Epigenetics - The Basics

A set of flashcards covering key concepts and mechanisms of epigenetics, gene expression, and chromatin structure.

What is epigenetics?

The study of changes in gene expression that occur due to chemical modifications of the genome, rather than a change to the DNA sequence itself.

How do different cells arise from a single genome?

Through unique gene expression profiles influenced by intrinsic and extrinsic factors.

What factors can regulate gene expression?

Gene expression can be regulated by extrinsic cues (like growth factors) and intrinsic cues (such as DNA modification).

What is the role of growth factors in gene expression?

Growth factors trigger intracellular signaling cascades that lead to changes in transcription.

What are the observable characteristics of cells influenced by?

They are influenced by unique gene and protein expression profiles, although all cells share the same genome.

What is gene expression?

The process by which cells convert the information encoded in DNA into functional products, such as proteins.

What are the two strands in DNA referred to in the context of transcription?

• The template or antisense strand (-)

• coding or sense strand (+)

What is the role of transcription factors in gene expression?

They interact with regulatory regions to help initiate transcription of specific genes.

What does the core promoter include?

• 'core' promoter region

• promoter proximal regions

• ie. TATA box.

What are enhancers and silencers?

• distal regulatory regions

• either enhance or repress the expression of specific genes.

What is the significance of the 30 nm chromatin fiber?

It is transcriptionally dormant and facilitates loops anchored to a protein scaffold for chromosome compaction.

What role do nucleosomes play in chromatin structure?

Nucleosomes are the units of chromatin that help to package DNA into a compact form.

How do chromatin remodeling complexes affect transcription?

They cooperate with DNA-binding proteins to repress or activate gene expression by altering the arrangement of nucleosomes.

What are posttranslational modifications (PTMs)?

Chemical modifications, such as acetylation and methylation, that occur on histone tails and influence transcription.

What happens during histone acetylation?

Acetyl groups are added to lysines, destabilizing chromatin structure and promoting gene activation.

What does DNA methylation do?

It represses transcription by preventing the binding of transcription factors to gene promoters.

What are CpG islands?

Regions of the genome with a high frequency of CpG dinucleotides, often found in gene promoters.

How does the environment influence the epigenome?

Environmental factors can promote or inhibit gene expression through changes in the epigenome.

What is the histone code hypothesis?

It postulates that patterns of histone modifications are interpreted by cellular mechanisms to regulate transcription.

What are the effects of DNA packing on gene expression?

Condensed chromatin is inaccessible to transcription machinery, while looser chromatin is permissive to transcription.

What do special transcription factors do?

Activators help initiate transcription by facilitating the binding of RNA polymerase to the core promoter, while repressors impede this binding.

What is the difference between euchromatin and heterochromatin?

Euchromatin is loosely packed and active in transcription, while heterochromatin is tightly packed and typically inactive.

What is the significance of combinatorial regulation in gene expression?

Multiple transcription factors can cooperate, with specific combinations required to induce expression or repression of a gene.

What is the relationship between experience and epigenetics?

Experiences can lead to epigenetic changes that alter gene expression, affecting behavior and phenotype.

What is the process of transcription initiation in eukaryotes?

It involves the binding of transcription factors to the core promoter and the recruitment of RNA polymerase to start transcription.

What happens when histone deacetylases (HDACs) act on chromatin?

They remove acetyl groups from histones, promoting chromatin compaction and gene repression.

What effect does phosphorylation of histone proteins have?

Phosphorylation can either activate or repress transcription depending on the context and specific amino acids involved.

How do chromatin remodeling complexes facilitate transcription?

By altering the structure of chromatin, they allow access to DNA-binding proteins and the transcriptional machinery.

What occurs during the process of nucleosome assembly?

Histones bind to DNA, forming nucleosomes that compact the DNA structure for efficient packaging.

What is the consequence of DNA packaging for gene expression?

Tightly packaged DNA limits the accessibility for transcription factors and RNA polymerase, thus repressing gene expression.

What is the main way environmental factors influence epigenetic regulation?

They can lead to changes in histone modifications and DNA methylation patterns that affect gene expression.

What are the functions of distal regulatory regions like enhancers?

They facilitate higher levels of gene expression by interacting with the core promoter from a distance.

What role do methyl-CpG binding domain (MBD) proteins play in gene regulation?

They bind to methylated DNA and function as repressors to inhibit gene expression.

What does the term 'phenotypic variation' refer to in the context of epigenetics?

Variations in observable traits that arise without changes to the underlying DNA sequence.

What is a nucleosome made of?

DNA wrapped around a core histone octamer composed of H2A, H2B, H3, and H4 proteins.

What are the two general mechanisms of chromatin structure modulation?

Posttranslational modification of histones and ATP-dependent chromatin remodeling enzymes.

What happens during histone demethylation?

Methyl groups are removed from histones, potentially activating previously silenced genes.

How can histone modification patterns influence gene expression?

Different patterns of histone modifications can signal whether a gene is activated or repressed during transcription.