Importance of proteomics and epigenetics Epigenetics Against Central

Importance of proteomics. . . … and epigenetics

Epigenetics Against Central Dogma or not? Why the definition of epigenetics has changed? Scope and terminology of epigenetics Chromatin Non-chromatin-based epigenetic mechanisms Conserved epigenes Roles of epigenetic information Epigenetics and evolution

Epigenetics Against Central Dogma or not? Why the definition of epigenetics has changed? Scope and terminology of epigenetics Chromatin Non-chromatin-based epigenetic mechanisms Conserved epigenes Roles of epigenetic information Epigenetics and evolution

Why it is interesting? It seems to go against the grain of the Central Dogma of Molecular Biology Genotype Phenotype

Genocentric view and Central Dogma ‘Genocentric’ view runs into problem when one start to deal with the multicellular organisms exhibiting the phenomenon of cellular differentiation Phenomenon of i. PS cell reprogramming and somatic cloning – genetic information is not sufficient to define the state of a cell. Importantly, there is no direct contradiction: Crick: The central dogma of molecular biology deals with the detailed residue-by-residue transfer of sequential information. It states that such information cannot be transferred from protein to either protein or nucleic acid. This leaves the door open for other types of information that could be required to specify the state of the organism/cell and might propagate independently from the DNA sequence

Epigenetics Against Central Dogma or not? Why the definition of epigenetics has changed? Scope and terminology of epigenetics Chromatin Non-chromatin-based epigenetic mechanisms Conserved epigenes Roles of epigenetic information Epigenetics and evolution

Epigenetics, past and present. I Conrad Waddington Epigenetic landscape Epigenetics - study of how interactions between genes creates stable trajectories of development Emphasis of relative decoupling of development from genes (phenocopies, tolerance to mutations)

Epigenetics, past and present. II Modern definition - ‘heritable variations in phenotype that cannot be accounted for by variations in DNA sequence’ Holy grail - stability of differentiated phenotypes in development Canonic models: Position effect variegation in drosophila Silencing in yeast DNA Methylation

Why change in definition of ‘epigenetic’? Result of a change in meaning of ‘genetic’ Genetics - science of inheritance Therefore, ‘epigenetic inheritance’ has no meaning (Oxymoron) After Watson & Crick Genes DNA (RNA) sequences, ‘All things genetic’ become associated with nucleic acids But how to describe stability of cell types after differentiation in development (cellular memory)? The concept of ‘epigenetic inheritance’ acquired meaning, as everything that is heritable, but not reducible to DNA sequence.

Epigenetics Against Central Dogma or not? Why the definition of epigenetics has changed? Scope and terminology of epigenetics Chromatin Non-chromatin-based epigenetic mechanisms Conserved epigenes Roles of epigenetic information Epigenetics and evolution

What is ‘Epigenetic’? Heritability requirement is too restrictive Types of epigenetic phenomena: 1. Germ-line epigenetic inheritance Meiosis 2. Epigenetic inheritance Mitosis, development 3. Epigenetic stability No replication, heritability criteria does not apply, but mechanisms the same muscle brain

What is ‘Epigenetic’? ‘Nonmendelian’ requirement is too loose Selfish genetic elements: Plasmids Viruses Organelle genomes Mitochondria Plastids

Working definition Epigenetic information - information that is necessary to specify the phenotype of an organism in addition to genetic sequence and the state of the environment Phenotype = F(genes, environment)? ? ? } + Epigenetic information!!! Important in: * Development and differentiation * Cancer and other pathologies * Therapeutic cloning

Is the notion of ‘epigenetic regulation’ useful or confusing? The value of a scientific concept depends on: (i) how well it can capture a particular class of phenomena by clearly distinguishing it from other phenomena, (ii) whether it can stimulate new directions of research (iii) whether it allows one to convey complicated ideas in a succinct and lucid fashion. Epigenetic regulation (control/circuits etc) - used to be called regulation of gene expression Genetic Switch was renamed to Epigenetic Switch by Ptashne himself Phage l system

Insights from ‘epigenetic information’ Genetic Epigenetic DNA/RNA replication Epigenetic channel Gene Epigene Allele/Mutation Epiallele/Epimutation DNA repair Repair of epigenetic information? DNA damage response epigenetic damage response?

Epigenetics Against Central Dogma or not? Why the definition of epigenetics has changed? Scope and terminology of epigenetics Chromatin Non-chromatin-based epigenetic mechanisms Conserved epigenes Roles of epigenetic information Epigenetics and evolution

Chromatin, the Nature’s Filing Cabinet Keeping most of the genetic information archived, and some accessible for immediate use Euchromatin Hetero chromatin

Epigenetic marks on chromatin 1. DNA methylation 2. Post-translational histone modifications Active chromatin: acetylation, H 3 K 4 methylation Silenced chromatin: H 3 K 9, 29 methylation 3. Chromatin proteins (alternative histones etc) Active chromatin: H 3. 3, H 2 A. BBD Silenced chromatin: macro. H 2 A 1, 2

Epigenetic templating Recruitment of machinery that deposits a particular epigenetic mark to sites on chromatin that contain the same mark Examples: Recruitment of bromodomain containing HAT complexes to acetylated chromatin Recruitment of chromodomain containing HMT complexes to methylated chromatin

Replication of inactive chromatin state Suv 39 h H 3 K 9 m Inactive chromatin HP 1 b chromo Chromodomain of HP 1 binds methylated K 9 of the histone H 3. During replication, the HP 1/Suv 39 complex is recruited to methylated nucleosome and directs methylation of the newly synthesized nucleosomes Inactive chromatin HP 1+Su. Var Methylation of adjacent nucleosome Propagation of methylated state Replication Newly synthesized nucleosomes Parental nucleosomes

Fields of chromatin and epigenetics are overlapping but not identical Further classification of epigenetic mechanisms

Epigenetics Against Central Dogma or not? Why the definition of epigenetics has changed? Scope and terminology of epigenetics Chromatin Non-chromatin-based epigenetic mechanisms Conserved epigenes Roles of epigenetic information Epigenetics and evolution

The chromatin based epigenetic mechanisms are cis-mechanisms, as particular locations of genome are marked Are there trans-acting epigenetic mechanisms?

Transacting epigenes: prions The transmission mechanism is similar to epigenetic templating: locally in space and time from one molecule to another

Transacting epigenes: memory Kandel E. Prion-like mechanisms might explain long term potentiation in neurobiological memory R D T I II III Crick F. Memory and molecular turnover. Nature. 1984

Are there epigenetic mechanisms that are global, i. e. do not involve templating? A a A 1 Pb Pa B B b A B 2

Genetic/Epigenetic switch Phage l system System has two alternative phenotypic states: (LOn, ROff) or (LOff, ROn) Generalization to many genes leads to genetic networks with many alternative states. Unlike in the case of templating mechanisms, the information is a global property of the system

Epigenetics Against Central Dogma or not? Why the definition of epigenetics has changed? Scope and terminology of epigenetics Chromatin Non-chromatin-based epigenetic mechanisms Conserved epigenes Roles of epigenetic information Epigenetics and evolution

Stability of Epigenetic information All examples of epigenetic information reviewed so far (chromatin, transcriptional switch), are less stable than genetic information Thus, epigenetics introduces an hierarchy of stabilities (times) in the description of a biological system However: Is all epigenetic information less stable than genetic information?

Conserved epigenes 1. Homochirality Proteins contain only L-aminoacids Nucleic acids contain only D-sugars Majority of enzymatic reactions are stereospecific and utilize and/or produce chiral molecules

Giant mirror experiment Reflection of the biosphere in a mirror will neither change processes in it nor the sequences of genomes

Chirality 1. Without the knowledge of chirality, apples from Mars could be dangerous Therefore, it is information necessary to specify the state of a living object, its integration into the ‘circle of life’ 2. It is information that is not contained in the sequence of genome, At least one additional bit of information is necessary to specify the chirality of biosphere (if each organism has racemases, need much more: 1 bit per each organism) Therefore, it is epigenetic information

Chirality Distinguishing features of chirality as epigenetic information Nonlocal character of reproduction Extremely stable. Unlike other types of epigenetic information, more stable than genetic information Is not a dynamical variable now, was fixed long time ago Should be a dynamical variable in description of origin of life

Conserved epigenes 2. Genetic code

The nucleotide sequence of aat. RNA synthetases is coded in genome, but the protein sequence cannot be deduced without a priory knowledge of the code ? Similarly, the correspondence between sound ‘a’ and a letter ‘A’ is not coded in a text

Conserved epigenes 2. Genetic code Arbitrariness of code General principle of functioning of a semiotic system The information about representation of a particular phoneme (A) by an alphabet symbol (a) cannot be transmitted between users (generations etc) through text alone Similarly, the information about the representation of aminoacid (Leu) by a codone (CTG) cannot be transmitted from one generation to another through DNA alone (aat. RNA synthetases should be present)

Epigenetics Against Central Dogma or not? Why the definition of epigenetics has changed? Scope and terminology of epigenetics Chromatin Non-chromatin-based epigenetic mechanisms Conserved epigenes Roles of epigenetic information Epigenetics and evolution

Roles of epigenetic information 1. Proper functioning of genetic information In general as a part of a semiotic system In development, helping to interpret it 2. Protection of genetic information

Roles of epigenetic information 1. Proper functioning of genetic information In general as a part of a semiotic system In development, helping to interpret it 2. Protection of genetic information

DNA methylation

Maintenance methylation Only semimethylated bases are coverted into fully methylated Replication Destruction

Epigenetic Templating D R T I II Crick F. Memory and molecular turnover. Nature. 1984 III

Protection of genetic information: 1. From foreign elements discrimination between ‘self’ and ‘other’ 2. From copying errors discrimination between ‘old and ‘new’

Mismatch Repair

Protection of genetic information: The Mismatch Repair mechanism in bacteria takes advantage of the difference in kinetics between replication of genetic and epigenetic information

Epigenetics Against Central Dogma or not? Why the definition of epigenetics has changed? Scope and terminology of epigenetics Chromatin Non-chromatin-based epigenetic mechanisms Conserved epigenes Roles of epigenetic information Epigenetics and evolution

Epigenetics and evolution

Epigenetics and evolution Which function of epigenetic information came first? Interpretation of genetic information or Protection of genetic information? Many epigenetic mechanisms appear to be related to mechanisms of suppression of parasitic genetic elements Epigenetic machinery was established by Life for ‘genome protection’ purposes first. In the further course of evolution, however, the mechanisms of processing of epigenetic information - which allow recognition of different epigenetic marks and channeling the signals encoded in these marks along appropriate response pathways - were recruited for other purposes, such as for stabilizing different alternative states of the same organism.

Epigenetics and evolution

Epigenetic mechanisms reviewed so far: Cis-, templating: chromatin-based Trans-, templating: prions Trans-, distributed: genetic networks Conserved: chirality, genetic code

All epigenetic information discussed so far was stored in molecular structure of some kind Structural versus dynamic invariants Covalent bond Conservation of momentum

Static versus dynamic epigenetic mechanisms Could information be stored dynamically? What about information associated with unequilibrium symmetry breaking? Living systems as open systems far from equilibrium Selforganization, Dissipative structures

Convection cells Dynamic flow organizes system to ensure ‘optimal performance’ Information/order is maintained by constant flow of free energy

Self-organization and evolution Waddington-Schmalhausen Adaptation on epigenetic level first Then Genetic assimilation But how adaptation can happen on epigenetic level? Via self-organization!

Self-organization and evolution An attractive aspect of ‘self-organization’ is that it implies that organism, as a physical structure, has a possibility to adapt before and independent from natural selection and thus provides an alternative model for natural evolution: 1. Dynamics/function determines structure 2. Structure becomes fixed by stabilizing/assimilating selection Contrary to the neodarwinian model: 1. Structure determines function/dynamics 2. In this way structures are tested by natural selection.