Epigenetics and Chromatin Overview
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Which of the following histone modifications is known to remove positive charge and loosen the nucleosome?

  • Acetylation of lysine (correct)
  • Trimethylation of lysine
  • Methylation of arginine
  • Serine phosphorylation

    • Histone modifications primarily occur at the C-terminal tail.

    False

    Name one enzyme responsible for the removal of acetyl groups from histones.

    Histone deacetyl complexes (HDACs)

    The recruitment of enzymes to modified chromatin often requires __________.

    <p>transcription factors</p> Signup and view all the answers

    Match the following histone modifications with their functions:

    <p>Acetylation = Loosens nucleosome Methylation = Can spread heterochromatin Phosphorylation = Involved in transcription regulation Trimethylation = Recruits HP1</p> Signup and view all the answers

    What does trimethylation of lysine or arginine residues primarily recruit?

    <p>HP1</p> Signup and view all the answers

    The histone code hypothesis is a simple concept with few modifications identified.

    <p>False</p> Signup and view all the answers

    What is the primary role of histone methyl transferases (HMTs)?

    <p>To add methyl groups to histones</p> Signup and view all the answers

    More than __________ side chain modifications have been discovered in the globular core of histones.

    <p>20</p> Signup and view all the answers

    Match the enzymes with their corresponding functions:

    <p>Histone acetyl transferases (HATs) = Add acetyl groups Histone deacetylases (HDACs) = Remove acetyl groups Histone methyl transferases (HMTs) = Add methyl groups Histone demethylases (HDMs) = Remove methyl groups</p> Signup and view all the answers

    What is the primary function of chromatin in eukaryotic cells?

    <p>To control gene expression</p> Signup and view all the answers

    Which domain is specifically associated with the recognition of methyl modifications?

    <p>Chromodomains</p> Signup and view all the answers

    Heterochromatin contains many genes and is less condensed than euchromatin.

    <p>False</p> Signup and view all the answers

    Writers, erasers, and readers refer to the same type of enzymes in histone modification.

    <p>False</p> Signup and view all the answers

    What are the fundamental subunits of chromatin?

    <p>Nucleosomes</p> Signup and view all the answers

    What does H3K4me3 modification indicate about gene activity?

    <p>It indicates that the gene is active and is located in the promoter region.</p> Signup and view all the answers

    The process of modifying histones through acetylation or methylation can influence __________ efficiency.

    <p>transcription</p> Signup and view all the answers

    The process of adding methyl groups to DNA cytosine is called __________.

    <p>DNA methylation</p> Signup and view all the answers

    Match the following histones with their corresponding roles:

    <p>H3 = Forms part of the core nucleosome H2A = Forms a dimer with H2B H4 = Smallest core histone H1 = Linker histone that stabilizes nucleosomes</p> Signup and view all the answers

    Match the following histone variants with their functions:

    <p>H2AX = DNA repair and recombination macroH2A = Transcriptional repression CENP-A = Kinetochore assembly H3.3 = Transcriptional activation</p> Signup and view all the answers

    Which of the following best describes the composition of a nucleosome?

    <p>147 bp of DNA wrapped around an octamer of paired histones</p> Signup and view all the answers

    What role does the SAGA complex play in histone modification?

    <p>Deubiquitination and acetylation</p> Signup and view all the answers

    Nucleosomes are designed to allow easy access to DNA for transcription.

    <p>False</p> Signup and view all the answers

    Histone chaperones are not necessary for nucleosome assembly.

    <p>False</p> Signup and view all the answers

    What role do histone tails play in chromatin structure?

    <p>They are important for modification such as methylation and acetylation.</p> Signup and view all the answers

    What is the estimated time frame for nucleosomes to be replaced in cells?

    <p>Every 1-2 hours</p> Signup and view all the answers

    The __________ are regions of chromatin that are densely packed and typically found near centromeres and telomeres.

    <p>heterochromatin</p> Signup and view all the answers

    ATP-dependent remodeling complexes use energy from __________ to move DNA.

    <p>ATP hydrolysis</p> Signup and view all the answers

    Which complex is known to stabilize replication forks and is involved in DNA damage repair?

    <p>INO80 complex</p> Signup and view all the answers

    What does paired-end tag sequencing help to identify?

    <p>Loci bound by protein and physical proximity in 3D space</p> Signup and view all the answers

    Hi-C is a low-throughput method of studying chromatin interactions.

    <p>False</p> Signup and view all the answers

    What are topologically associated domains (TADs)?

    <p>Regions of the genome where genes tend to be activated at the same time.</p> Signup and view all the answers

    Hi-C captures interactions across all chromosomes __________.

    <p>simultaneously</p> Signup and view all the answers

    Match the following terms with their definitions:

    <p>Paired-end tag sequencing = Identifies interacting regions of the genome Hi-C = High-throughput method for mapping chromatin interactions Topologically associated domains (TADs) = Regions coordinating gene expression Genome-wide mapping = Capturing interactions across all chromosomes</p> Signup and view all the answers

    What must you do to determine interactions when reading a Hi-C map?

    <p>Read in the direction of the arrows</p> Signup and view all the answers

    What is the purpose of crosslinking in the context of DNA interactions?

    <p>To freeze interactions in place</p> Signup and view all the answers

    Restriction enzymes are used to crosslink DNA.

    <p>False</p> Signup and view all the answers

    What do fragments that are physically close in 3D space have a higher likelihood of doing?

    <p>Ligating together</p> Signup and view all the answers

    The process used to enrich for DNA interactions mediated by specific proteins is called __________.

    <p>chromatin immunoprecipitation (ChIP)</p> Signup and view all the answers

    Match the following terms to their descriptions:

    <p>3C = Technique to analyze DNA interactions ChiA-PET = Specialized type of 3C for DNA-protein interactions Restriction enzyme = Cuts DNA at specific sites Ligation = Joining of DNA fragments</p> Signup and view all the answers

    What is one of the uses of understanding gene regulation through proximity?

    <p>To understand how enhancers loop to their promoters</p> Signup and view all the answers

    Hybrid molecules are analyzed to determine gene interactions.

    <p>True</p> Signup and view all the answers

    What type of domains are mapped during chromatin studies?

    <p>Topologically associating domains (TADs)</p> Signup and view all the answers

    In ChiA-PET, the first step is __________ to freeze the interactions.

    <p>crosslinking</p> Signup and view all the answers

    What role does digestion play in chromatin analysis?

    <p>To cut DNA at specific sites and keep interacting regions together</p> Signup and view all the answers

    Study Notes

    Epigenetics and Chromatin

    • Epigenetics studies how environmental and behavioral factors affect gene function.
    • For example, chromatin structure affects transcription efficiency. Histones need to be acetylated or methylated to allow transcription.
    • Chromatin is tightly packed eukaryotic DNA and proteins.
    • It controls gene expression and chromosome segregation during mitosis.
    • It also protects DNA from damage.
    • Heterochromatin is a highly condensed form typically near centromeres and telomeres.
    • Heterochromatin makes up about 10% of mammalian DNA and contains fewer genes.
    • Euchromatin is less condensed, and its changes can relate to differential gene expression.
    • Nucleosomes are fundamental chromatin subunits.
    • Each nucleosome is made up of about 147 base pairs of DNA wrapped around a histone octamer.
    • Histones are proteins (H3, H4, H2A, H2B).
    • DNA stretches between nucleosomes are 38-53bp long.
    • Nucleosomes can be studied using micrococcal nuclease (MNase).
    • Nucleosome structure is beads-on-a-string.
    • Nucleosome structure resists nuclease digestion.

    Histones

    • Histones are highly conserved, small, basic proteins.
    • Core histones are H3, H4, H2A, and H2B.
    • Linker histone H1 is the largest, H4 being the smallest.
    • Linker DNA is 38-53bp long.
    • Histones have a high lysine and arginine content, important for DNA binding.
    • H3 and H4 combine to form a dimer.
    • H2A and H2B combine to form a dimer.
    • Two dimers combine to form an octamer.
    • A nucleosome is 11nm in diameter and 5.7nm thick.
    • 147bp of DNA wraps around the histone octamer in a left-handed, superhelix pattern.
    • Primary interactions occur with the phosphodiester backbone and lysines or arginines.

    Histone Tails

    • Histones have variable tails on their N-terminals.
    • Histone tails can be modified to alter DNA interaction.
    • Examples of modification:
      • Acetylation of lysine residues.
      • Methylation of lysine or arginine residues.
      • Serine phosphorylation.

    Histone Modifications

    • Enzymes drive modifications.
      • Acetylations are driven by HATs, removed by HDACs.
      • Methylations are driven by HMTs, removed by HDMs.
    • Modifications can spread heterochromatin.
    • Various modification combinations occur, each with different functions.

    Histone Code Hypothesis

    • Different combinations of chemical modifications on histones guide gene expression.

    Histone Variants

    • Histones have variable forms.
    • Common examples include H2AX and H2AZ.
    • Functions include recombination and expression control.

    High Order Chromatin Organization

    • 3C assays are used to study genome-wide interaction maps.

    • Chromatin organization is studied by

      • Crosslinking DNA and proteins.
      • Digesting the chromatin.
      • Ligation of fragments.
      • Identifying interactions using detection methods.

    • Hi-C is a high throughput method for measuring chromatin interactions.

    • Topologically associating domains (TADs) are areas of chromatin with high interaction frequency.

    • Genes in a TAD often have the tendency to be expressed similarly.

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    Chromatin and Epigenetics PDF

    Description

    This quiz explores the complex topics of epigenetics and chromatin structure, focusing on how they influence gene expression and chromosome behavior. Discover the roles of histones, nucleosomes, heterochromatin, and euchromatin in cellular processes and DNA protection.

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