Mutations, Gene Expression, and RNA Modifications

Mutation Significance

• Mutations are a significant function of cells.
• They drive evolution and influence biological processes.
• Mutations are the source of genetic variation.
• Cell division presents the potential for mutations.
• The frequency of mutation occurrences depends on DNA repair, cell division rate, and environmental exposures.

Gene Expression Regulation

• Gene expression can be regulated independently of DNA mutations through:
  • Histone Modification: impacts gene accessibility chemically.
  • Chromatin Remodeling: repositions nucleosomes affecting gene accessibility.
  • DNA Methylation: influences gene expression without altering the DNA sequence.

RNA Modifications & Consequences

• mRNA is modified through capping, polyadenylation, splicing, and RNA editing.
• These modifications are essential for stability, nuclear export, and translation efficiency.
• RNA editing results in changes to protein sequences, alternative splicing, and altered miRNA activity.
• Splicing consequences include generating protein isoforms, affecting gene expression, and potentially causing diseases.

Mutations in Protein Coding Regions

• Mutations in protein coding regions lead to changes in protein structure and function.
• Mutations can cause loss of function, gain of function, or disease.

Mutations Outside Protein Coding Regions

• Mutations elsewhere in the genome can have varying consequences.
• Consequences range from no effect to causing genetic disorders or increasing disease risk.
• Most mutations occur during DNA replication or due to environmental factors.
• Mutations can be categorized as somatic.

AMES Test

• The AMES test assesses the mutagenic potential of chemical compounds.
• Uses Salmonella typhimurium with a defective histidine gene.
• Bacteria are mixed with a test chemical and plated on a histidine-deficient agar.
• Colonies indicate restored ability to synthesize histidine.
• A high number of colonies indicates strong mutagenic potential.

Copy Number Variants (CNVs)

• CNVs are sections of the genome repeated.
• Copy numbers varies between individuals.
• CNVs are a major contributor to genomic diversity in humans.
• CNVs can affect gene dosage, traits, and susceptibility to conditions.
• CNVs can disrupt genes or regulatory elements, causing:
  • Gene dosage imbalance
  • Altered gene expression
  • Fusion genes or disrupted coding sequences.

Spontaneous or Replication Error Mutations

• Base Substitutions: Transitions and transversions occur due to errors in DNA replication.
• Frameshift Mutations: Insertions and deletions disrupt the reading frame.
• Strand Slippage: newly synthesized strand separates temporarily and re-anneals at a different location
• Tautomeric Shifts: changes in the structure of DNA bases lead to incorrect base pairing during replication.
• Replication errors are a major source of spontaneous mutations

Chemical Mutagens

• Base analogs (like 5-bromouracil).
• Alkylating agents (like ethyl methanesulfonate).
• Intercalating agents (like acridine orange).

Environmental Exposure & Cancer Risk

• Substances in the environment can damage DNA and disrupt normal cell functions leading to cancer.
• Hormone Disruption: interferes with hormone signaling, promoting abnormal cell growth.
• Chronic Inflammation: triggers inflammation, increasing cancer risk.
• Cell Proliferation: altering cell cycles or suppressing apoptosis that creates conditions for cancer to develop.

Viruses and Cancer

• Viruses cause cancer by directly altering cellular genes.
• Viruses cause cancer by suppressing the immune system.
• Viruses cause cancer by causing chronic inflammation.

RAS Genes

• RAS genes encode proteins that act as molecular switches.
• They relay signals from the cell surface to the nucleus.
• Regulate cell growth, proliferation, and differentiation.
• Growth signals are received by receptors at the cell surface.
• The activated receptor transfers the signal to intracellular Ras protein.
• After receiving a signal, normal Ras protein binds guanosine triphosphate (GTP).

P53

• P53 regulates:
  • DNA Repair
  • Cell Cycle Arrest
  • Apoptosis
  • Senescence
  • Metabolism Regulation
• Mutations are found in the DNA-binding domain of active cancer.
• Mutations prevent p53 from binding DNA properly, disabling its tumor-suppressing functions.
• P53 is always present at low levels but is kept inactive by MDM2.
• Phosphorylates control DNA repair and cell cycle arrest.
• DNA damage inhibits MDM2, leading to P53 stabilization and accumulation.

Inflammation & Cancer

• Increased Cell Proliferation: Inflammatory signals drive excessive cell division.
• Genomic Instability: Reactive oxygen and nitrogen species from inflammation cause DNA damage.
• Angiogenesis: Inflammatory factors stimulate new blood vessel formation.

Environmental Agents & Inflammation

• Tobacco Smoke: Contains carcinogens that cause chronic inflammation and DNA damage.
• Chronic Infections: Viruses like HPV, H. pylori, and hepatitis viruses trigger persistent inflammation.
• Radon: radioactive gas that's colorless and odorless and can be a health hazard.

Cancer Phenotypes

• Sustaining proliferative signaling.
• Evading growth suppressors.
• Resisting cell death.
• Enabling replicative immortality.
• Inducing angiogenesis.
• Activating invasion and metastasis.
• Reprogramming cellular metabolism.
• Avoiding immune destruction.

Gene Fusions

• Gene fusions occur when two separate genes join together.
• They create hybrid genes with altered functions.
• They result from chromosomal rearrangements like translocations, deletions, or inversions.
• RNA sequencing (RNA-seq), fluorescence in situ hybridization (FISH), and reverse transcriptase PCR (RT-PCR) are used to detect
• Gene fusions can function as cancer drivers, leading to oncogenesis (BCR::ABL1 fusion in leukemia for example).

Rabbit Effect

• Purpose of study was to research how social environment can act as a factor in diet-induced atherosclerosis.
• Rabbits were chosen because they develop atherosclerosis more easily versus other mammals.
• Rabbits with high levels of care and attention showed significantly less atherosclerosis.
• Their bodies were accustomed to less stress.

Rat Grooming

• Mother A would pair with pup B and mother B would pair with pup A.
• Mother A does not exhibit the behavior of grooming the young while Mother B does.
• Older pups showed changed behavior as it was epigenetic.
• Epigenetic changes are genetic modifications that impact gene activity.

Epigenetics

• Epigenetics are changes in gene expression that do not involve alterations in the DNA sequence.
• Changes are influenced by environmental factors and can be inherited.
• Examples of epigenetic effects in humans include:
  • Genomic Imprinting
  • Cancer
  • Effects of Early-Life Environment

Genome Sequencing

• Precision medicine in cancer refers to ID individual approaches to Tx of individual's cancer.
• Whole genome sequencing can obtain the following genetic information
  • Mutations
  • Copy Number Variations (CNVs)
  • Structural Variations
  • Epigenetic Changes

RNA Sequencing

• Information obtained through this includes:
  • Gene Expression Levels
  • Splice Variants
  • Fusion Transcripts
  • Non-coding RNA Activity