S. cerevisiae copies. Red genes are conserved only in S. cerevisiae copy 1 .Blue genes are conserved only in S. cerevisiae copy 2.The lost genes are in light grey.
EMERGENCE OF SPECIES-SPECIFIC TRANSPORTERS
DURING EVOLUTION OF THE HEMIASCOMYTE PHYLUM
Benoît De Hertogh*[1], Frédéric Hancy†[2], André Goffeau‡ and Philippe V. Baret*
Université catholique de Louvain
www.gena.ucl.ac.be
Evolution of the yeast genome
Wolfe KH, Shields DC. Molecular evidence for an ancient duplication of the entire yeast genome. Nature. 1997;387:708-13.
Kellis M, Birren BW, Lander ES. Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature. 2004;428:617-24.
Dujon B, Sherman D, Fischer G, Durrens P, Casaregola S, Lafontaine I, De Montigny J, Marck C, Neuveglise C, Talla E, Goffard N, Frangeul L, Aigle M, Anthouard V, Babour A, Barbe V, Barnay S, Blanchin S, Beckerich JM, Beyne E, Bleykasten C, Boisrame A, Boyer J, Cattolico L, Confanioleri F, De Daruvar A, Despons L, Fabre E, Fairhead C, Ferry-Dumazet H, Groppi A, Hantraye F, Hennequin C, Jauniaux N, Joyet P, Kachouri R, Kerrest A, Koszul R, Lemaire M, Lesur I, Ma L, Muller H, Nicaud JM, Nikolski M, Oztas S, Ozier-Kalogeropoulos O, Pellenz S, Potier S, Richard GF, Straub ML, Suleau A, Swennen D, Tekaia F, Wesolowski-Louvel M, Westhof E, Wirth B, Zeniou-Meyer M, Zivanovic I, Bolotin-Fukuhara M, Thierry A, Bouchier C, Caudron B, Scarpelli C, Gaillardin C, Weissenbach J, Wincker P, Souciet JL. Genome evolution in yeasts. Nature. 2004;430:35-44.
Epigenomics
Egger G, Liang G, Aparicio A, Jones PA. Epigenetics in human disease and prospects for epigenetic therapy. Nature. 2004;429:457-63.
Costello JF. Comparative epigenomics of leukemia. Nat Genet. 2005;37:211-2.
Membrane Classification (MC)
Membrane Proteins
A
C
10
F
10.A Lipid Metabolism
10.B Anchoring
10.C Polysaccharide Metabolism
10.D Trafficking
10.E Signaling
10.F Oxidoreductases
10.G Subtelomeric Conserved
10.H Chaperones
B
D
E
G
H
Genomesequencing
Deletomics(systematic)
Overexpressionics(systematic)
Transcriptomics(DNA chips)
Proteomics(2D gels/2 hybrids)
PhysiologistsPathologists
Structuralists Biologists BiochemistsREDUCTIONICS
(SPECIFIC)
NEW TOOLS(GLOBAL)
GENOMICS(GLOBAL)
Genomemapping
Genomecomparison
Genomology
Databases
Conclusions
• Analysis of the 28.000 protein sequences obtained from 14 hemiascomycetes illustrates the usefulness of the functional/ phylogenetic TC system proposed by MILTON SAIER • A similar system for non - transport membrane proteins is proposed (179 members)• S. cerevisiae contains contains 11 channels, 211 permeases,
•16 P-ATPases and 22 ABC-ATPases•They contain also 28 putative transporters families and 112 singletons of unknown function• Speciation of hemiascomycetes is accompanied by the emergence of membrane proteins not represented in S. cerevisiae• Similar analysis of TMS 1 and 2 proteins is required•Our database has been used for identification of novel putative yeast transporters• Our database will serve as reference for the automatic annotation of membrane proteins from recently sequenced yeast genomes
TC - Class 9
Incompletely Characterized Transport Systems
Functionally Characterized Transporters Lacking Identified Sequences
9.C
Recognized Transporters of Unknown Biochemical Mechanism
9.A
Putative Uncharacterized Transport Proteins9.B
The Membrane Proteins of Unknown Function
9.D
9
9.E Questionable ORFs with TMS>2
10.A Lipid Metabolism 13 28
10.B Anchoring 9 10
10.C Polysaccharide Metabolism 8 32
10.D Trafficking 11 39
Total : 55 146
10.E Signaling 4 7
10.F Oxidoreductases 5 11
10.G Subtelomeric Conserved 1 12
10.H Chaperones 4 7
Subfamilies ORFs
S. Cerevisiae Membrane Classification
Table 1 Global statistics of membrane proteins in Hemiascomycete species
Species Y. lipolytica D. hansenii K. lactis C. glabrata S. cerevisiae
Total
Code YALI DEHA KLLA CAGL SACE
Strain CLIB122 CBS767 CLIB210 CBS138 S288c
Database Génolevures Génolevures Génolevures
Génolevures
SGD
Release 22 may 2004 22 may 2004 22 may 2004
22 may 2004
22 may 2004
Natural substrate fats salted fish milk blood grapes
ORFs 6666 6896 5331 5272 5800 29965
Classified transporters 597 538 439 398 508 2480
% 9.0 7.8 8.2 7.5 8.8 8.3
Possible transporters (9.B.X.Y.Z) still unannotated
296 295 226 236 243 1296
Table 2 Functional distribution of the “established and putative” transporters in the Hemiascomycete phylum
YALI DEHA KLLA CAGL SACE Total
1.A Alpha-Type channels 46 32 26 26 38 168
1.B Beta Barrel porins. 1 1 1 2 2 7
2.A Porters (uniporters, symporters, antiporters)
316 281 206 162 218 1183
3.A P-P-bond-hydrolysis-driven transporters 94 89 91 87 107 468
3.B Decarboxylation-driven transporters 2 1 1 2 0 6
3.D Oxidoreduction-driven transporters 21 27 18 15 25 106
3.E Light absorption-driven transporters 0 0 0 3 3 6
8.A Auxiliary transport proteins 5 7 5 3 10 30
9.A Recognized transporters of unknown mechanism
82 75 76 81 85 399
9.B Putative uncharacterized transport proteins 30 25 15 17 20 107
Total 597 538 439 398 508 2480
Table 4 Mean and standard deviation of the subfamily size according to the different modes of evolution within the Hemiascomycete phylum
Mode of evolution Number of subfamilies
Mean number of ORF per subfamily
Minimum number of ORF
Maximum number of ORF
UBIQUITOUS 107 19.9 ± 25.8 5 146
SPECIES-SPECIFIC UNIQUE
15 1.5 ± 1.6 1 7
SPECIES-SPECIFIC ABSENT
20 7.9 ± 7.0 4 28
PHYLUM-GAINED 13 3.2 ± 1.0 2 6
PHYLUM- LOST 36 2.6 ± 2.6 1 16
HOMOPLASIC 13 3.1 ± 1.0 2 5
Table 7 Hemiascomycete Mitochondrial Carrier subfamilies that are absent in S. cerevisiae
Y. lipolytica D. hansenii K. lactis C. glabrata
Subfamily
2.A.29.6 YALI0A20944g DEHA0G14454g KLLA0E02750g
2.A.29.Y14 DEHA0E08349g KLLA0A09383g CAGL0F08305g
2.A.29.Y15 CAGL0B03883g
2.A.29.Y16 YALI0A16863g
2.A.29.Y17 YALI0A20988g DEHA0G19437g KLLA0E09680g
2.A.29.Y18 YALI0B05852g
2.A.29.Y19 YALI0E33341g YALI0F00418g
2.A.29.Y20 YALI0F20262g DEHA0E11022g
2.A.29.Y21 YALI0F15609g DEHA0B16401g DEHA0E09691g
2.A.29.Y22 YALI0E06897g
2.A.29.Y23 YALI0D06798g
ORF number
10 6 3 2
Figure 2B Identification principles of the different evolution patterns distinguished in Figure 2A
Symbols used in
Figure 2 A
Mode of evolution Species A Species B Species C Species D
Ubiquitous
? 1 ORF
? 1 ORF
? 1 ORF
? 1 ORF
Unique
no ORF
? 1 ORF
no ORF
no ORF
Absent
? 1 ORF
no ORF
? 1 ORF
? 1 ORF
Gained
? 1 ORF
? 1 ORF
no ORF
no ORF
Lost
no ORF
no ORF
? 1 ORF
? 1 ORF
Homoplasic
? 1 ORF
no ORF
? 1 ORF
no ORF
Main characteristics Species Y. lipolytica D. hansenii K. lactis C. glabrata S. cerevisiae Total
Code YALI DEHA KLLA CAGL SACE
Natural substrate fats salted fish milk blood grapes
ORFs 6666 6896 5331 5272 5800 29965
Classified transporters
597 538 439 398 508 2480
% 9.0 7.8 8.2 7.5 8.8 8.3
Possible transporters (9.B.X.Y.Z) still unannotated
296 295 226 236 243 1296
Our objective : a consistent annotation
• Key elements– Consistent databases– The TCDB system of classification– A well-known evolutive context
• Output– A subfamily by subfamily discussion– Dynamic species vs. Quiet species
• Extension– Other species– Different levels of annotation
Databases Knowledge Models
DescriptionProcesses
Annotation Evolution
The TCDB Classification
• Based on five digits• Consistent across species• Extensible• An example
– 2 Electrochemical Potential-driven transporte• 2.A Porters (uniporters, symporters,
antiporters)– 2.A.1 The Major Facilitator (MFS) Superfamily
» 2.A.1.Y2 Undefined Subfamily
In practice – the most variable families
Subfamily YALI DEHA KLLA CAGL SACE Mean Variance
2.A.1.1 Sugar Porter (SP) 27 48 20 17 34 29.2 153.7
2.A.1.14 Anion Cation Symporter (ACS) 39 27 13 6 10 19.0 187.5
2.A.1.2 Drug Proton Antiporter 1 (DHA-1) 33 24 8 10 12 17.4 114.8
9.A.5.1 Peroxisomal Protein Importer (PPI) 27 7 10 11 10 13.0 63.5
2.A.67.1 Oligopeptide Transporter (OPT) 17 4 3 0 2 5.2 45.7
2.A.1.16 Ferrioxamine H+ symporter (SIT) 14 5 4 1 6 6.0 23.5
2.A.1.13 Fructose uniporter (FRU) 5 8 12 3 0 5.6 21.3
9.B.17.1 The Putative Fatty Acid Transporter (FAT-1)
14 3 3 5 5 6.0 21.0
3.D.1.2 NADH Dehydrogenase I (NDH 1) 8 8 0 0 0 3.2 19.2
2.A.3.10 AminoAcid-Polyamine-Organocation Yeast Transporter( APC-YAT )
14 24 16 14 18 17.2 17.2
1.A.20.5 Yeast Metal Channel ( Cyt B-FRE ) 11 7 5 1 7 6.2 13.2
Our objective : a consistent annotation
• Three elements– The Genolevure database– The TCDB system of classification– A well-known evolutive context
• Our material– Five species of Hemiascomycetes– 2480 identified transporter proteins
• Our objective– To understand how subfamilies of transporters emerge along the
evolutionary process
The chosen phylum
Figure 2. The Yeast MIT Family (Metal Ion Channels). TC # 1.A.35.
0.1
DEHA-0E11616g
YALI-0B05148g
KLLA-0F26895g
CAGL-0M13233g
SACE-MNR2
YALI-0F06248g
DEHA-0B05445g
KLLA-0F02519g
CAGL-0E05368gSACE-MRS2
DEHA-0E05731g
YALI-0D19514g
CAGL-0M07249gKLLA-0F28017g
SACE-LPE10
DEHA-0F17776g
YALI-0D00319g
YALI-0E00462g
KLLA-0E07249g
SACE-ALR2
SACE-ALR1
CAGL-0E01617g
1.A.35.5mitochondriaMg, (Zn, Mn, Cu?)
1.A.35.2plasma membrane Mg, Zn, Mn, Cu
Figure 4. The Yeast CDF Family (Cation Diffusion Facilitator). TC # 2.A.4.
0.1
DEHA-0G14113g
KLLA-0F20746g0
CAGL-0F05401g
SACE-MSC2
CAGL-0E06006g
SACE-MMT2
KLLA-0C16181g
CAGL-0H08822gSACE-MMT1
DEHA-0A03553g
YALI-0C12254g
YALI-0C18359gSACE-COT1
DEHA-0G03828g
YALI-0F00176g KLLA-0F08723g
CAGL-0K07392gSACE-ZRC1
2.A.4.2vacuoles, mitochondriaZn, Co
2.A.4.4endoplasmic reticulum, nucleusZn
2.A.4.Y1mitochondriaFe
Figure 5. The Yeast ZIP Family (ZINC Iron Porters). TC # 2.A.5.
0.1
DEHA-0B16335g
DEHA-0E25388g
SACE-ZRT1
YALI-0F21659gDEHA-0B07337g
CAGL-0E01353gKLLA-0D16434g
CAGL-0M04301g
SACE-ZRT2
YALI-0D00759g
YALI-0E00748g
YALI-0F15411g
SACE-YKE4
KLLA-0F17886g
YALI-0D19008g
DEHA-0E06105g
KLLA-0A07601g
SACE-ATX2
CAGL-0K05577g
2.A.5.Y1GolgiMn
2.A.5.2endoplasmic reticulumZn
2.A.5.1plasma membraneZn
2.A.5.Y2no datano data
Figure 6. The Yeast Nramp Family (Metal Ion Transporters). TC # 2.A.55.1
0.1
DEHA-0D06996g
KLLA-0D09581g
CAGL-0J00407g
SACE-SMF2
YALI-0D26818g
DEHA-0G09251g
KLLA-0F17391g
CAGL-0A03476g
SACE-SMF3
YALI-0C04411g
DEHA-0F25234g KLLA-0A03740g
CAGL-0E01969g
SACE-SMF1
2.A.55.1.2vesicles, mitochondriaMn
2.A.55.1.3vacuolesFe
2.A.55.1.1plasma membrane, vacuolesMn
0.1
DEHA-0D05269gDEHA-0E13211g
KLLA-0A03025g
CAGL-0I06743g
SACE-FTR1
YALI-0A04917g
DEHA-0C06226g
DEHA-0C07117g
KLLA-0F28039gCAGL-0M05511gSACE-FTH1YALI-0D06688gYALI-0D07304g
YALI-0D06754g
YALI-0D07282g
YALI-0A20273g
CAGL-0J08481g
KLLA-0C01694g
SACE-YDR506
KLLA-0F26400gDEHA-0E13332gKLLA-0D05489gCAGL-0K12738gSACE-FET5DEHA-0G05720gCAGL-0F06413gSACE-FET3
Figure 8. The Yeast OFeT Family (Oxydase-dependant Iron Transporters). TC # 9.A.10.
9.A.10.1plasma membrane, vacuolesFe
9.A.10.Y1plasma membrane, vacuolesFe
Figure 9. The Yeast CTR (Copper Transporters). TC # 9.A.12.
0.1
SACE-CTR3
KLLA-0A09207gDEHA-0G15268g
SACE-CTR2
CAGL-0I02508g
DEHA-0B00407g
DEHA-0F16390g
YALI-0C20295g KLLA-0B11407g
CAGL-0D04708g
SACE-CTR1
9.A.12.Y1,2,3no datano data
9.A.12.1vacuolesCu
9.A.12.Y4plasma membraneCu
9.A.12.2plasma membraneCu
CVYALI DEHA KLLA CAGL SACE name
39 27 13 6 10 9,87 2.A.1.14 The Anion: Cation Symporter (ACS) Family17 4 3 0 2 8,79 2.A.67.1 Subfamily of the Oligopeptide Transporter (OPT) Family0 0 0 0 7 7,00 8.A.9.Y1 Subfamily of the rBAT Transport Accessory Protein (rBAT) Family
33 24 8 10 12 6,60 2.A.1.2 The Drug:H+ Antiporter-1 (12 Spanner) (DHA1) Family8 8 0 0 0 6,00 3.D.1.2 Subfamily of the Proton-translocating NADH Dehydrogenase (NDH) Family
27 48 20 17 34 5,26 2.A.1.1 The Sugar Porter (SP) Family27 7 10 11 10 4,88 9.A.5.1 Subfamily of the Peroxisomal Protein Importer (PPI) Family14 5 4 1 6 3,92 2.A.1.16 The Siderophore-Iron Transporter (SIT) Family5 8 12 3 0 3,80 2.A.1.13 The Monocarboxylate Porter (MCP) Family
14 3 3 5 5 3,50 9.B.17.1 The Putative Fatty Acid Transporter (FAT-1) Type 1 Subfamily3 0 0 0 0 3,00 3.A.1.201 The Multidrug Resistance Exporter (MDR) Family (ABCB)7 3 1 1 1 2,62 2.A.17.2 Subfamily of the Proton-dependent Oligopeptide Transporter (POT) Family0 0 0 3 3 2,25 3.E.1.4 The Fungal Subfamily of the Ion-translocating Microbial Rhodopsin Subfamily6 3 2 0 1 2,21 2.A.1.12 The Sialate:H+ Symporter (SHS) Family
11 7 5 1 7 2,13 1.A.20.5 Subfamily of the Human Phagocyte NADPH Oxidase Cyt b558 H+ Channel
Nbr of Orfs in each subfamily
The variation coefficients of transporters in subfamilies
TC/YETI Family or Subfamily Identificator
Top Related