Applied Genetics and Epigenetics GNSA 503 PDF

## Applied Genetics and Epigenetics - GNSA 503 ### Course Information - Lebanese University-R. Hariri University Campus - Sciences Faculty/EDST-Hadat - Biology/Biochemistry Department - 2024-2025 - Office: 2-45 - Master 2R: GNSA ## Genome Stability - Diagram of cell cycle and mitosis showing:...

## Applied Genetics and Epigenetics - GNSA 503 ### Course Information - Lebanese University-R. Hariri University Campus - Sciences Faculty/EDST-Hadat - Biology/Biochemistry Department - 2024-2025 - Office: 2-45 - Master 2R: GNSA ## Genome Stability - Diagram of cell cycle and mitosis showing: - Chromosomes condensing - Sister chromatids - Centromere - Mitotic spindle - Sister chromatids separating - Daughter cells forming - G1, S, G2, M phases of the cell cycle - DNA damage checkpoints - DNA replication - Cytokinesis - Describes the process of genome stability being maintained through the cycle. ## Genome Instability Levels - Genomic instability describes a state in which there is an increased tendency to acquire hereditable genetic alterations that may influence phenotype. - Depiction of a circle divided into: - **Genome Instability** - **Microsatellite Instability** - Microsatellite expansion/deletion - **Chromosomal instability (CIN)** - Structural CIN - Duplication - Inversion - Translocations - Deletion - Numerical CIN - Aneuploidy - **Nucleotide Instability** ## Genome Instability Levels - Explained in Detail - **Nucleotide Instability** - Shows original DNA sequence and changes that cause instability: - Substitution - Insertion - Deletion - **Microsatellite Instability** - Shows a "CACACACACACACACA" 8 repeat sequence - Shows different conditions of the sequence: - Normal MMR - Aberrant MMR - Repaired - Irreparable - **Chromosomal Instability** - **Numerical Chromosomal Instability** - Small-scale gains - Small-scale losses - Monosomy - Large-scale gains - Extra set (polyploidy) - **Structural Chromosomal Instability** - Deletions - Amplifications - Inversions - Translocations ## Factors Causing Genome Instability - **Genomic Instability** - **External Factors** - **Genotoxic Agents** - Depiction of DNA and genotoxic agents. - **Exogenous Agents** - **Ultraviolet (UV) radiation** - Diagram shows UV radiation interacting with DNA. - Depiction of Thymine Dimer - **Alkylating Agents** - Depiction of of the structural change that occurs with alkylating agents - **Ionizing Radiation (IR)** - diagram showing ionizing radiation interacting with DNA and causing direct and indirect damage. - **Toxins** - Depiction of AFB1, 8, 9-exo-epoxide and DNA interaction and the formation of AFB1-N7-Gua - **Internal Factors** - **Endogenous chemicals** - Depiction of DNA with ROS. - **DNA repair defects** - Depiction of DNA with repair defects. - **Mitotic defects** - Depiction of abnormal chromosome segregation - **Replication defects** - Depiction of DNA replicating. - **Cell cycle defects** - Depiction of cell cycle. - **Epigenetic alterations** - Depiction of DNA with altered epigenetic information ## Factors Causing Genome Instability - Explained in Detail - **Endogenous Genotoxic Agents** - Depiction of DNA and a description of mismatch bases. - **Base & Sugar Damage** - Description of the processes: - Base Depurination - Depiction of the hydrolysis process - Base Oxidation - Base Deamination - Depiction of Thymine, Thymine Glycol, Cytosine, Uracil, Guanine and O-methylguanine. - Base Methylation - Intrastrand crosslink - Interstrand crosslink - DNA-Protein crosslink - **Exogenous Genotoxic Agents** ## External Factors Causing Genome Instability - **Exogenous Agents** - **Ultraviolet (UV) radiation** - **Alkylating agents** - **Ionizing Radiation (IR)** - **Toxins** ## Table 1. Factors Causing DNA damage - Table showing the estimated frequencies of DNA lesions caused by endogenous and common environmental sources of DNA damage. ## The ATM/ATR Signaling Network - Diagram showing how ATM/ATR signaling network functions. - **DNA damage** and its detection - **Recognition** - **Signal transduction** - **Signal amplification** - **Activation of Effector molecules** - **Cellular Decisions** - Explains how DNA damage is recognized, processed and leads to DNA repair or cell death. ## DNA Damage Response / DNA Repair Pathways - Diagram detailing the DNA damage response and repair pathways. - **Sensor** - Describes the sensor machinery that identifies DNA damage - **Transducer** - Describes how the signal is transduced - **Effector** - Describes how the signal leads to the appropriate cellular response - Describes how DNA damage is repaired through different pathways: - **Nucleotide excision repair (NER)** - **Mismatch repair** - **Homologous recombination repair (HDR)** - **Nonhomologous end joining (NHEJ)** - **Base excision repair (BER)** ## Factors Causing Genome Instability - 2 - DNA Repair Defects - **DNA damage & cancer evolution** - Diagram depicting how damage, mutation or chromosome aberrations lead to cancer. - **ATM alterations in cancer** - Diagram showing the different outcomes of ATM alterations in cancer: - Ataxia-telangiectasia - Breast cancer predisposition - No specific phenotype - Graph depicting the prevalence of the **ATM** gene alterations in the general population, in breast cancer and in Ataxia-telangiectasia. ## Internal Factors Causing Genome Instability - 3 - Replication Dysfunction - **Replication dysfunction** - Diagram of the replication fork formation with the involved proteins: - CDK - DDK - CDT1 - CDC6 - ORC1-6 - MCM2-7 - CDC45 - GINS - Description of the replication process: - initiation - licensing - activation. - **Low replication initiation density** - Diagram showing a replicated strand with: - MCM2-7 - DNA with TOP1, TOP2, MCMlow, Cln20/e, Sic1-, TER - **Untimely initiation causing Re-replication** - Diagram depicting untimed initiation leading to replication fork collisions. ## Internal Factors Causing Genome Instability - 3 - Replication Dysfunction - Explained in Detail - **Fork reversal** - Diagram depicting fork reversal. - **Untimely initiation causing Re- Replication** - Diagram depicting re-replication. - **Transcription-Replication Collision** - Diagram showing collision of transcription and replication. - **Unusual DNA structures** - Depiction of trinucleotide repeats - G-quadruplexes - R loops. ## Internal Factors Causing Genome Instability - 4 - Mitotic Defects - **Mitotic defects** - Diagram depicting prometaphase, metaphase and anaphase of the cell cycle. - Describes the mitotic checkpoint: - **Prometaphase** - **Metaphase** - **Anaphase** - Explains how the mitotic checkpoint ensures proper cell cycle progression and genome stability. ## Internal Factors Causing Genome Instability - 5 - Epigenetic Regulation - Diagram depicts: - A mitotic chromosome - Nucleosome - Histone modification - DNA methylation - Nucleosome remodeling - Noncoding RNA regulations - Explanation of the various epigenetic mechanisms that regulate genome stability. ## Internal Factors Causing Genome Instability - 5 - Epigenetic Disregulation - Diagram depicting the link between epigenetics and genomic instability through: - Histone modifications - DNA modifications - DNA repair - TE regulation - Noncoding RNA - Explains how disruptions in these epigenetic mechanisms can lead to genomic instability. ## DNA Methylation Alterations Drives Genomic Instability - **DNA hypomethylation/hypermethylation** - Diagram showing the following: - **Normal state** - Depiction of the properly methylated state - **Hypomethylated state** - Depiction of the hypomethylated state - Depiction of TE repeats - Insertional mutagenesis - Aberrant gains in CTCF binding - Multiradial chromosomal configurations - **Hypermethylated state** - Depiction of the hypermethylated state - Increased deamination - Loss of proper CTCF/cohesin binding - Telomere shortening - Altered sister chromatid cohesion - Explains how alterations in DNA methylation can contribute to genomic instability. ## Nucleosome Remodeling - Explains the process of nucleosome remodeling: - **Nucleosome assembly** - Free DNA - Prenucleosome - Mature nucleosome - **Chromatin access** - **Nucleosome editing** ## Histone Modifications - Diagram depicting the nucleosome and histone modifications. - Depiction of closed chromatin, HATS, relaxation, HOACS, open chromatin. - Explains the various histone modifications and their impact on chromatin structure and gene expression. ## Epigenetic Modification in DNA Repair Pathway - Diagram showing the impact of epigenetic modifications on the different DNA repair pathways: - **Normal state** - Mobilty - Chromatin Dynamics - Transcription - Structure - DDR processes - **Damaged state** - Efficient DNA repair (HR/NHEJ) - Explains the role of epigenetic mechanisms in DNA repair pathway choice and efficiency. ## Epigenetic Modification in DNA Repair Pathway - Explained In Detail - **Histone Phosphorylation: y-H2AX** - Diagram showing y-H2AX phosphorylation. - **Histone methylation: H3K36me2** - Diagram showing H3K36me2 methylation. - Explains the role of histone phosphorylation and methylation in directing DNA repair pathways. ## Histone PTM-Mediated 53BP1 and BRCA1 DSB Repair Pathway Choice Regulation - Diagram showing how 53BP1 and BRCA1 are regulated through histone modification. - Explains how histone PTMs, such as methylation and acetylation, influence the choice between NHEJ and HR repair pathways. ## Epigenetic Modification in DNA Repair Pathway - **SWI/SNF complex and DNA repair** - Diagram showing how the SWI/SNF complex functions. - Explains the role of the SWI/SNF complex in regulating DNA repair pathways. ## Epigenetic Modifications in DNA Replication - Diagram explaining histone modifications at stalled replication forks. - **Replisome obstacle** - Tight protein-DNA complex(es) - DNA damage - Torsional stress - Chemical DNA lesions - Secondary DNA structures - Explains the role of chromatin remodelers in responding to stalled replication forks and the potential consequences of faulty replication. ## Epigenetic Control of Centromeres/Genomic Instabilities - Depiction of the chromosome structure: - Sister Chromatids - Kinetochore - Centromere. - Diagram depicting the centromere region. - Diagram showing the processes related to centromere function: - Prometaphase - Metaphase - Anaphase - Diagram depicting how misregulation of the centromere leads to genomic instability and human diseases. ## Epigenetic Control of Centromeres/Genomic Instabilities - Explained in Detail - **Histones post-translational modifications at centromeres** - Diagram depicting how histone modifications occur in the centromere region. - Diagram depicting CENP-A localization. - **Centromeric Non-coding RNAs** - Diagram depicting the role of centromeric non-coding RNAs. ## Epigenetic Control of Telomeres/Genomics Instabilities - Diagram depicting: - Telomere - T-loop - D-loop - Diagram showing a model for how telomere-tethered HP1a impacts telomere maintenance. - Diagram depicting how telomeres are shortened in dividing cells and the role of telomerase in maintaining telomere length. ## Epigenetic Control of Telomeres? Genomic Instabilities - Explained in Detail - Depiction of how telomeres are regulated at the molecular level. - Diagram showing how telomerase functions in maintaining telomere length. - Diagram depicting subtelomeres and telomeres and their role in TPE-OLD. ## Epigenetic Control of Transposable Elements/Genomic Instabilities - Diagram depicting: - Abundance of Transposable elements in humans (H. sapiens) - Active elements - LINE - SINE - Retrotransposon (class 1) - Transcription - RNA intermediate - Reverse Transcription - DNA intermediate - Integration - DNA Transposon (class 2) - Excision - DNA intermediate - Integration - Explains the different classes of transposable elements and their role in genome evolution and instability. ## Epigenetic Control of Transposable Elements/Genomic Instabilities - Explained in Detail - **Histone modifications and TE** - Diagram showing H3K9me2/3 - coupled DNA methylation - Diagram depicting how histone modifications and DNA methylation regulate TE activity. - **DNA methylation and TE** - Diagram depicting how DNA methylation regulates TE activity and how TE insertion can impact gene expression. - Explains how epigenetic mechanisms, namely histone modifications and DNA methylation, contribute to the regulation of transposable element activity.