1. The Importance of Epigenetic Phenomena in Regulating Activity of the Genetic Material
Sin Chan

2. Genetics Study of genes, heredity and variation
Traditional focus for genetic analysis has been DNA-centric (DNA as blueprint for life)
Genetics is the study of genes, heredity, and variation
The traditional focus of genetic analysis has been DNA centric for the majority of history
Modern genetics was founded by the work of Gregor Mendel and his investigations into the inheritance pattern in pea plants in 1866
Following his work was the development of molecular studies in genetics with the discovery of DNA as the carrier of genetic material and its structure
Throughout this progression in the field of genetics, DNA has always been considered the blueprint for life
Within it lies the genes that encode for the various functions of life
Throughout the timeline of genetics the one main and stable body of idea has been that DNA was the sole determinant of life

3. Epigenetics Genes as destiny?
Defined as the study of factors affecting gene expression, but not the DNA sequence
May be acquired, and not only inherited
Jean-Baptiste Lamarck ( )
French scientist
Theory that acquired
traits/characteristics may be
passed on
Mechanisms:
Histone Modification
DNA methylation
But evidence started surfacing that made researchers question if genes really were destiny.
The study of epigenetics brought to question if there were other possible factors that could change how the information in our DNA could be expressed differently
Epigenetics is the study of factors that change the expression genes, without altering the DNA sequence itself
These factors can be acquired throughout the lifespan of an organism, and does not necessarily have to inherited from parents
One of the first people to have come up with this idea was a french scientist named Jean-Baptiste Lamarck
Lamarck had a theory that acquired traits/characteristics may be passed on from one generation to the next
He described this specifically in the case of giraffes
Originally he proposed that giraffes had a short neck and that the need to reach leaves on the higher elevated branches caused them to acquire longer and longer necks
This trait was then passed down from one generation to the next, until you end up with the giraffes we know today with their very long necks
How these changes occur in altering the gene expression can be described by two main mechanisms; histone modification and DNA methylation

4. Histone Modification Histones Histone code hypothesis
Proteins
Involved in DNA packaging
H2A, H2B, H3, and H4
Histone code hypothesis
Genetic information is partly regulated by chemical modifications to unstructured ends
5 kinds of histone modifications
Acetylation, methylation, ubiquination, phosphorylation, and sumoylation
Histone modification is the first one I will be describing
Histones are proteins that is involved in DNA packaging.
DNA is wrapped around the histones and this structure is known as the nucleosome, which is them packaged into the chromosomes
In each nucleosome complex is two sets of the H2A, H2B, H3, and H4 histones
The histone code hypothesis proposes that histone modifications does more than to just stabilize and destabilize the interactions between histones and the underlying DNA,
It also recruits proteins that have a hand in altering the whether genes get expressed or not
5 kinds of histone modifications

5. Histone Acetylation Important role in gene regulation
Acetylation and deactylation of lysine residues on N-terminus tail and histone core
Reaction catalyzed by enzymes histone acetyltransferases (HATs) and histone deacetylase (HDAC)
Acetylation removes positive charge on histone
Causes N-terminus to loosely bind to negatively charged DNA phosphate group
Allows easier access to DNA for transcription factor
Genes more readily expressed
Acetylation reversed by HDAC
Histone acetylation has important role in gene regulation
Acetylation and deacetylation of lysine residues occur on the N-terminus tail and histone core
This reaction is catalyzed by the enzymes histone acetyltransferases and histone deacetylase
Acetylation removes the positive charge on the histone
This causes the N-terminus end to loosely bind to DNA, which has a negative charge due to the phosphate group
The loosening of the interaction between the N-terminus tail of the histone and the phosphate group of the DNA allows easier access for transcription factors to bind
Genes therefore become more readily expressed due to acetylation
Deacetylation by histone deacetylase does the opposite, where it tightens the bond and makes the genes less accessible to the transcription factors

6. DNA Methylation Best understood epigenetic modification
Methyl groups attach to backbone of genome at CpG sequences
Cytosine bases5-methylcytosine
DNA methyltransferases (Dnmt)
Represses gene expression
Silences genes; (ex. - tumor suppressor genes)
DNA methylation is the best understood mechanism of epigenetics
Methyl groups are added to the backbonee of the genome at CpG sequences, which are sites where cytosine and guanine bases of the DNA occur in a linear sequence side by side
The addition of the methyl group converts the cytosine bases to 5-methylcytosine
This conversion is catalyzed by the enzymes DNA methyltransferases.
There are three main kinds of methyltransferases
DNA methylatlion causes genes to not be expressed
This repression of genes can have huge impacts on an individual overall, such as the repression of tumor suppressor genes

7. Human Epigenome Project
Epigenomics
Study of chemical tags that control
activities of genes
Human Epigenome Consortium
Collaboration of public and private institutions
Goal of project
Identify, catalogue and interpret genome-wide DNA methylation patterns
The human genome project started in the late eighties sequenced the entire DNA
And mapped and identified genes to better understand their physical and functional aspects
But with the understanding that there was more than one way the genetic material could be read, it called for a mapping of these factors that altered how genes were expressed
Thus starting the human epigenome project
Epigenomics is defined the study of chemical tags that control the activities of genes
The project was started by the human epigenome consortium and is a collaboration of both public and private sectors
The goal of the project was to identify, catalogue, and interpret genome wide DNA methylation patterns.

8. Bisulfite Sequencing identification of DNA methylation patterns
The method in which DNA methylation patterns were identified was through bisulfite sequencing
Dna sequences were treated with bisulfite and this converted cytosine bases to uracil.
However the methylated cytosines were unaffected.
Through pcr sequencing the uracils were then further converted to thymine, but the methylated cytosines lose their chemical tags
From this scientists were able to identify where dna methylation could have occurred along the genome by the presence of cytosine bases.

9. Behavior Environmental factors/adaptations passed on to offspring
Paternal Effects
Environment experienced by paternal lineage can indirectly affect descendants
Ex.) Swedish community
Shortage of food
Malnutrition between 9-12 years old in grandfather increased lifespan of grandchildren
Adequate nutrition and food decreased lifespan
Heart disease and diabetes
Diet plays a part in methylation of DNA
Epigenetic modifications have been known to have consequences in various aspect of studies in organisms
These include behavior, stem cell, and disease studies
In Behavorial studies environmental factors and adaptations have a large role in the shaping an individual and as well as their descendents
It is well known that maternal

10. Agouti Mouse Diet of mother shapes epigenome of offspring
Unmethylated agouti gene leads to obesity and more susceptible to cancer and diabetes
Yellow coat color
Normally agouti gene methylated
Healthy and brown coat color
Explain how father’s genes can indirectly affect the offspring, even if taken out of the care of the offsprings
Explain how certain traits and genes come from dad and not mom-paternal effects

11. Agouti Mouse Experiment: Pregnant yellow mouse fed methyl rich diet
Offspring brown and healthy, did not inherit yellow coat color or susceptibility to disease
Concluded health determined by environmental factors of what our parents eat

12. Twinning Phenomenon
Talk about how epigenetics shape the differences among identical twins
Talk about how this comes from different environmental factors, physical activities and diet

13. Stem Cells Two important properties Pluripotency reduced over
Self renewal
Pluripotency
Pluripotency reduced over
time and cell division
Epigenetic modifications
stabilize the lineage-specific
fate of cells

14. DNA Methylation of Stem Cells
DNA methylation low in regions of DNA sequence that are CpG rich (CpG islands) in stem cells
DNA methylation increase during lineage-specification of cells
Methylation targeted at promoter regions
Increase causes loss of pluripotency

15. Cancer Why study epigenetics in cancer? Epigenetic effects: Prevention
Detection
Treatment
Epigenetic effects:
Silencing of tumor suppressor genes
Activation of oncogenes (gene with potential to cause cancer)

16. DNA Methylation & Cancer
DNA methylation in normal cells
CpG island before promoter region of gene is unmethylated
DNA methylation in tumor cells
CpG island before promoter region of gene is hypermethylated

17. Hypermethylation
Basically, an over abundance of methylation at CpG islands
Hypermethylation causes silencing of genes
Silencing of tumor suppressor genes
Causes tumorigenesis (production and formation of tumors)

18. Histone Modifications & Cancer
Healthy and cancer cells differ in histone modification profiles
Cancer cells:
Decrease monoacetylated and trimethylated H4 (one of four types of histones involved in DNA packaging)
Decrease of acetylation on H3 and trimethylation of H3 Lysine 4 (H3K4me3)
Silence tumor suppressor gene, although there’s noted demethylation of CpG islands

19. Controlling Epigenetic Modifications in Cancer Cells
DNA methylation inhibitor 5-aza-2’-deoxycytidine
Prevents methylation of CpG islands
Inhibits all three DNA methyltransferases (Dnmt1, Dnmt3a, Dnmt3b)
In clinical trials, proven to be effective in low dosage and increasing survival rates
Histone deacetylase inhibitors
Problem: deacetylase proteins other than target histones

20. Epigenetics Alter the way we view DNA expression Major role in:
Behavior
Stem Cell and Development
Disease