** Epigenetics

    Cards (46)

    • Epigenetics
      Study of heritable changes in gene expression that do not involve changes to the underlying DNA sequence
    • Epi- (Greek)

      On top of or in addition to
    • Epigenetic changes are potentially stable and heritable
    • Epigenome
      A collection of all the chemical compounds that have been added to the entirety of one's DNA (genome) as a way to regulate the activity (expression) of all the genes within the genome
    • Genetically Identical Cells
      • Different epigenetic modifications can lead to different expression patterns and phenotypes
    • Epigenetic changes
      • Often reversible, unlike genetic mutations
    • Nucleosome
      Fundamental unit of DNA packaging, consisting of a segment of DNA wound around eight histone proteins
    • Nucleosome Structure
      • DNA wraps around a histone octamer (2x H2A, H2B, H3, H4)
    • Further Packaging
      Nucleosomes coil to form chromatin fibers, which condense into chromosomes during cell division
    • Condensed Chromatin (Heterochromatin)
      Tightly packed, transcriptionally inactive
    • De-condensed Chromatin (Euchromatin)
      Loosely packed, transcriptionally active
    • Epigenetic Tags (Marks)
      Chemical modifications to DNA or histones that affect gene expression
    • Epigenetic Tags (Marks)
      • DNA methylation, histone modification
    • Epigenetic Modifiers
      Enzymes that add or remove epigenetic tags
    • Epigenetic Modifiers
      • DNA methyltransferases (DNMTs), histone acetyltransferases (HATs), histone deacetylases (HDACs)
    • DNA Methylation
      Addition of a methyl group to the 5th carbon of cytosine residues, forming 5-methylcytosine (5mC)
    • CpG Sites
      Cytosine followed by guanine; common sites for DNA methylation
    • CpG Islands
      Regions with a high frequency of CpG sites, often located near gene promoters
    • DNMT1
      Maintenance methyltransferase, preserves methylation during DNA replication
    • DNMT3A and DNMT3B
      De novo methyltransferases, establish new methylation patterns during development
    • Functions of DNA Methylation
      • Gene silencing, Transposon suppression, X-chromosome inactivation
    • Active Demethylation
      Enzymes like TET proteins oxidize 5mC to 5-hydroxymethylcytosine (5hmC), which can be further processed and removed
    • Passive Demethylation
      Failure to maintain methylation during DNA replication
    • Bisulfite Sequencing
      Treat DNA with bisulfite to convert unmethylated cytosines to uracil, then sequence the DNA to distinguish between methylated and unmethylated cytosines
    • Methylation-Specific PCR (MSP)

      PCR technique to amplify and detect methylated DNA sequences
    • Histones
      Proteins around which DNA is wrapped, forming nucleosomes
    • Types of Histones
      • H1, H2A, H2B, H3, H4
    • Histone Tails
      Extend from the nucleosome and are sites for post-translational modifications
    • Acetylation
      Addition of acetyl groups by HATs; generally associated with gene activation
    • Deacetylation
      Removal of acetyl groups by HDACs; associated with gene repression
    • Methylation
      Addition of methyl groups by histone methyltransferases (HMTs); can either activate or repress gene expression depending on the specific residue methylated
    • Phosphorylation
      Addition of phosphate groups by kinases; involved in chromatin remodeling and gene expression regulation
    • Ubiquitination
      Addition of ubiquitin molecules; involved in DNA damage response and chromatin structure regulation
    • Writers
      Add modifications (e.g., HATs, HMTs)
    • Erasers
      Remove modifications (e.g., HDACs, histone demethylases)
    • Readers
      Recognize and bind to specific histone modifications, influencing downstream processes
    • Histone Code
      The idea that specific combinations of histone modifications can lead to distinct chromatin states and gene expression patterns
    • Chromatin Remodeling
      • Epigenetic modifications can alter chromatin structure, making DNA more or less accessible to transcription factors and RNA polymerase
    • Gene Activation
      • De-condensed chromatin with activating marks (e.g., H3K4me3, H3K27ac) is more accessible for transcription
    • Gene Repression
      • Condensed chromatin with repressive marks (e.g., H3K27me3, DNA methylation) is less accessible, leading to gene silencing
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