Epigenetics: Gene Expression and Regulation

• Lecture covers Epigenetics
• Presented by Associate Professor Zanda Daneberga

Epigenetic Trait

• Stably heritable phenotype
• Results from chromatin changes
• Does not alter the DNA sequence

Characteristic of Changes

• Stable in cell division
• Reversible

Timing of Epigenetic Reprogramming

• Occurs during germ cell development
• Occurs during early embryogenesis in mammals

Epigenomics

• These are epigenetic changes at the whole genome level

Epigenetics vs Epigenomics

• Epigenetics focuses on processes like chemical modifications
• These regulate gene expression and genomic stability
• The epigenome has chemical compounds that instruct the genome
• Both epigenetics and epigenomics provide a program for gene expression
• Factors like environment, lifestyle, age, and disease state can influence gene expression

Regulation

• Eukaryotic organisms gain precise and stable control of gene expression and genomic regulation through multiple generations

Genomic Stability

• Epigenetic traits play a crucial role in genomic stability
• This is achieved through the silencing of centromeres, telomeres, and transposable elements

Genomic Stability is Ensured Through:

• Proper microtubule attachment to centromeres
• Reducing excessive recombination between repetitive elements
• Preventing the transposition of transposable elements

Epigenitor

• Changes in the environment trigger epigenetic changes in the cell
• The environmental signal is considered an epigenator
• Epigenators activate initiators

Epigenetic Initiator

• The initiator translates the epigenator signal
• It identifies locations on chromosomes
• This is where epigenetic marks are established
• DNA binding proteins and noncoding RNAs act as initiators
• Initiators are DNA sequence-specific

DNA-Binding Proteins

• DNA-binding proteins bind to specific DNA sequences
• From this noncovalent interactions with an α-helix in the DNA-binding protein domain
• Atoms on the base edges in a DNA major groove allow binding to occur
• DNA sugar-phosphate backbone atoms are also involved
• Atoms in a DNA minor groove also contribute to binding

Non Coding RNA

• ncRNA is a functional RNA molecule transcribed from DNA
• ncRNA molecules are non-translated into proteins
• Epigenetic-related ncRNAs can be short or long
• ncRNAs regulate gene expression at the transcriptional and post-transcriptional levels

Short ncRNAs Involved in Epigenetic Processes

• Less than 30 nucleotides long
• MicroRNAs bind to target messenger RNA with a complementary sequence
• Binding leads to cleavage, degradation, and translation blocking

short interfering RNAs (siRNAs):

• Leads to post-transcriptional gene silencing which results in mRNA degradation

piwi-interacting RNAs (piRNAs):

• Used for chromatin regulation and suppression of transposon activity in germline and somatic cells

long ncRNAs

• Made of more than 200 nucleotides
• Forms a complex with chromatin-modifying proteins
• Recruits the proteins catalytic activity to specific sites in the genome
• Modification of chromatin state and gene expression follow

ncRNA Functions

• Chromatin remodeling
• Transcriptional regulation
• Post-transcriptional regulation
• Serve as precursors for siRNAs

Epigenetic Maintainer: DNA Methylation

• Methyl Group is added to the 5-carbon of the pyrimidine base cytosine in CpG islands.
• Three DNA methyltransferases (DNMTs) methylate CpG sites.
• Methylation of a gene's CpG island represses gene expression
• Different cell methylation creates different expression in different cell types

Non-CpG Cytosine Methylation:

• Found in high levels in stem cells
• Loss of this methylation is thus important to cell differentiation
• Global and non-CpG methylation level are inversely proportional to stem cell differentiation levels

Histone Modification

• Histone modification and DNA methylation are coordinated processes
• Histone modification is a covalent post-translational modification (PTM) to histone proteins.
• PTMs regulate chromatin structure to affect gene expression, DNA repair, and chromosome condensation

Histone modifications:

• Methylation - addition of a methyl group (CH3)
• Phosphorylation - addition of a phosphate group (PO4)
• Acetylation - addition of an acetyl group (CH3CO)
• Ubiquitylation - addition of ubiquitin protein
• Sumoylation - addition of Small Ubiquitin-like Modifier protein

Histones

• Histones consist of a globular core
• Histones have a loosely structured n-terminal tail that protrudes of the nucleosome
• Most histone PTMs occur on the N-terminal tails
• Due to their chemical properties, epigenetic modifications alter chromatin condensation
• They also alter the accessibility of DNA to transcriptional machinery

Acetylation

• Histones become acetylated on lysine (K) residues
• histone acetyltransferases (HATs) and histone deacetylases (HDACs) are the key enzymes
• The addition of the acetyl group neutralizes the positive charge of lysine
• Leads to weakened affinity between to histone tail and negatively charged DNA

Methylation

• Occurs on both lysine and arginine (R) residues
• This epigenetic modification transcribed and or silenced genes.
• Arginine residues can be mono or di-methylated
• Lysine residues can be mono, di or tri-methylated
• histone methyltransferase (HMTs) and histone demethylases (HDMs) control the process

Phosphorylation

• Occurs on serine (S), threonine (T), and tyrosine (Y) residues
• Commonly associated with transcriptional activation
• Repulsion is created between repulsive histone and negatively charged DNA
• Phosphorylation is reversible
• Protein kinases (PKs) add phosphate groups
• Protein phosphatases (PPs) removes phosphate groups

Ubiquitination

• Attachment of ubiquitin to core histones: H2A and H2B.
• H2A ubiquitination is repressive, H2B can be active or repressed
• Epigenetic phenomenon, H2A/B and histone methylation often cross-talk
• H2B starts methylation, but H2A inhibits

Sumoylation

• Addition of Small Ubiquitin-like Modifiers (SUMO)
• Similar to ubiquitin, about 100 amino acids long
• Actions are reversed by proteases
• Sumoylation is another mark of transcriptional repression

Histone Variants

• They are coded by different genes as histones
• Reflect amino acid differences in tails and globular central domains
• They feature specific expression, localization, and distribution patterns
• The function affects chromatin remodelling and post-translational modifications.
• Underlying mechanisms not fully understood

Nucleosome Remodeling

• Refers to chromatin structure changes
• Requires ATP energy input
• Carried out by ATPase enzymes
• It can lead to complete or partial nucleosome disassembly
• It can lead to an exchange of histones for variants
• It can lead to assembly of nucleosomes
• It can lead to the movement of histone octamers on DNA

Example: Hippo-campus

• The hippocampus is an area of the brain involved in stress response
• Glucocorticoids are primary stress hormones necessary regulate life processes
• The GR gene encodes the glucocorticoid receptor
• DNA methylation in the promoter region of the glucocorticoid receptor (GR) gene leads to decreased GR expression
• Transcription factor NGF1-A can bind the GR promoter region to start gene expression

Conclusion

• Epigenetic and gene expression changes persist into adulthood
• This leads to a heightened stress response, at least in rat models