BMS 532 Principles and Processes of Epigenetics PDF

Principles and Processes of Epigenetics CHANGES IN GENE EXPRESSION WITHOUT CHANGING THE GENETIC CODE BMS 532 BLOCK 2 LECTURE 7  Objectives 1. Define the following terms: epigenetics, euchromatin, heterochromatin, imprinting, and X-inactivation/Lyonization 2. Compare and contras...

Principles and Processes of Epigenetics CHANGES IN GENE EXPRESSION WITHOUT CHANGING THE GENETIC CODE BMS 532 BLOCK 2 LECTURE 7  Objectives 1. Define the following terms: epigenetics, euchromatin, heterochromatin, imprinting, and X-inactivation/Lyonization 2. Compare and contrast euchromatin and heterochromatin and Compare and contrast constitutive and facultative heterochromatin 3. Summarize the process of Methylation and Chromatin remodeling and Compare and contrast DNA and histone methylation ◦ Identify the role of the following players: CRCs, Histone methyltransferases, DNA methyltransferases, and histone deacetylases 4. Outline the importance of heterochromatin to gene regulation and chromosome function and the role remodeling plays in development 5. Assess the consequences for gene regulation following or as induced by changes in chromatin structure 6. Evaluate imprinting and the role of imprinting in gene regulation and human health ◦ Define imprinting and differentially methylated regions ◦ Compare and contrast maternal and paternal imprinting ◦ Explain the process of imprinting in gametogenesis ◦ Summarize the role of demethylation and re-methylation in imprinting ◦ Compare and contrast Prader-Willi and Angelman Syndromes in terms of inactivation, loss of genetic information, and genes involved in the disorders (from the perspective of which are expressed and which are lost) 7. Evaluate lyonization/x-inactivation in terms of process and effects on gene expression ◦ Explain the process of lyonization/X-inactivation and its connection to inactive chromatin ◦ Compare and contrast imprinted lyonization from random lyonization ◦ Summarize the process of x-inactivation and explain the role of mRNA in the process ◦ List and explain the consequences/effects of X-inactivation (define dosage compensation and explain its role in proper cell function) 8. Define mosaicism and explain the role of x-inactivation in generating mosaic phenotypes LO1 Terminology Epigenetics ◦ The study of the manner in which expression of heritable genetic traits are modified by environmental influences or other mechanisms without a change in DNA sequence Euchromatin ◦ The state of chromatin in which it is partially or fully uncoiled and genetically active; light- staining Heterochromatin ◦ The state of chromatin in which it is tightly coiled and considered molecularly inactive; dark- staining ◦ Constitutive Chromatin ◦ Region of heterochromatin that is never transcribed ◦ Facultative Chromatin ◦ Region of heterochromatin that is silenced and can become active ◦ Regions that become heterochromatic in certain cells/tissues Lyonization/X-Inactivation ◦ Inactivation of genes on the X chromosome that exhibit dosage effects LO1, LO2 Euchromatin Loosely coiled during interphase ◦Beads-on-a-string conformation Condensed during mitosis Often undergoing active transcription G-banding: Light Bands LO1, LO2 Heterochromatin Late Replicating; highly inaccessible by the replication machinery Remains condensed from prophase through the mitotic cycle Can be constitutive or facultative NOT transcriptionally active G-banding: dark bands LO1, LO3, LO4, DNA Methylation LO5 Addition of methyl group to cytosine or adenine DNA bases Cytosine methylation is associated with heterochromatin formation and repression of gene expression Important process in epigenetics and in genetic disease LO3, Ability of a methylated DNA to influence an adjacent promoter is a function of the number of LO4, modified sites. LO5 7 Michela Curradi et al. Mol. Cell. Biol. 2002;22:3157-3173  Methylation Process LO3 8 LO3, LO4, LO5 HISTONE Methylation Histone Methyltransferases add methyl groups to specific histone residues ◦ This correlates with changes in heterochromatin and euchromatin as well CHROMATIN REMODELING The molecular mechanism of chromatin remodeling frequently involve repositioning, acetylation, methylation, and/or replacement of histone variants Several different multi-protein complexes, known as chromatin-remodeling complexes (CRCs), can restructure chromatin to increase or decrease transcription CRCs use energy derived from ATP to initiate changes CRCs can disrupt nucleosome structure without displacing them or reposition the nucleosomes making key DNA-binding sites accessible LO1, Heterochromatin vs LO2, LO3 Euchromatin LO1, LO2, LO3, Euchromatin vs Heterochromatin LO4, LO5 11 LO1, LO2, LO3 Facultative Heterochromatin SILENCED euchromatin Deactivated by multiple processes ◦Changes in Methylation ◦Hypoacetylation ◦Changes in the timing of DNA replication Mono and Dimethylated H3-Lys9 LO1, LO2, LO3 Constitutive Heterochromatin DNA which is theoretically never transcribed but plays critical structural roles Highly repetitive sequences Significant percentage of human genome (15-20%) Trimethylated H3-Lys9  Chromatin Remodeling LO1, LO3, Complex: LO5 Activity and Consequences Remodeling does not solely have to be about heterochromatin and euchromatin transitions Shifting the material associated with nucleosomes can also influence gene expression even when not tightly coiled Chromatin Remodeling Complex: Activity and Consequenc es LO1, LO5 Importance of Heterochromatin Originally thought to be a repository of “junk” DNA Findings now indicate that is has structural and functional importance ◦ Believed to confer strength and protection to centromeres ◦ May protect against change in sequence; can prevent crossing over ◦ May aid in alignment and separation of chromosomes during mitosis and meiosis ◦ Heterochromatic regions of Y-chromosome have been shown to contain fertility factors ◦ Heterochromatin also serves to more “permanently” turn off genes that were used in development and are no longer needed ◦ Role in cellular specialization and differentiation LO1, LO3, LO5 Model for the molecular mechanisms of gene silencing mediated by DNA methylation. 18 Michela Curradi et al. Mol. Cell. Biol. 2002;22:3157-3173 LO1, LO6 Epigenetics and Imprinting Core phenotypic changes due to changes in gene expression WITHOUT changes in the core DNA sequence Differentially methylated domains of imprinted genes contain CpG-rich, imperfect tandem repeats resulting in a RELATED DNA STRUCTURE implicated in imprinting ◦ Specifically, the establishment and maintenance of parent of origin-specific methylation patterns PATERNALLY imprinted ◦ Paternal gene is OFF ◦ Maternal gene is ON MATERNALLY imprinted ◦ Maternal gene is OFF ◦ Paternal gene is ON LO1, LO6 Imprinting in Gametogenesis Original imprinting in the gamete is erased prior to spermatogenesis and oogenesis Selective silencing Different genes are silenced during oogenesis than spermatogenesis leading to specific maternal vs paternal imprinting patterns De-methylation and Re-methylation cycles to add and erase imprinting LO1, LO6 Imprinting in Gametogenesis Erasure via DEMETHYLATION (active or passive) Multiple mechanisms including deamination followed by repair and exclusion or regulation of key maintenance molecules like LO1, Differentially Methylated LO6 Regions and Disorders (23 DMRs exist) White circle = maternal differentially methylated regions Black circle = paternal differentially methylated regions BWS = Beckwith-Wiedemann Syndrome AS= Angelman Syndrome PWS= Prader-Willi Syndrome SRS= Silver-Russell Syndrome TNDM transient neonatal diabetes mellitus RB Retinoblastoma Important considerations for imprinting UPD14 uniparental disomy 14 in the use of assisted reproductive PHP1b pseudohypoparathyroidism type technologies https://www.ncbi.nlm.nih.gov/pmc/article 1b s/PMC4182590/pdf/RMB2-13-193.pdf LO1, LO7 X-Inactivation Introduction First described by Geneticist Mary Lyon Lyonization = X chromosome inactivation Necessary for maintaining the balance of X-linked genes Happens early in development during embryogenesis X-inactivation in human tissues is either RANDOM or imprinted Some genes on the inactive X (Xi) are still transcribed LO1, LO7 Effects of X-Inactivation Dosage Compensation ◦Total amount of gene product between males and females is made essentially equal Mosaicism ◦Different cells within an individual can have different chromosomal make-up Variable Expression ◦Females heterozygotes for disease alleles can have different or varying manifestations LO1, LO7 Structure of Inactive X Chromosome X-chromosome inactivation is a form of epigenetics Facultative Heterochromatin Hypermethylated and hypoacetylated histones 85% silenced with genes escaping inactivation primarily located on the short (p) arm Inactivated X’s pick up stain more due Inactive X = Barr Body to increased presence of methyl groups  Process of LO1, LO7 X- Inactivation Determine Number of Xs Choose extra X to inactivate Initiate Inactivation Expand/Spread the Inactivation Signal along appropriate regions of chromosome Maintain the inactivation LO1, LO7  Mosaicism LO1, LO7, LO8 Anhidrotic Ectodermal Dysplasia ◦ Patches of skin without sweat glands ◦ It is similar to the mosaicism observed with calico cats Other diseases are also observed to be mosaic due to random X-inactivation LO5, Summarizing Methylation and LO6, LO7 X-inactivation LO5, LO6, Errors in Heterochromatin LO7 Formation and/or Epigenetics and Human Disease Facioscapulohumeral muscular dystrophy ◦ Characterized by weakness and atrophy of particular muscle groups (predominantly face, shoulders, and upper arms) Friedreich’s ataxia ◦ Characterized by impaired or uncoordinated muscle movement Fragile X syndrome ◦ Characterized by developmental delays and learning difficulties ◦ Expansion of CGG sequence repeats in FMR1 gene ◦ More CGG = More Methylation Potential Prader-Willi Syndrome and Angelman Syndrome LO5, LO6, LO7 Disease Examples NOTE: These are not necessarily diseases of imprinting but rather diseases that differentially manifest due to patterns of imprinting MATERNALLY IMPRINTED PATERNALLY IMPRINTED Prader-Willi Syndrome ANGELMEN SYNDROME Maternal copy is OFF; Paternal is Paternal Copy is OFF; Maternal is deleted or lost or inappropriate pattern deleted, or lost or inappropriate pattern placed placed Loss of 15q11-13 Loss of 15q11-13 Gene Expression Lost = SNRPN and Gene Expression Lost = UBE3A NDN Developmental and intellectual Hypotonia, obesity, hypogonadism deficiencies, epilepsy and tremors LO5, Prader-Willi vs. Angelman LO6, LO7 Questions What type of DNA would be expected near areas that structurally at the Chromosome level need to be protected from rearrangement and what chromatin is expected as a result? (previous lecture and LO2) A gene normally located in an area of euchromatin is identified to be repositioned to an area of heterochromatin. (LO1, LO2, LO3, LO5, LO6) ◦ What could account for this change/How could this change occur? ◦ What is the consequence for this change in terms of gene activity? ◦ If that change occurs in a differentially methylated region, what would that mean for the organism or cell?