Lecture 8
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Questions and Answers

What is the role of a mediator in transcription?

  • It binds to the promoter, thus controlling the expression of genes.
  • It acts as a linker, allowing for proper localization of general and specific transcription factors to the promoter. (correct)
  • It is a specific transcription factor that activates or inhibits transcription based on cellular demand for specific proteins.
  • It is a component of the transcription pre-initiation complex which binds to the enhancer or silencer and forms a loop.

    • What is the primary function of general transcription factors (GTFs)?

  • To bind to the promoter region of a gene and initiate transcription in all cells. (correct)
  • To form a loop between the enhancer/silencer and the promoter, allowing for the regulation of transcription.
  • To bind to specific DNA sequences and activate or repress transcription based on cellular needs.
  • To act as a mediator between the enhancer/silencer and the promoter, facilitating the interaction of specific transcription factors with the promoter.

    • What is the main difference between general transcription factors (GTFs) and specific transcription factors (STFs)?

  • GTFs are protein complexes, while STFs are single proteins
  • GTFs bind to the promoter, while STFs bind to the enhancer or silencer.
  • GTFs are involved in the initiation of transcription, while STFs are involved in the elongation of the transcript.
  • GTFs are always active and involved in basal transcription, while STFs are activated based on specific cellular demands. (correct)

    • What is the purpose of the loop formed between the enhancer/silencer and the promoter?

    <p>To create a physical connection between the enhancer/silencer and the promoter, allowing for regulation of transcription.</p> Signup and view all the answers

    Which of the following are true about transcription regulators? (Select all that apply)

    <p>They bind to DNA regulatory sequences.</p> Signup and view all the answers

    How do transcription regulators recognize specific DNA sequences?

    <p>By recognizing specific base pairs in the major groove of DNA.</p> Signup and view all the answers

    What is the structural motif called that is formed by transcription regulators with at least three α helices that fit into the major groove of DNA?

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

    What is the significance of dimerization in transcription regulators?

    <p>It increases the contact area between the transcription regulator and DNA, strengthening the interaction.</p> Signup and view all the answers

    What is combinatorial control in gene expression?

    <p>The coordinated action of multiple transcription regulators working together to determine the expression of a specific gene.</p> Signup and view all the answers

    Which of the following statements about trans regulatory sequences are true? (Select all that apply)

    <p>They function to act as switch regulating transcription.</p> Signup and view all the answers

    What is the primary function of a gene in eukaryotic cells?

    <p>To code for a sequence of nucleotides in mRNA</p> Signup and view all the answers

    What percentage of DNA in humans consists of protein-coding genes?

    <p>1.5%</p> Signup and view all the answers

    Which statement about housekeeping proteins is true?

    <p>They include proteins that are essential for basic cellular functions.</p> Signup and view all the answers

    What is the key regulatory step for most genes during gene expression?

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

    Which of the following is a characteristic of cis-regulatory sequences?

    <p>They influence the gene they are located next to.</p> Signup and view all the answers

    What role do transcription regulators play in gene expression?

    <p>They act as switches to regulate transcription.</p> Signup and view all the answers

    Which type of regulatory sequence typically acts over long distances?

    <p>Silencers and enhancers</p> Signup and view all the answers

    How can eukaryotic cells regulate their protein synthesis?

    <p>By controlling transcription and degradation of mRNA.</p> Signup and view all the answers

    Which type of RNA is encoded by a gene that produces a polypeptide?

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

    What characterizes the differentiated cells in a multicellular organism?

    <p>They can express a variable number of genes depending on their function.</p> Signup and view all the answers

    What distinguishes trans-acting regulatory elements from cis-regulatory elements?

    <p>Trans elements can act on different chromosomes.</p> Signup and view all the answers

    Which mechanism primarily facilitates the transport of mRNA from the nucleus to the cytoplasm?

    <p>Nuclear pore complex</p> Signup and view all the answers

    Which gene expression regulation involves proteins that inhibit transcription?

    <p>Transcription repressors</p> Signup and view all the answers

    What is the relationship between the structural differences of tissues and gene expression?

    <p>Different genes are expressed in different tissues, resulting in functional variations.</p> Signup and view all the answers

    What is the main difference between euchromatin and heterochromatin?

    <p>Euchromatin is less tightly packed than heterochromatin.</p> Signup and view all the answers

    Which of the following is NOT a common histone modification?

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

    Which of the following is NOT a function of DNA methylation?

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

    What is the role of methyl-CpG binding domain (MBD) proteins?

    <p>Recognizing and binding to methylated CpG sequences in DNA.</p> Signup and view all the answers

    What is the significance of the CpG dinucleotide in DNA methylation?

    <p>It is the most common site for methylation in vertebrates.</p> Signup and view all the answers

    What is the role of histone acetyltransferases (HATs) in chromatin remodeling?

    <p>HATs add acetyl groups to histone tails, leading to gene activation.</p> Signup and view all the answers

    What is the role of histone deacetylases (HDACs) in chromatin remodeling?

    <p>HDACs remove acetyl groups from histone tails, leading to gene silencing.</p> Signup and view all the answers

    What is the main mechanism of "histone octamer shift" in chromatin remodeling?

    <p>The histone octamer slides along the DNA strand.</p> Signup and view all the answers

    What is the role of RNA interference (RNAi) in epigenetic regulation?

    <p>RNAi can indirectly affect DNA methylation and histone modifications, leading to gene silencing.</p> Signup and view all the answers

    How do epigenetic patterns change during development?

    <p>Epigenetic patterns are erased and re-established at various stages of development.</p> Signup and view all the answers

    Which of the following is an example of epigenetic regulation contributing to cellular identity?

    <p>The difference in gene expression patterns between a muscle cell and a nerve cell.</p> Signup and view all the answers

    What is the main function of the "barrier sequences" that are mentioned in the context of chromatin remodeling?

    <p>Barrier sequences block the spread of heterochromatin formation, preventing gene silencing.</p> Signup and view all the answers

    Which of the following statements about histone modification during DNA replication is TRUE?

    <p>Newly synthesized DNA receives a mixture of modified and unmodified histones, with the patterns influenced by the parent strand.</p> Signup and view all the answers

    What is the main difference between "chromatin remodeling" and "histone modification"?

    <p>Chromatin remodeling involves altering the structure of the nucleosome, while histone modification involves altering the chemical composition of histone proteins.</p> Signup and view all the answers

    Which of the following is NOT a typical participant in chromatin remodeling?

    <p>RNA polymerase</p> Signup and view all the answers

    What is the main outcome of the epigenetic reprogramming cycle during gametogenesis and early embryogenesis?

    <p>The selective erasure of some epigenetic patterns and the establishment of new patterns, specific to germline or somatic cells.</p> Signup and view all the answers

    What is the role of multiple transcription regulators in eukaryotes?

    <p>They help in the coordination of mediator assembly and transcription factors.</p> Signup and view all the answers

    What occurs as a result of alternative promoter usage?

    <p>Different transcripts and proteins from the same gene depending on the tissue.</p> Signup and view all the answers

    How does alternative splicing contribute to protein diversity?

    <p>By producing different combinations of exons.</p> Signup and view all the answers

    Which statement about poly(A) sites is true?

    <p>Use of different poly(A) sites can lead to variations in mRNA stability and location.</p> Signup and view all the answers

    What is the primary function of the RISC complex formed by miRNA?

    <p>To degrade target mRNA or inhibit its translation.</p> Signup and view all the answers

    In what context does RNA editing alter gene expression?

    <p>By inserting or deleting nucleotides in the mRNA sequence.</p> Signup and view all the answers

    What distinguishes lncRNAs from other types of RNA?

    <p>They play significant regulatory roles in gene expression.</p> Signup and view all the answers

    Which of the following describes the characteristic of heterochromatin?

    <p>It is tightly packed and transcriptionally inactive.</p> Signup and view all the answers

    What is the primary outcome of the action of small interfering RNA (siRNA)?

    <p>Degrading target mRNA to inhibit its production.</p> Signup and view all the answers

    What mechanism allows a single pre-mRNA molecule to produce multiple protein forms?

    <p>Alternative polyadenylation.</p> Signup and view all the answers

    What is an example of the effects of transcriptional regulators during embryonic development?

    <p>They contribute to the differentiation of various cell types.</p> Signup and view all the answers

    What role do transcription factors play in the process of gene expression?

    <p>They assist in the binding of RNA polymerase to DNA.</p> Signup and view all the answers

    Which of the following correctly describes gene expression regulation via epigenetic mechanisms?

    <p>It can be modified by external factors without changing the DNA sequence.</p> Signup and view all the answers

    How does the use of specific RNA editing in liver and intestinal cells affect ApoB protein synthesis?

    <p>Liver cells produce a longer ApoB while intestinal cells produce a shorter one.</p> Signup and view all the answers

    What role does the mediator protein play in transcription?

    <p>It connects transcription factors to the transcription pre-initiation complex.</p> Signup and view all the answers

    Which statement about general transcription factors (GTFs) is true?

    <p>GTFs are the same across different types of eukaryotic genes.</p> Signup and view all the answers

    What defines a transcription regulator's ability to recognize DNA sequences?

    <p>It relies on the precise fitting of the protein’s surface to the DNA structure.</p> Signup and view all the answers

    Which of the following statements about combinatorial control is accurate?

    <p>Multiple transcription factors work together to express genes under specific conditions.</p> Signup and view all the answers

    How do specific transcription factors (STFs) differ from general transcription factors (GTFs)?

    <p>STFs can be activated or inhibited based on cellular needs, unlike GTFs.</p> Signup and view all the answers

    What type of interaction do transcription regulators primarily use to bind to DNA?

    <p>Hydrogen bonds, ionic bonds, and hydrophobic interactions through dimerization.</p> Signup and view all the answers

    In the context of transcription regulation, what is the function of trans regulatory sequences?

    <p>They encode transcription factors that work through DNA-protein and protein-protein interactions.</p> Signup and view all the answers

    What is the significance of the major groove in DNA for transcription regulators?

    <p>It is the site where transcription regulators form specific connections with base pairs.</p> Signup and view all the answers

    Why is dimerization of regulatory proteins important in transcription regulation?

    <p>It increases the binding specificity and interaction area with DNA.</p> Signup and view all the answers

    Which type of bond is least likely to be formed between transcription regulators and DNA?

    <p>Covalent bonds</p> Signup and view all the answers

    What is a primary consequence of DNA methylation on gene expression?

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

    In the context of X chromosome inactivation, what is the role of DNA methylation?

    <p>Prevents transcription of genes on one X chromosome</p> Signup and view all the answers

    What characterizes the inheritance of DNA methylation patterns during cell division?

    <p>One strand is inherited as methylated and the other as unmethylated</p> Signup and view all the answers

    Which of the following histone modifications is associated with decreased gene expression?

    <p>H3 K9 methylation</p> Signup and view all the answers

    Which mechanism allows for the modification of newly synthesized histones during DNA replication?

    <p>Proteins binding to previous modified histones</p> Signup and view all the answers

    What is the primary action of histone acetyltransferases (HATs) in chromatin remodeling?

    <p>To add acetyl groups to histone tails, increasing transcription</p> Signup and view all the answers

    What effect does histone deacetylation have on chromatin structure?

    <p>Condenses chromatin and inhibits transcription</p> Signup and view all the answers

    Which type of modification is NOT a common histone modification?

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

    Which of the following describes a function of RNA interference (RNAi)?

    <p>Regulates transcription through methylation and histone modifications</p> Signup and view all the answers

    How does histone methylation contribute to chromatin remodeling?

    <p>By promoting either euchromatin or heterochromatin formation</p> Signup and view all the answers

    What is the initial mechanism of chromatin remodeling involving the histone octamer?

    <p>Loosening of nucleosomal DNA via ATP hydrolysis</p> Signup and view all the answers

    In the process of chromatin remodeling, what do barrier sequences help prevent?

    <p>Further spreading of heterochromatin formation</p> Signup and view all the answers

    What common function do histone modifications serve in transcription regulation?

    <p>Induce structural changes in chromatin accessibility</p> Signup and view all the answers

    What is a critical feature of histone tails that allows for modification?

    <p>They extend beyond the nucleosome's globular structure</p> Signup and view all the answers

    What best describes the functional difference between housekeeping proteins and specialized proteins in differentiated cells?

    <p>Housekeeping proteins facilitate basic metabolic functions, while specialized proteins are involved in specific roles.</p> Signup and view all the answers

    Which statement accurately characterizes eukaryotic gene expression?

    <p>Transcription occurs independently of translation in eukaryotes.</p> Signup and view all the answers

    How do long-range cis-regulatory sequences function in gene expression regulation?

    <p>They can influence transcription regardless of their orientation relative to the promoter.</p> Signup and view all the answers

    What role do transcription regulators play in cis-regulatory sequences?

    <p>They must recognize specific DNA sequences to effectively regulate transcription.</p> Signup and view all the answers

    What is a primary mechanism by which differentiated cells can change their gene expression patterns?

    <p>By responding to both intracellular and extracellular signals.</p> Signup and view all the answers

    What defines the significance of enhancers and silencers in gene transcription?

    <p>They can function independently of their distance to the promoter.</p> Signup and view all the answers

    Which of the following is true about the transcription factors associated with cis-regulatory sequences?

    <p>They can interact with DNA at regulatory sequences to modulate gene expression.</p> Signup and view all the answers

    What primarily characterizes the process of alternative splicing in gene expression?

    <p>It alters the final protein product by generating different combinations of exons.</p> Signup and view all the answers

    Why is the organization of genes and regulatory elements significant in eukaryotic cells?

    <p>It allows for the specific activation of genes required in particular cell types.</p> Signup and view all the answers

    What would be an incorrect assumption about the encoding capability of eukaryotic genes?

    <p>The majority of a eukaryotic genome is made up of protein-coding regions.</p> Signup and view all the answers

    What is the primary reason for the variability of protein expression levels in different cell types?

    <p>Different cells have unique sets of regulatory proteins that control gene transcription.</p> Signup and view all the answers

    In the context of gene expression regulation, what is a critical factor affecting mRNA degradation?

    <p>The specific regulatory proteins that bind to the mRNA.</p> Signup and view all the answers

    Which of the following is a misconception about the role of non-coding DNA in eukaryotes?

    <p>Non-coding DNA has no regulatory function.</p> Signup and view all the answers

    What is the primary advantage of combinatorial control in gene regulation during embryonic development?

    <p>It ensures that multiple genes can be regulated simultaneously with fewer regulators.</p> Signup and view all the answers

    Which mechanism allows a gene to produce different mRNA transcripts in different tissues?

    <p>Alternative promoters</p> Signup and view all the answers

    How does alternative splicing contribute to the generation of protein diversity?

    <p>By altering exon arrangements and resulting in different protein variants.</p> Signup and view all the answers

    What is one consequence of using different poly(A) sites in gene expression?

    <p>Formation of mRNA with varying lengths and stability.</p> Signup and view all the answers

    Which of the following best describes the role of regulatory RNAs, such as miRNA?

    <p>They mediate RNA degradation or inhibit translation.</p> Signup and view all the answers

    What is the primary function of the RITS complex in relation to RNA interference?

    <p>To inhibit transcription of complementary sequences.</p> Signup and view all the answers

    In the context of RNA editing, which type of change primarily occurs in mammals?

    <p>Changes of cytosine to uridine.</p> Signup and view all the answers

    What condition leads to the synthesis of two forms of apolipoprotein B in different tissues?

    <p>RNA editing resulting in different mRNA forms.</p> Signup and view all the answers

    Which aspect of chromatin structure is affected by epigenetic mechanisms?

    <p>The degree of condensation of chromatin.</p> Signup and view all the answers

    Which statement about long non-coding RNAs (lncRNAs) is true?

    <p>lncRNAs can influence chromatin structure and gene expression.</p> Signup and view all the answers

    What is primarily monitored during the decision-making process after each cell division in embryonic development?

    <p>The synthesis of regulatory proteins.</p> Signup and view all the answers

    What distinguishes the action of alternative promoters from alternative splicing in gene expression control?

    <p>Alternative promoters affect transcription in a tissue-specific manner.</p> Signup and view all the answers

    Why is the concept of epigenetics important in understanding gene expression changes?

    <p>It accounts for inheritable expression changes not involving DNA sequence alterations.</p> Signup and view all the answers

    In humans, what is the impact of glucocorticoid hormones like cortisol on gene regulation?

    <p>They coordinate the expression of multiple genes through shared regulatory sequences.</p> Signup and view all the answers

    Study Notes

    Control of Gene Expression

    • Lecturer: Dr. Michelle Kuzma
    • Adapted from: Dr. Danuta Mielżyńska-Švach
    • Book reference: Essential Cell Biology, 6th Edition by Bruce Alberts
    • Focus on content discussed in lectures
    • Chapters: 8 (Control of Gene Expression), 9 (How Genes and Genomes Evolve)

    Gene Expression in Eukaryotes

    • Cells in multicellular organisms became interdependent, sacrificing individual independence for the common good
    • Multicellular organism activities resemble a large metropolis
    • Prokaryotic cells resemble a small cottage in the middle of nowhere

    Human Genome

    • Nuclear genome: 3000 Mb, 30,000 genes
    • Mitochondrial genome: 16.6 kb, 37 genes
    • Coding DNA: 10%
    • Non-coding DNA: 90%
    • Genes and gene-related sequences: 30%
    • Extragenic DNA: 70%
    • Two rRNA genes: 80%
    • 22 tRNA genes:
    • 13 polypeptide-encoding genes: 20%
    • Pseudogenes, gene fragments, introns, untranslated sequences, etc.
    • Unique or low copy number
    • Tandemly repeated or clustered repeats
    • Moderate to highly repetitive interspersed repeats

    Eukaryotic Gene

    • A gene is a fragment of DNA that encodes a product
    • A gene carries information for polypeptide structure (mRNA)
    • A gene carries information for functional non-coding RNA (e.g., rRNA, tRNA, snRNA, miRNA)

    Eukaryotic Gene Sequences

    • Coding sequences (exons)
    • Non-coding sequences (introns)
    • Regulatory sequences
    • Promoter
    • Enhancers
    • Silencers

    Eukaryotic Gene Structure

    • DNA 5' --> 3'
    • Upstream regulatory sequence
    • Distal control elements
    • Proximal control elements
    • Open reading frame (ORF)
    • Downstream regulatory sequence
    • Intron
    • Poly-A signal sequence
    • Exon
    • Promoter (TATA box)
    • Enhancer/Silencer
    • Terminator

    Gene Expression in Eukaryotes

    • Genetic material of somatic cells is identical
    • Differentiated human cell expresses 5,000-1,000 genes out of 25,000 protein-coding genes
    • Protein-coding genes represent 1.5% of DNA, while 98.5% is non-protein-coding.
    • Gene expression is the process where cells synthesize proteins and RNA from their DNA.
    • In each differentiated cell type, the set of expressed genes remains constant.
    • Cells can alter gene expression patterns in reaction to intracellular and extracellular signals

    Expression of Genes in Eukaryotes

    • In somatic cells, most proteins are the same.
    • Called "housekeeping proteins" and include:
      • DNA and RNA polymerases
      • DNA repair enzymes
      • Ribosomal proteins
      • Enzymes associated with basic metabolic processes

    Gene Expression in Eukaryotes - Examples

    • Pancreatic ß-cells produce insulin
    • Pancreatic α-cells produce glucagon
    • B cells (lymphocytes) produce antibodies
    • Red blood cells synthesize hemoglobin

    Gene Expression in Eukaryotes - Steps

    • DNA --> RNA transcript (transcriptional control)
    • RNA processing (RNA processing control)
    • mRNA transport and localization (mRNA transport and control)
    • mRNA translation (translation control)
    • protein activity, degradation
    • mRNA degradation (mRNA degradation control)

    Gene Expression Regulation

    • Cells regulate protein sets by
      • Controlling when and how often a given gene is transcribed
      • Controlling transcript maturation steps
      • Selectively exporting mRNAs to cytoplasm.
      • Regulating mRNA degradation speed
      • Selecting mRNAs for ribosome translation
      • Regulating protein degradation rate

    Types of Expression Regulation

    • Key regulatory step, largely: transcription
    • Transcription begins when RNA polymerase and transcription factors bind to the gene promoter.
    • Most genes have additional DNA regulatory sequences for transcription control

    Types of Regulatory Sequences

    • Cis-type: on the same chromosome as the regulated gene
    • Trans-type: on a different chromosome

    Cis-Regulatory Sequences

    • Divided into short-range and long-range sequences
    • Short-range: promoters, enhancers, and silencers in the 5' UTR region Long-range sequences act over larger distances

    DNA Regulatory Sequences

    • Regulators do not function independently.
    • Recognition by a transcription regulator protein turns them on or off

    Models for Action "at a Distance"

    • Activator or repressor protein binds to enhancer or silencer sequences far from promoter
    • DNA loops connect enhancer (silencer) and promoter to let the regulator protein contact transcriptional pre-initiation complex
    • Mediators act as linkers for correct localization of general or specific transcription factors to the promoter region with RNA polymerase.

    Transcription Factors

    • GTFs (general transcription factors) remain active throughout the cell's lifetime
    • STFs (specific transcription factors) are activated/inhibited in response to cell requirements for specific proteins

    General transcription factors associated with a promoter are the same for all genes transcribed by RNA polymerase.

    Specific transcription factors and DNA-binding sites vary between genes.

    Combinatorial control

    • Most eukaryotic transcription regulators cooperate in complex systems
    • The combination of proteins determines expression of specific genes

    In Eukaryotes, expression generally is controlled by multiple factors together

    Types of Expression Regulation (continued):

    • Promoter is first regulatory sequence where RNA polymerase and transcription factors bind

    Cis-regulatory sequences

    • Short-range regulatory sequences, like promoters, enhancers, and silencers influence nearby genes
    • Long-range sequences act over larger distances

    Regulatory Sequences (continued)

    • Binding by transcription regulators acts as a switch

    Regulatory Trans Sequences

    • They are sequences that encode transcription factors that influence other genes via interactions (DNA-protein, protein-protein, RNA-protein)

    Transcription Regulators

    • Transcription regulator proteins recognize DNA regulatory sequences
    • Their binding acts as a switch that regulates transcription

    Transcription Regulators (continued)

    • They are proteins whose surfaces tightly fit DNA surfaces
    • Noncovalent bonds with nucleotides in the major groove of DNA
    • Interactions may also occur in the minor groove with bases
    • Strong and specific DNA/protein interactions
    • Use at least three a helices, fitting into DNA major groove and connecting with base pairs
    • Asparagine side chain of third helix forms hydrogen bonds with adenine bound to thymine

    Transcription Regulators (continued)

    • DNA-protein interface contains 10-20 interactions, involving varying amino acids
    • Interactions include hydrogen, ionic, hydrophobic bonds

    Dimerization

    • Protein dimers increase the surface area for DNA-protein interaction

    Chromatin Remodeling

    • Remodeling alters chromatin structure (condensation/loosening) by histone-modifying enzymes and chromatin-remodeling complexes

    Chromatin Remodeling (continued)

    • Some gene activators/repressors recruit proteins to promoters by:
    • Histone acetyltransferase — adds acetyl groups, increasing gene transcription
    • Histone deacetylase — removes acetyl groups, reducing gene transcription

    Chromatin Remodeling (continued)

    • Modifications create waves
    • Barrier sequences prevent heterochromatin spread.

    Histone Octamer Shift

    • A chromatin remodeling mechanism that moves histone octamers to alter DNA access.
    • Protein complexes use energy ATP hydrolysis to loosen nucleosomal DNA and push it out of the nucleosome, making it accessible to enable transcription.

    RNA Interference (RNAi)

    • A defense mechanism against viruses present in eukaryotes.
    • Some RNAi inhibit transcription of specific genes via DNA modifications, RNAi-dependent DNA methylation, and histone protein modifications.

    Epigenetics

    • The study of changes to gene expression without altering the DNA sequence
    • Epigenetic mechanisms include inheritance and modification by external factors.

    Epigenetic Regulation

    • DNA with proteins create chromatin that can be condensed to varied degrees.
    • Condensation affects protein accessibility for DNA transcription.
    • Heterochromatin (tightly packed) — inactive
    • Euchromatin (loosely packed) — active

    Epigenetic Regulation (continued)

    • Changes in chromatin structure alter transcription without altering DNA sequence. These mechanisms include:
      • DNA methylation
      • Histone modification
      • Chromatin remodeling
      • Non-coding RNA synthesis

    DNA Methylation

    • Methylation adds a methyl group to cytosine.
    • Formation 5-methylcytosine due to participating of DNA methyltransferases
    • In vertebrates limited to CpG sequences (cytosine next to guanosine)
    • About 60% of cytosine nucleotides in mammals are methylated and recognized by MBD proteins (Methyl-CpG Binding Domain).
    • Methylation causes closure of chromatin area and blocks gene transcription.
    • Examples relate to cellular identity, X-chromosome inactivation, gene reprogramming, and genomic imprinting

    Cellular Identity

    • DNA methylation patterns pass through cell division
    • Conservative methyltransferases interact with unmethylated strands for methylation of CpG sequences

    X-chromosome inactivation

    • In female mammals, one X chromosome is inactivated in each cell.
    • Inactivation occurs randomly and is passed to daughter cells (e.g., calico cats)

    Epigenetic Reprogramming

    • Methylation patterns erased in germline
    • Paternal and maternal methylation imprinted after development

    Chromatin Structure

    • DNA and proteins form chromatin, which can condense
    • Condensed chromatin (heterochromatin) — transcriptionally inactive
    • Loose chromatin (euchromatin) — transcriptionally active

    Histone Modification

    • Nucleosome histones can be modified covalently.
    • Common modifications — phosphorylation, acetylation, methylation, ubiquitination
    • Modified amino acids numbered (36 of H3 near the N-terminus), can be methylated
    • Modification patterns can be propagated through cell division and influence function of proteins.

    Histone Modification (continued)

    • Histone acetylation — increases gene expression by relaxing chromatin
    • Histone deacetylation — reduces gene expression by tightening chromatin

    Histone Modification (continued)

    • Methylation on lysines has different effects
    • Increased expression: H3 K4 me3, K36 me3, K79 me3
    • Decreased expression: H3 K9 me3, K27 me3, H4 K20 me3

    Histone Modification (continued)

    • During DNA replication, histones are distributed randomly to daughter chromosomes.
    • Proteins responsible for histone modifications keep the patterns by binding, adding modifications

    Chromatin Remodeling

    • Involves condensation/loosening of chromatin
    • Used by histone/chromatin-modifying complexes to influence gene expression

    Chromatin Remodeling (continued)

    • Gene activators/repressors recruit proteins to promoters for specific interactions — e.g., histone acetyltransferase (adds acetyl groups), histone deacetylase (removes acetyl groups)

    Chromatin Remodeling (continued)

    • Modifications in regions can propagate.
    • Barrier sequences block the spread

    Histone Octamer Shift

    • A chromatin remodeling mechanism involves shifting histone octamers to alter DNA access.
    • ATP dependent remodeling protein complexes cause DNA loosening and movement.

    Regulatory RNA

    • Noncoding RNAs, such as miRNAs, siRNAs, and IncRNAs, play diverse roles in regulating gene expression.

    mi RNAs

    • miRNA is small hairpin RNA that is processed.
    • Single-stranded miRNA, protein complex (RNA-induced silencing complex, RISC)
    • RISC recognizes complementary bases in the target mRNA and can degrade or reduce translation by mRNA

    si RNA

    • formed from double-stranded (usually exogenous/endogenous) large RNA
    • Cleaved by protein DISCER
    • Forms siRNA-RITS complex that attaches to pre-mRNA
    • Transcription elongation inhibited

    IncRNA

    • Long non-coding RNAs (IncRNAs) are more than 200 nucleotides long.
    • Xist (17,000 nucleotides) plays a key role in inactivating one of the two X chromosomes.
    • Some IncRNAs fold into specific structures and place proteins on DNA/RNA sequences

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    This quiz explores the roles of mediators, general transcription factors (GTFs), and specific transcription factors (STFs) in gene regulation. Additionally, it covers mechanisms such as enhancer/silencer interactions, transcription regulators, and combinatorial control. Test your knowledge on these essential components of transcription.

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