Epigenetics and Epigenomics

Lecture 5 - Epigenetics and Epigenomics

• Epigenetic traits lead to stably heritable phenotypes that stem from chromosomal changes without DNA sequence alterations.
• Epigenetic changes are stable during cell division but can also be reversed.
• Epigenetic reprogramming is vital during germ cell development and early embryogenesis in mammals.
• Epigenomics studies epigenetic changes at the whole genome level.
• The epigenome acts as a crucial interface between the environment and the genome.
• Chemical tags attached to the genome form the epigenome.
• Epigenetics maintains tissue identity by determining which genes are active or inactive.

Epigenetic Regulation in Eukaryotes

• Eukaryotic epigenetic events provide precise control over gene expression and genomic stability across generations.
• Epigenetic modifications in eukaryotes involve histone-binding epigenetic factors that affect DNA packing or directly alter DNA.
• Epigenetic traits maintain genomic stability by silencing centromeres, telomeres, and transposable elements.
• Silencing ensures proper microtubule attachment, reduces recombination between repetitive elements, and prevents transposable element transposition.
• Environmental cues trigger cell epigenetic changes
• Epigenators refer to environmental signals responsible for initiating these changes.
• Epigenator signals activate initiators.
• Initiators translate epigenator signals and pinpoint chromosomal locations for epigenetic marks.
• DNA-binding proteins, noncoding RNAs, are sequence-specific initiators.

Epigenetic Initiators

• DNA-binding proteins' ability to bind specific DNA sequences is due to noncovalent interactions between the α-helix in the DNA-binding protein domain and atoms within the DNA major groove.
• Sugar-phosphate backbone atoms and atoms in the DNA minor groove also facilitate this binding.
• Non-coding RNA (ncRNA) molecules are transcribed from DNA but not translated into proteins.
• Epigenetic-related ncRNAs, including short and long ncRNAs, regulate gene expression at transcriptional and post-transcriptional levels.

ncRNAs in Epigenetic Processes

• Short ncRNAs, specifically microRNAs (miRNAs) target mRNA with complementary sequences.
• microRNAs induce cleavage, degradation, or blocked translation, leading to gene silencing and mRNA inactivation.
• RNA-induced silencing complex (RISC) is formed when precursor miRNA is transported to the cytoplasm and processed by Dicer.
• Dicer cleaves stem-loops to form short double-stranded miRNA molecules, which Ago 2 binds, unwinds, and releases one strand,
• The remaining guide strand interacts with Ago 2 and additional proteins to form RISC, inactivating genes via mRNA cleavage or translation inhibition.
• Short interfering RNAs (siRNAs) mediate post-transcriptional gene silencing, resulting in mRNA degradation and induce heterochromatin formation via RISC.
• Piwi-interacting RNAs (piRNAs) regulate chromatin and suppress transposon activity in germline and somatic cells.
• Long ncRNAs (> 200 nt) form complexes with chromatin-modifying proteins.
• Long ncRNAs recruit catalytic activity to specific genomic sites, modifying chromatin state and gene expression.
• ncRNAs function in chromatin remodeling, transcriptional regulation, and post-transcriptional regulation, acting as precursors for siRNAs.

Epigenetic Maintainers

• DNA methylation involves adding a methyl group to the 5-carbon of cytosine within CpG islands.
• DNA methyltransferases (DNMTs) perform CpG site methylation, leading to gene expression repression.
• Different cell types exhibit distinct methylation patterns, influencing gene expression variations.
• Stem cells have high levels of non-CpG cytosine methylation, and a loss of this methylation is critical in differentiation.
• Total global methylation and degree of non-CpG methylation are inversely proportional to the level of differentiation.

Histone Modification

• Histone modification and DNA methylation coordinate in correlated processes.
• It is a covalent post-translational modification (PTM) to histone proteins.
• PTMs regulate chromatin structure, affecting gene expression, DNA repair, and chromosome condensation.
• The majority of histone PTMs occur on the N-terminal tails.
• Chemical properties of epigenetic modifications alter chromatin condensation, thus impacting DNA accessibility to the transcriptional machinery.
• Histone protein PTM include methylation, phosphorylation, acetylation, ubiquitylation, and sumoylation.
• Acetylation neutralizes the positive charge of the amino group of lysine, decreasing affinity between the tail and negatively charged DNA, leading to a more open chromatin structure.
• Histone methylation can occur on lysine and arginine residues and can lead to transcribed and silenced genes.
• Arginine residues can be mono- and di-methylated.
• Lysines can be mono-, di-, tri-methylated,
• These degrees of histone methylation can have differing roles on gene expression regulation.
• Histone methylation is controlled by histone methyltransferases (HMTs) and histone demethylases (HDMs).
• Phosphorylation typically associates with transcriptional activation due to the repulsion between the phosphate group and negatively charged DNA.
• Protein kinases regulate histone phosphorylation by adding phosphate groups, while protein phosphatases remove them.
• Ubiquitination is the attachment of the 76-amino acid protein ubiquitin to the histone core proteins H2A and H2B.
• H2A ubiquitination is repressive.
• H2B ubiquitination is active and repressive.
• Sumoylation refers to the addition of SUMO proteins, similarly 100 amino acids long, histone sumoylation serves as a mark of transcriptional repression.

Histone Variants

• Histone variants are non-allelic and coded by different genes, representing differences in amino acids in tails or in the globular central domains.
• They have specific expression, localization, and distribution patterns and impact chromatin remodeling.
• Histone variants affect post-translational modifications.

Nucleosome Remodelling

• Nucleosome remodeling is a change in chromatin structure requiring ATP energy input.
• Enzymes known as ATPases carry out nucleosome remodeling through complete or partial nucleosome disassembly, histone exchange, nucleosome assembly, or histone octamer movement on DNA.

Epigenetics and Human Health

• Key points surrounding early life environment epigenetically shapes the stress response later in life in both rates and humans
• Erasers remove marks from the chromatin, and enzymes work simultaneously.
• Hippocampus is implicated in the stress response.
• Glucocorticoids are stress hormones which are necessary for life. They also regulate numerous physiological processes to maintain homeostasis.
• DNA methylation in the promoter region of the glucocorticoid receptor (GR) gene leads to decreased GR expression.

Epigenomics and Allelic Imbalance

• The study of epigenetic changes at the level of the whole genome.
• Allelic imbalance occurs when gene expression levels from two alleles in a diploid genome aren't equal.
• It affects 5-20% of autosomal genes, often during early embryogenesis.
• Monoallelic expression means that only one of two gene copies is active, while the other is silent.
• Somatic rearrangement involves changes in DNA organization that lead to functional gene at only one copy.
• Between 0.5% and 15% of autosomal exhibit random monoallelic expression.
• Random choice of one gene copy is expressed, like immunoglobulin genes and T-cell receptor genes.
• Genomic imprinting occurs when all epigenetic silencing affect the gene copy present in imprinted regions. There are >100 genes and the function is for developmental.
• Parental gametogenesis means if the maternal copy id methylated, paternal copy is active.
• In X chromosome inactivation the Epigenetic silencing of X chromosome affects linked genes on one female chromosome

Human Genome Variation

• Variation is caused by the process of mutation which affects somatic and germline cells.
• Human genome variation can be observed in alteration of numerical/structural chromosomal aberrations and alteration of structure on a DNA sequence.
• The human genome project was completed in 2003.

Chromosomal v DNA Alterations

• A chromosomal aberration changes in the number/structure of chromosomes and DNA sequence.
• DNA alterations affect DNA sequence.
• To fix errors in DNA polymerase uses its proofreading function

Allelic Variants and Mutation Rates

• A missense allelic variant involves a single nucleotide substitution in the coding region, altering the genetic code.
• Silent allelic variants alters the genetic code where the synonymous replacement of one amino acid occurs.
• In nonesense variants a single altered nucleotide effects the genetic code by one of a three stop codes.
• The process of fixing mismatch errors in a DNA is mismatch repair
• Physical and ionized radiation causes induced mutations
• Average human germ cells rate of mutation is 1.1 to 1.7*10^8 per nucleotide

Pathological and Functional Consequences

• In the blood, sickle cell is from symptoms of anemia tissue infractions and multiple infections
• Silent code alters genetic code by synonymous replacement
• Nonsense code alters genetic code of stop codons

PCR Terms and Types

• Basic steps I denaturation (unwinding) of DNA II. Primer finds single DNA stranded DNA and attaches to its annealing
• DNA template DNA sequence specific, primers.
• In 3rd step new DNA is synthesized only 2 enzymes Taq.
• Human DNA range of 1.1-1.7 *10’s per nucleotide.
• Main step is initial Denaturation initial step to get DNA prepared.
• Next is, Denaturation where synthesis will be repeated.
• Amplifying more copies increase the yield.

Cell Division- Cytoskeleton Functions

• Cell division ensures Ability eukaryotic cell to cell shape deformation and intracellular cargo.
• Changes shape during movement and communication signals assisted.
• Microtubules are composed of protein tubulin composed diameter of 25nm.
• Composed subunit of Alpha Beta tubulin Assembled into linear protofilaments.
• Microtubules Rapid Grow during polymerization and shrinking.

Cell Cycle

• Somatic division results in two genetically identical cells.
• Mitosis Consist of five phases.
• Interphase cell performs it’s function
• Five phases called karyokinesis- Division of nucleus followed by Cytokinesis, cell separates.
• Cytokinesis result and rest of cell separates.
• Regulation controlled by CDK proteins.
• M phase to regulation proteins
• Metaphase cells arranged in linear fashion on plate.
• Anaphase cells migrate to be oppposite poles connected by chromosome
• The spindle checkpoint in case a mistake happens in spindle.
• Each chromosomes Sister chromatids move to the opposite poles of the cell.
• Each chromatics break to separate as daugher chromosome.

Meiosis

• In Prophase chromosomes condenses attahcment condesin at each sides for compact organization
• Anaphase centromere chromosomes move to mid line spinder and move together
• Cnetrosomes move during S phase

Cellular Components

• Mircotubles move pole to pole, kinetochore attahc chromotids, interplar microtubules,
• In Telophase chromosomes at poles and dissembles to a mitotic spindle.
• There is phosphate which results in a membrane surrounding chromosome
• Cytokinesis is a process of splitting a cell, membrane pinches cell at equal divide

Meiosis Details

• Creates diploid cells -> Haplodi gamemates and has two rounds of cell division has one single DNA replication.
• Begins two phases with a four stage
• Prophase phase is a complicated process w several detailed stages: Leptote Zyotene.
• Homologous counterparts for information and create align with pairings.
• Exchange from cross overs will leads to genetic alleic combos.
• Homologous recombination results in non chromatids with result in different cell death.
• Telophase is two hapliod sets of chromosomes.

Human Pathology Chromosomal Abnormalities

• The most common are down syndrome results with different face charatertics
• In chromsome, is not paired = nondisjunction and can lead to chromosome transolcations
• Somatic mosaicism effects