Exam 2 Flashcards
Mechanisms of epigenetics
DNA methylation - transcriptional Histone modification - transcriptional miRNA - post-transcriptional siRNA - post transcriptional Prions
Heritability
Epigenetic changes ARE heritable
- non-mutational changes that are transmitted from one cell to its daughter cell
- transmitted between generations
Epigenetics defintion
structural adaptation of chromosomes so as to register, signal, or perpetuate altered activity states
Factors that affect the epigenome
Diet (higher effect in utero, eg. methyl deficiency prevents necessary methylation marks from occurring)
Toxins/chemicals (bisphenol A - aberrant imprinting)
Environment (maternal behavior)
Aging (histone acetylation and deacetylation)
Drugs/pharmaceuticals
Epigenetic defects
Imprinting disorders (Angelman, Prader-Willi, Beckwith-Wiedemann) Cancer Multifactorial disorders (autism, bipolar disorder)
DNA methylation and histone modification
Control availability of chromatin to transcriptional machinery
Types of chromatin
Euchromatin - decondensed, may be silent or active
Heterochromatin - highly compacted and silenced
Constitutive heterochromatin - Always silenced (centromeres and telomeres)
Facultative heterochromatin - repressed but may be active for specific parts of the cell cycle or development
Chromatin organization
- Nature of DNA sequence is important
- Quality of RNA produced determines whether it is a fully functional mRNA or if it will be earmarked for use in RNA interference to target heterchromatin
Histones
- Very small, highly basic, make up the nucleosome
- Highly conserved - serve critical functions
- Histone tails are subject to post-translational modification
- Majority of modifications occur at N-terminal tail of histones (many lysines and arginines here) - typically methylation but can also see acetylation, phosphorylation, and ubiquitination
- H1 histone is the “bar” that holds the nucleosome together
Histone modifications
- Cis effects - Changes in physical properties of modified tails (acetylation and phosphorylation)
- Trans effects - Recruitment of modification-binding partners to chromatin (bromo and chromo domains)
- Modifications can be activating or repressive
- May lead to decrease or increase in contacts between nucleosome leading to increased of decreased access to chromatin respectively
DNA Methylation
- Typically occurs in CpG islands
- Catalyzed by methyltransferases (DNMT1, DNMT3a, DNMT3b)
- Inverse relationship between CpG methylation and transcriptional activity
- Serves mainly as a host defense mechanism to silence much of the genome of foreign origin
- Silencing
- Some can be reversed
- Hypermethylation can lead to changes in structure and silencing of tumor supressor genes
- Important in X inactivation
- Bivalent domains mark CpG-rich promoters of developmental genes in embryonic stem cells
- Trithorax group methylates histone H3K4
- Polycomb complexes methylate histone H3K27
RNA interference
A conserved silencing mechanism whereby dsRNA induces specific down-regulation/silencing of homologous sequences
RNAi mechanisms
miRNA or siRNA (in lower organisms)
- dsRNA cleaved into siRNA by DICER
- bind RNA-induced silencing complex (RISC)
- RISC-RNA complex binds mRNA of interest and argonaute protein cleaves the mRNA leading to degradation
miRNA vs siRNA
siRNA - usually exogenous, come from viruses
miRNA - genomically encoded to help regulate gene expression, particularly during development
Purpose of RNAi
-plays a role in immunity in lower organisms/plants
-maintenance of undifferentiated or incompletely differentiated types
-imprinting
-cell cycle
can be applied to medicine and biotechnology
Enhancer
-set of short sequence elements which stimulate transcription and whose function is not critically dependent on their location
Promoter
Combination of short sequence elements typically just upstream of a gene to which RNA polymerase binds to initiate transcription
Locus control region
stretch of DNA containing regulatory elements which control the expression of genes in a cluster that may be far away
Insulator/boundary element
DNA elements that act as barriers to the spread of chromatin changes or the influence of cis-acting effects
Transcription factor
Upregulates or downregulates transcription
ChIP
chromatin immuno-precipitation sequencing
-examines histone modifications and protein binding
DNA footprinting
Use an enzyme with random cleavage activity to determine binding sites for specific proteins
-if protein binds, it produces a “footprint” on gel where protein protected sequence from cleavage
Databases
ENCODE
ORegAnno - Open regulatory annotation
TRED - Transcriptional Regulatory Element Database
ReulomeDB
What are the goals of identifying genetic risk factors for eye diseases?
Developing clinically useful gene-based screening tests and new therapeutic strategies with the final goal of reducing the global burden of visual impairment from these conditions.
What are two loci with substantial effect on AMD risk?
- 1q32
- 10q26
What are the 5 pathways involved in AMD?
- inflammation, specifically the innate immune system disregulation & enhanced complement activation
- lipid transport
- ECM remodeling
- angiogenesis
- cell survival, including DNA repair, apoptosis, and stress response
Which immune system (innate or adaptive) is involved in SLE and AMD?
AMD - innate only!!!
SLE - both innate and immune
Which region is important for several diseases including AMD and SLE? (The most important genetic factors influencing susceptibility to autoimmune diseases are located at the)
MHC (major histocompatibility complex) - 6p21
Which member of the innate immune system involved in a number of pathways is involved in SLE and AMD?
Complement system/complement cascade
Describe the signature that plays a central role in the initiation and progression of SLE
Interferon-alpha (IFN-alpha) levels have been consistently shown to be elevated in sera from SLE patients and the type-I IFN system-regulated genes (inducible by IFN-alpha) have been found to be upregulated in their peripheral blood mononuclear cells (so called ‘interferon signature’)
