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What are the major & minor grooves of the DNA molecule? Discuss the significance of the major and minor grooves as they relate to gene regulation.
Major groove has its bases more accessible. Methyl groups lie in the MAJOR groove of DNA. Proteins such as transcription factors can also bind to the major groove, giving it an important role in gene regulation
What are the different components of eukaryotic chromatin, how do they interact and what is the importance of chromatin organization to eukaryotic organisms?
- Composed of multiple histones which aids in the condensing and looping of DNA (described in previous question).
- Euchromatin: DNA wrapped around histone, forming nucleosome (aka: beads on a string), fairly open form, higher gene regulation activity vs more compact form
- Euchromatin form: residues in histone tails affect nucleosome interactions, chromatin packing, etc.
- Heterochromatin: 30nm chromatin fibers, COMPACT form, less gene regulation activity (still accessible to transcription machinery)
What are the common types of histone modifications and what effect do they have on chromatin structure? What classes of enzymes are responsible for these modifications?
- Histones help to coil and pack the chromatin structure thereby affecting gene regulation
- Histone modifications are often interdependent (ie: phosphorylation of H3S10 promotes acetylation and INHIBITS meth. Of H3K9)
- 1. nucleosome: DNA wrapped around histones. These separated by linker DNA, which H1 histone interacts with
- 2. solenoid structure: 30nm chromatin fiber, although still accessible to transcription machinery
- 3. looped domain: loops of the 30nm chromatin fiber, which can uncoil to give high-gene expression
- Enzymes responsible for modifications:
- Acetylase: Lysine, when acetylated is open and more active.
- Deacetylase: Lysine, when hypoacetylated, coiled up and closed, inactive gene regulation
- Methylases and demethylases: Lysine and Arginine, with promoters..when methylated, low gene expression. and when demethylated, high gene expression
- Kinases and phosphatases: Serine, when phosphorylated (thru kinase) adds a phosphate group
Briefly explain what is meant by the term histone code and what is some of the evidence for the existence of such a code?
- Histone code: refers to the idea that transcription of DNA is regulated by modification of histones that interact with specific proteins
- Modified histones:
- 1. Phosphorylation example: Phos. Of H3S10 can promote ACETYLATION and METH. Of H3K9
- 2. Ubiquitination example: Ubiq. Of H2AK119 is required for METH of H3K4
- Protein interactions with modified histones
- 1. H3K4: associates with promoter sites
- 2. Bromodomains bind acetylated lysines
- 3. Chromodomains bind methylated lysines: aid in stabilizing chromatin in its condensed state
- 4. PHD domains bind more generally
What is DNA methylation (be specific) and how/why is it important to gene regulation?
- DNA methylation: occurs at specific nucleotides (CpG). The process involves converting the cytosine to 5MeC
- Methyl groups lie in the MAAJOR groove of DNA: can affect binding of activator and silencing proteins
- Interaction with MeCpG-binding proteins: play a role in chromatin STRUCTURE and gene REGULATION
- Also MeCpG important in epigenetics and genetic memory
- Binding of siRNAs can trigger histone methylation: resulting in non-expressed chromatin
Defend or argue against the following statement. Genome/chromatin modifications in the parent are never passed on to the offspring. Alternatively this might be worded as, with each fertilization, the genome slate is wiped clean. Answers to either should be in terms of epigenetics, imprinting, etc.
- Chromatin modification may be present in the offspring, as the DNA sequences that may be present and passed on through transposition or tandem duplications, in which the child inherits these DNA sequences, may result in similar modifications.
- Modifications that can be inherited may result from the inherited DNA sequences leading to:
- 1. the same chromatin structure formation due to modifications of histone tails, or RITS-RNA incuded transcriptional silencing for example.
- 2. similar targets for DNA methylation and other histone modifications
What is meant by the phrase the nucleus is not just a bag of chromatin?
- Chromosome regions localize within the nucleus and are involved in chromatin structure and gene regulation: diff. chromosomes occupy distinct territories within nuclei active toward center and inactive in periphery
- rRNA synthesis and ribosome assembly in nucleus
- RNA synthesis and splicing in sites w/in nucleus
- Chrom. Tethering to nuclear lamina can result in: altering gene expression of associated genes and mutations in lamina (cause genetic diseases, ie progeria)
What is known about the role(s) of various ncRNAs in chromatin structure/gene regulation? Provide some specific examples.
- Piwi-RNAs: REPRESS transposition by targeting RNAs made from transposons. Only expressed in germ line.
- Large/long ncRNAs: play a role in X-chromosome inactivation
- Binding of siRNAs: can trigger histone methylation (lead to non-expressed chromatin) or regulating of transposons
- miRNA: important in gene regulation, esp. w/development, and involved in cancers. miRNAs processed from large precursors (which become cleaved and one strand removed to get miRNA)
- Heterochromatic regions are coated with RNAi-induced transcription silencing complex (RITS)
What is epigenetics and what mechanisms are involved in epigenetic changes to the chromatin? What are some specific examples of epigenetics and what are the consequences of epigenetics in these examples.
- Epigenetics: the study of heritable changes in gene expression, caused by changes in DNA sequences.
- Mechanisms: Histone modifications that result in DNA methylation (CpG cytosine replaced with 5MeC). Highly methylated areas are less transcriptionally active
- H3K4 methylation plays a role in preventing gene silencing via DNA methylation, by preventing DNA methyltransferase from binding to nucleosomes where H3K4 is bound.
Briefly describe the mechanism(s) by which piRNAs are thought to protect our genomes by suppressing transposon activity. Be sure to also include the proteins that are involved in generation and/or functioning of piRNAs.
- 1. piRNA scans RNAs to identify targets.
- 2. piRNA triggers generation of small RNAs (ie, 22G-RNAs in C elegans) that associate with WAGO protein.
- 3. Transposon transcript is cleaved
- 4. piRNA can associate with WAGO proteins: Result in SUPPRESSING action of transposons mRNA in cytoplasm & silence transposon expression via chromatin remodeling.