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

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

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 (1744-1829) 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

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

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

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

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.

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.

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

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

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

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

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

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

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)

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

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)

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

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

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