Chapter 1 (Epigenetics)

2 common mechanisms for epigenetic modifications

-Methylation and histone modification, each of which influences gene expression without altering the DNA sequence

What is epigenetics?

-*Environmental factors* can alter the way our genes are expressed, making even identical twins different -Once nurture seemed clearly distinct from nature. Now it appears that our diets and lifestyles can change the expression of our genes -How? By influencing a network of *chemical switches* within our cells collectively known as the *epigenome*

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-*Methylation of lysines and arginines* (by histone methyl transferases) -Can either close or open chromatin, depending on specific amino acid modified -For example, adding methyl group to H3 lysine 9 favors heterochromatin formation -Demethylation reverses

Behavioral epigenetics- cognition in humans

-A drug that promotes acetylation of histone proteins improved learning and memory in mice that have a disorder similar to Alzheimer's disease -Other studies have found that histone acetylation decreases with age in mice, with diminished expression of genes related to learning and memory -When researchers injected mice with a drug that is an inhibitor of deacetylase activity, acetylation of histones increased, transcription of genes involved in memory increased, and memory of mice improved -These studies suggest that changes in chromatin structure may be involved in learning and memory

Histone modification and disease

-A mutation has been identified in the CREB-binding protein (CBP) -We know that CBP binds to the cAMP-response element-binding protein (CREB) in a transcriptional complex -This mutation cause Rubinstein-Taybi syndrome, which is characterized by short stature, distinctive facial features, and mental retardation

Histone modification

-Acetylation of lysines by histone acetyl-transferases -Prevents close packing of nucleosomes -Favors expression of genes in euchromatin -De-acetylation results in reduced transcription

Histone modification and cancer

-Alterations in histone modification have also been found to promote tumor growth -A common alteration is the global reduction of an acetylated lysine residue in histone H4

Histone modification drugs

-Are called histone deacetylase (HDAC) inhibitors -HDACs are enzymes that remove the acetyl groups from DNA, which condenses chromatin and stops transcription -Blocking this process with HDAC inhibitors turns on gene expression -The most common HDAC inhibitors include phenylbutyric acid, SAHA, depsipeptide, and valproic acid

Epigenetic effects of the environment

-Because some chemicals are capable of modifying chromatin structure, researchers have looked for long-term effects or environmental toxicants on chromatin structure and epigenetic traits

Histone modification and disease

-CBP has histone acetyltransferase activity and opens the chromatin structure -CRP-cAMP complex makes direct contact with RNA polymerase -Without interaction with CRP-cAMP, RNA polymerase can bind to the promoter, but is less likely to unwind DNA and initiate transcription

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-Certain nutrients were protective -Supplementing the mothers' diets with methyl-donating substances, such as folic acid and vitamin B12 counteracted the reduction in DNA methylation caused by the bisphenol A -It is not known if this would actually reverse epigenetic effects, as these supplements occurred at the same time as the bisphenol A exposure -Regardless, these data demonstrate how profoundly the environment can affect gene expression and phenotype

DNA methylation and transcription

-CpG islands are frequently found in the 5' region of genes (at promoter regions) -Usually DNA methylation is associated with the silencing of gene expression (transcriptionall inactive gens- methylated at CpG islands) -Active genes are usually unmethylated -Transcriptionall active genes- hypomethylated at CpG islands

DNA methylation and DNA replication

-DNA methylation is stably maintained during cell division -The parental DNA strand directs the generation of the identical methylation pattern in its daughter strand -This process, also known as maintenance methylation -It is mediated mainly by the DNA methyltransferase DNMT1 and results in the stable inheritance of methylation patterns in a cell line -All the cells will have the identical differentiated phenotype

DNA methylation- drug modification

-Drugs are available that affect the epigenetic modulation of CpG motifs -An example, decitabine, hypomethylates DNA by inhibiting the DNA methyltransferase -This drug is indicated for myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML) -However, since the unspecific inhibition of DNA methylation ahs widespread consequences, the drug has many toxic side effects in treated patients

Environmental epigenetics- endocrine disruptors

-Endocrine disruptors mimic or interfere with natural hormones -They are capable of interfering with processes regulated by natural hormones such as sexual development and reproduction -Ex: vinclozolin, a common fungicide used to control fungal disease in grapes, fruits, and veggies, and to treat turf on golf courses -Vinclozolin acts as an antagonist at the androgen receptor, preventing testosterone from binding -But vinclozolin dose not properly activate the receptor, so it inhibits the action of androgens and prevents sperm production -In one study with rats, vinclozolin not only lead to reduction in sperm production in exposed rats, but it caused reduced sperm in several subsequent generations -There was increased DNA methylation in the DNA of sperm exposed to vinclozolin and these patterns were inherited

Histone modification

-Histones are positvely charged proteins that package and order genomic DNA -Modifications at the N-terminal tails of the histones influence the ability of genes to transcribe DNA into RNA and also affect replication, DNA repair, and chromosomal condensation -Posttranslational modification of histone proteins is carried out by *histone acetyltransferases* (HATs) -The processes are reversible by *histone deacetylases* (HDACs)

SES leaves a mark on the genome

-In a 2019 study, researchers found evidence that poverty can become embedded across wide swaths of the genome -They disocvered that lower SES is associated with levels of DNA methylation at more than 2,500 sites, across more than 1,500 genes (~10% of the genome) -This pattern highlights a potential mechanism through which poverty can have a lasting impact on a wide range of physiological systems and processes -Follow-up studies will be needed to determine the health consequences of differential methylation at the sites the researchers identified, but many of the genes are associated with processes related to immune responses to infection, skeletal development, and development of the nervous system

Early stress cont

-In one study, researches examined the brains of 24 people who had commited suicide, half of whom had experienced childhood abuse and found that those who had experienced childhood abuse had a greater degree of methylation of the glucocorticoid receptor gene than those who had not experienced childhood abuse -Other studies have found that growing up in a lower socioeconomic environment before age 5 altered expression of over 100 genes related to immune function of adults -A different study concluded that growing up in an orphanage alters telomere length

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-It was hypothesized that the same type of receptor might also be present in a mouse's brain -The researchers discovered melanocortin receptors in an area of the mouse brain known to be involved in feeding behavior and body weigh set point -Thus the agouti protein appears responsible for both phenotypic differences in mouse twins: coat color and body weight

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-Many cancer cells also have a distorted epigenetic landscape -Typical changes include a global loss of DNA methylation at CpG islands of certain gene promoters -Hypermethylation at the CpG islands of tumor suppressor genes further favors tumor initiation and progression, whereas hypomethylation can induce aberrant expression of oncogenes

Behavioral epigenetics- early stress in humans

-Numerous studies have demonstrated that stress during childhood and adolescence produces a number of adverse effects that persist into adult life -Ex: child abuse increases the probability that the child will experience depression, anxiety, and suicide as an adult

DNA methylation

-Occurs at cytosines -Occurs largely in dinucleotides of cytosine and guanosine -Abbreviated as *CpG dinucleotides* where p indicates the phosphate group connecting the nucleosides -CpG dinucleotides tend to cluster in regions called *CpG islands* -*DNA methyltransferase (DNMT) enzymes* transfer a methyl group to the C5 position of cytosines -The methyl group can be removed by *demethylases*

Environmental epigenetics-plastic contaminant

-One suspected trigger is a chemical found in many plastic drinking bottles: *bisphenol A* -*Agouti mice*: genetically identical siblings that can look entirely different in both size and color (one may be yellow and obese, another small and brown , and another a medium weight and mixed color -They have the same genome, but gene expression is different -In *healthy brown mice*, the agouti genes are kept in the "off" position by the epigenome, which attaches methyl groups to specific regions in the DNA, preventing transcription -In the *yellow/obese mice*, the same genes are not methylated, and so they are "turned on" or transcribed. These yellow mice are also more likely to suffer from diabetes and cancer as adults

Socioeconomic status leaves a mark on the genome

-Previous research has shown that socioeconomic status (SES) is a powerful determinant of human health and disease, and social inequality is a ubiquitous stressor for human populations globally -Lower SES is also associated with physiological processes that contribute to the development of disease, including chronic inflammation, insulin resistance, and cortisol dysregulation

Chromatin remodeling: with so much DNA compaction, how does transcription occur?

-Promoters of transcribed genes are located in nucleosome free regions -Promoters of non-transcribed genes wrapped in nucleosomes -When transcription required, promoters are exposed by removing or repositioning nucleosomes

Behavioral epigenetics

-Research has shown that life experience, especially those in early life, can have long-lasting effects on behavior -In some cases, these effects can last into future generations -Some of these effects are mediated by epigenetic changes where the life experiences alter chromatin structure

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-Researches exposed pregnant agouti mice to bisphenol A -More offspring developed into obese/yellow mice than expected -Researchers determined that DNA methylation at the agouti gene sites was decreased by 31% -In fact, DNA methylation was reduced on other genes as well -These results supported the hypothesis that bisphenol A alters the action of organism's epigenomes by removing methyl groups from DNA

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-Researches infused the brains of rats with deacetylase inhibitors, which prevents removal of acetyl groups from histone proteins -The rats then showed less responses to fear and stress as adults -Taken together, these studies show that the mother's grooming behavior brought about an epigenetic change in the offspring, which was a long-lasting effect

Human nutrition

-Swedish scientists conducted investigations examining whether nutrition affected the death rate associated with cardiovascular disease and diabetes (the "Swedish food study") -Also, whether these effects were passed from parents to their children and grandchildren -These researchers estimated how much access individuals had to food by examining records of annual harvests and food prices in Sweden across three generations of families, starting as far back as the 1890s -These records were for those in isolated communities, where, if the harvest was bad, people starved -The starving years were all the crueler for their unpredictability

Environmental epigenetics- human nutrition

-The external environment's effects upon genes can influence disease, and some of these effects can be inherited in humans -Studies investigating how environmental factors impact the genetics of an individual's offspring are difficult to design -However, in certain parts of the world in which social systems are highly centralized, environmental information that might have influenced families can be obtained

Histone modifications

-The histone tails can undergo covalent modification with chemical groups -Enzymes can add chemical groups (methyl or acetyl groups, etc.) -Modified tails can alter nucleosomes and bind chromatin modified proteins

Epigenetic regulation of gene expression

-The term "epigenetics" describes heritable changes in the DNA sequence -In a broader sense, epigenetics also refers to stable, long-term alterations in transcriptional levels that are not necessarily heritable -Epigenetic processes are crucial for cellular differentiation -All cells of an organism contain the identical genetic information, but the selective activation and inhibition of genes determines their differentiation into a specific cell type, for example, a liver cell, a muscle cell, or a neuron

Intro to epigenetics

-These are mitotically heritable alterations in the pattern of gene expression -Mediated by mechanisms other than changes in the primary sequence of a gene -Epi= greek prefix which means "on top of"

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-These researchers found that if a father did not have enough food available to him during a critical period in his development (just before puberty), his sons were less likely to die from cardiovascular disease -Remarkably, death related to diabetes was associated with food availability of elders during the critical period -It *increased* for children if food was plentiful for the paternal grandfather, but *decreased* when excess food was available to the father -These findings suggest that diet can cause changes to genes that are passed down through generations by the males in a family -These alterations can affect susceptibility to certain diseases via epigenetic changes

DNA methylation and cancer development

-This occurs through induction of classic genetic mutations -Methylated cytosines mutate to thymidines at a compartively high frequency, which is a mutational change frequently found in human cancers -These mutations may convert proto-oncogenes to oncogenes or inactivate tumor suppressor genes

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-Through careful study, the scientists found that the amount of DNA methylation was fairly consistent through an individual mouse's body -This result suggested that the demethylation that led to yellowness and obesity occured in early development -Despite this suggestion, not all the mice pups grew to be unhealthy. In other words, bisphenol exposure didn't guarantee obesity in mice; rather, it simply increased the risk of developing obesity

Behavioral epigenetics- induced by maternal behavior

-Typically a good mother rat will lick and groom her pups and nurse them -The offspring of mothers who display more licking and grooming behavior show reduced hormonal responses to stress compared with offspring of mothers who lick and groom less -These long-lasting differences in the offspring are not due to changes in nucleotide sequence inherited from their mothers -Offspring exposed to more grooming develop a different pattern of DNA methylation compared with offspring exposed to less grooming -These differences in both methylation and acetylation persist into adulthood of the rat offspring -It was found that these changes affect many stress-response genes, including the glucocorticoid receptor -So how do we correct this?

Histone modification and cancer drugs

-Vorinostat (trade name Zolinza), used for the treatment of cutaneous T-cell lymphoma, was the first HDAC inhibitor that was approved by the FDA -In some cases, chromosomal translocations modulate the activity of histone acetylases and affect the global balance of histone acetylation

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-What are the implications of this study? -With the rise of obesity in the US, and the coincident widespread use of bisphenol A in everything from water bottles to dental sealants, it is tempting to wonder if there is a casual connection -Researchers are cautious to say that this cannot be definitely demonstrated until evidence shows that bisphenol A indeed affects the expression of the human genes involved in obesity

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-What do we know in mice? Pigment -It was first discovered that the agouti protein binds to a melanocortin receptor located on a mouse's skin cells -This blocks those cells from making black pigment -Thus, because the agouti gene is constantly turned on in mutant mice, the melanocortin receptor is always blocked and the animals are yellow

DNA methylation and embryo development

-While methylation patterns are maintained during somatic cell division, they vary during the stages of embryologic development -Initially, the level of DNA methylation is high in mature gametes, but it is nearly eliminated in the blastocyst stage of development (~200-300 cells, when the embryo embeds itself into the uterine wall) -The level of DNA methylation then rises again in all cells except the germ line that remain largely unmethylated throughout life

Transcription

-is controlled by chromatin structure and nucleosome position -Spacing and structure of nucleosomes affects transcription; more compacted DNA= less transcription -Mechanisms that can regulate chromatin patterns: 1. *Remodeling complexes* can alter nucleosome patterns; change accessibility of promoter sequences; remove or reposition promoter-blocking nucleosomes 2. *Histone modifications*- addition of methyl or acetyl groups

Features of epigenetics

1. Stable pattern that is continued through many rounds of mitosis 2. There is control of gene expression at the transcriptional of post-transcriptional level via chemical modifications 3. A dynamic process that can be influenced by development, environment, other factors