Lecture 5 Flashcards
What does molecular psychiatry include?
looking at changes in specific cell types, proteins, genetics, or gene expression.
what are the 4 original tenets of molecular psychiatry?
- There is pathology in cellular function which account for pathological behaviors.
- We must understand the molecular and cellular response; i.e. how psychotropic drug act and reverse pathological behaviors.
- The vulnerability to pathology results from the combination of individual genetics with a host of environmental factors.
- This information must be translated to a clinical population.
what are genetics?
The study of genes and heredity.
what is heredity?
passing of genetic information and traits (eye colour) from parent to offspring.
what is DNA?
Carries genetic information encoded by DNA bases
what are the 4 DNA bases?
Adenosine, cytosine, guanine, thymine
what is chromatin?
DNA wrapped around proteins (histones)
what are the two states of chromatin?
- Euchromatin (Open state)
- Heterochromatin (Closed state)
what are chromosomes? (4)
composed of compacted dna
Receive one from each parent
22 identical pairs
1 pair of sex chromosomes (X, Y)
what two stages are necessary for gene expression?
transcription and translation
what is the genetic architecture of complex disorders? (2)
Large number of small-effect variants primarily located in non-coding regions.
It is likely that the disease risk stems from altered gene expression.
where are the majority of genetic variants ?
fall into regions of the genome that do not code for a gene but influence how a gene is expressed (intergenic).
This is part of the functional genome.
what is the definition of epigenetics?
Processes that alter gene expression without altering the underlying DNA sequence.
“The study of molecules and mechanisms that can
perpetuate alternative gene activity states in the
context of the same DNA sequence.”
why can we say that DNA methylation determines cell fate?
Every cell in your body has the same DNA, therefore something is required to direct the DNA into unique expression patterns, resulting into different transcriptomes.
what is the role of dna methylation in cell fate?
at the early phase, many genes are accessible (not methylated) and as cells differentiate into specific cell types (methylation patterns become really well defined)
give 3 examples of epigenetic processes
- dna methylation
- post-translational histone modifications
- micro RNA
what is the link btw dna methylation and dna structure?
various signaling on chromatin recruites methylation or vice versa so you get a change in the conformation of the chromatin
what protein interaction can dna cytosine methylation affect?
histones, transcription factors, enhancers, repressors,…
what does dna cytosine methylation result in?
changes to levels of gene transcription
whats the difference btw dna cytosine methylation and gene body methylation?
Repressive in the gene promoter, whereas gene body methylation positively associate with gene
expression
is dna methylation a stable modification?
yes
what process does the following refer to:
A stable chemical modification influences the way DNA will be expressed without altering the underlying genomic
sequence
dna cytosine methylation
what role does dna methylation have in early development?
X-chromosome inactivation
Genomic imprinting
Differentiation and development of tissues
what role does dna methylation have in childhood +?
Mediates the relationship between the environment and gene expression
Susceptibility/resilience to complex diseases
Relevant to diseases and illnesses as a therapeutic agent or biomarker
(T/F): methylation states cannot be altered or reversed
false
how does nutrition and methylation relate in rats? explain the study
coat-colour of the Agouti
mouse can be influenced by
methyl-group supplementation of the
maternal diet (makes agouti rats yellow)
Associated with increased
methylation of the IAP
retrotransposon
how does nutrition and methylation relate in humans?
- Effects of maternal undernutrition on DNA methylation also observed in humans
- Children conceived during the Dutch famine display numerous metabolic differences compared to their same-sex siblings
- Elevated BMI and serum cholesterol, impaired glucose tolerance
- Several genes show persistent differences in methylation
regulation of hippocampal ___ expression by _____ care affects behavioural phenotypes in adult rats
glucocorticoid receptor; maternal
- high LG pup and put it with low LG mom -> increase in methylation
- high LG pup with other LG mom -> stays same
- low LG pup with other low LG mom -> still high
- low LG pup with high mom -> low methylation
GR expression is ____ in the hippocampus of abused suicide completers
decreased
site-specific ____ in hGR1F promoter in abused suicide completers
hypermethylation; methylation was really increase but only in the people with ELA
what s intergenerational ?
occurs when an organism in which a change is triggered, passes this change to its immediate offspring.
what is transgenerational?
an epigenetic signal that is being maintained in the absence of the original
stimulus.
what type of methylation inheritance in mammals do we have confirmed examples of?
CpG
what are nucleosomes?
dna wrapped around histones
what two post-translational modifications do histones go through?
- methylation
- acetylation
histones have long ____ rich tails
lysine
what are H3K9me domains?
often termed as
constitutive heterochromatin and is strongly associated with DNAme.
what is H3K24me?
widespread repressive mark – silencing genes during development, acting in
opposition to H3K4me3.
what do chromatin states in mental illness suggest?
that diff genes get regulated differently in diff contexts and characterizes where you see this modifications
what region of chromatin are we interested in?
open region of chromatin as these are considered ACCESSIBLE
what type of info is available from accessible regions of treated dna?
TF footprinting
Histone code
Open chromatin.
what have we found when studying chromatin in mental disorders? (3)
Most variants identified through genome-wide association studies related to neurological and psychiatric disease have been found in non-coding regions.
Difficult to assess function.
Examining a SNPs within the landscape of open chromatin and distally related chromatin regions can provide insight into the functional impact of the
variant.
how is chromatin related to MDD?
DARs in Excitatory neurons tended to be distal to any
TSS (77%), while DARs in microglia tended to be
proximal to a TSS (73%).
The closed regions overlapped more with marks of promoter accessibility, while the open regions, with enhancer marks
what can we do with cell specific GWAS enrichment?
have all these diff cell types based on whats open and closed
can define these diff cell types based on chunks of dna that we can map back to genome
means we can identify where the genetic heritibility is
what is microRNA?
Short (17-22 nt) RNA
Influence gene expression through interactions with target RNA molecules
Require high complementarity between “seed region” (2-7nt) and target RNA
Target regions of a gene are generally within the 3’UTR
what is miRNA Biogenesis?
Transcribed by RNA Pol II (primiRNA)
Cleaved by Drosha (pre-miRNA)
Pre-miRNAs transported to cytoplasm and are processed by Dicer (mature miRNA)
what is miRNA nomenclature?
alleles all express same mature microRNA
how do you measure miRNA on a large scale?
Small RNA-sequencing
- 3’ adapter targets microRNAs and other small RNAs that have a 3’ hydroxyl
group resulting from enzymatic cleavage by Dicer or other RNA processing enzymes
Microarrays
- Small RNAs are isolated and labeled prior to hybridization to chip
how do you measure miRNA on a medium scale?
Firefly
- Particles contain a region complementary to miRNA of interest, as well as a barcode and fluorescent signal that is quantified using flow cytometry
how do you measure miRNA on a small scale?
RT-PCR
- Primer-specific cDNA synthesis (one miRNA, or random priming)
- Typically use RNU6B (snRNA) as endogenous control
(T/F): miRNA is specific to tissues
true
what is the relation btw miRNAs in psychiatry?
Display differential expression in psychiatric disorders; schizophrenia, bipolar disorder, major depressive disorder
Altered expression in the brain; majority of studies have investigated the frontal cortex
Altered expression in the blood
Influenced by treatment; may mediate treatment response
what miRNA is related to MDD? explain
miRNA 1202; less in mdd
