Epigenetics Flashcards
Epigenetics
Heritable changes in gene function that occur without a change in the DNA sequence
Can be inherited but not DNA changes; can change with different environment
3 modifications of the genome
1) DNA methylation
2) histones modification
3) non-coding RNA
DNA methylation: lack of methylation means….
Transcription is active
DNA methylation: if methylated….
Transcription OFF
Reader recognizes methyl group, enhance blocking of the gene
CpG islands thought out genome, most are methylated
Epigenetics phenomena are characterized by chemical modifications to __ or ___
DNA or histones
DNA methylation typically occurs at ____
Cytosine bases of DNA, within CpG dinucleotides
CpG islands are associated with
5’ regulatory regions of almost al housekeeping genes and 1/2 of almost all housekeeping genes
What happens when promoter CpG islands are methylated
Associated genes tend to be transcriptionally inactive
_____ process for maternal demethylation
______ for paternal demethylation
Passive for maternal
Active for paternal
As form zygote, everything will be demethylated
Father is actively demethylated in 1-2 division cycles; mother is passively demeythylated until blastocyst (dilution)
*blastocyst –> embryo, maintaining CpG methylation
DNA methylation during mammalian development
Wave of demethylation during cleavage, genome-wide methylation after implantation
Extent of methylation in genome of gastrulating embryo is high owing to _____
De novo methylation
*tends to decrease in specific tissues during differentiation
*de novo methylation rarely occurs after gastrulation; seen frequently in cancer though
What does dMTase activity do?
Demethylase
What does DNA methyl transferase do?
De novo methylation
- need to maintain methylation pattern of cells
- as replication proceeds, DNAP does not add methyl group on daughter strand; gotta do DNMT maintenance
Transcription factor binding to methylated DNA sequences ____regulates transcriptional output
Negatively
TF binds to methylated –> no transcription
DNA sequence regulates TF binding (genetic and fixed)
DNA methylation regulates TF binding (Epigenetic and dynamic)
2 roles of DNA methylation in mammals
1) regulation of gene expression
- tissue specific transcription, twin studies, MeCP2: Rett Syndrome
2) Genomic Imprinting
DNA methylation and gene expression twin studies
Twins can have Epigenetic tags in different places as they age;
Ex: 50 yr olds have more different Epigenetic tags; rheumatoid arthritis and breast cancer more affected by Epigenetic changes (due to environmental influence) more so than other stuff
Rett Syndrome
Autism spectrum disorder with mono genie origin
-progressive neurological developmental disorder
-one of the most common causes of mental retardation in females (1 in 15k females)
-X linked dominant
-period of apparent normalcy: 6-18mos
Life expectancy= 40 years
Mutation in Rett Syndrome
MECP2 (CpG binding protein)
MECP2 binds to….
Methylated DNA & represses transcription from methylated gene promoters
MECP2 is most abundantly expressed in the
Brain
Loss of function of MECP2 in differentiated post-mitotic neurons results in innapropriate_____
Over expression of genes with potentially damaging effects during central nervous system maturation
Imprinted genes are expressed how?
Preferentially or completely from only one allele (paternal or maternal) depending on the specific imprinted gene under consideration
Genomic imprinting is the
Unequal expression of the maternal and paternal alleles of a gene
Do Epigenetic tags on imprinted genes stay put for life of organism? Exception?
YES; but they are reset during egg and sperm formation
If came from mother, will remain maternal; same with dad
What happens to imprints in sperm?
Erased and rewritten with the paternal pattern, even with the genes that came from mom
What happens to imprints in eggs?
Erased and rewritten with the maternal imprint, even the genes that came from dad
If the allele inherited from the father is imprinted it is thereby ___ and only the allele from the ____ is expressed
If the allele inherited from the father is imprinted is is thereby silenced and only the allele from the mother is expressed
Which 3 vital roles to imprinted genes play?
1) embryonic growth
2) neonatal behavior
3) tissue or developmental stage specific monoallelic expression patterns
Prader-Willi Syndrome
- disorder of genomic imprinting
- mental retardation
- hyperplasia
- paternal deletion of SNRPN; maternal allele of SNRPN is imprinted by methylation (inactivated)
- no SNRPN protein at all
Angelman Syndrome
- disorder of genomic imprinting
- excessive laughter
- seizures
- mental retardation
- maternal deletion (angelman, mothers are angels) (SNRPN, UBE3A)
- -
Histones can be ___modified in their ____ which protrude from nucleosomes core particle
Histones can be REVERSIBLY modified in their amino terminal tails
How can histones be REVERSIBLY modifieD?
Acetylation of lysine; opens zipper, allows for transcription
Phosphorylation of serine
Methylation of lysine and arginine residues (prevents transcription)
Sumoylation
What happens when histones methylated and who does this?
Closed chromatin Heterochromatin Inactive transcription Writers: methyltransferases Erasers: Histones deacetylases (HDACs)
What happens when Histones acetylated? Who does this?
Compact chromatin
Euchromatin
Active transcription
Writers: Histones acetyltransferases (HATs)
Erases: Demethylase
*acetylation increase transcription form (euchromatin) and inactivate transcription thru methylation
N termini of core Histones proteins have many lysine residue that have a very ____ charge; these bind tight with negative DNA
Tight binding with DNA and Histones associated with
Gene inactivity
Positive lysine charge is neutralized by _____ and interaction with DNA is weakened –> transcription can occur
Acetylation
Non-COding RNA
NcRNA is a functional RNA molecule that is transcribed from DNA but not translated into proteins
MiRNA, siRNA, piRNa, IncRNA
Long ncRNAs function in
Chromatin remodeling
Transcriptional regulation
Post-transcriptional regulation
Precursors for siRNAs
Ex: X chromosome inactivation (XCI)
-2 lncRNAs (Xist and antisense Tsix, negative regulator of Xist)
Xist is a ____ transcribed from Xic of inactive C chromosome
LncRNA
Xist RNA does what
Covers the entire chromosome and. Silences gene expression through Epigenetic modification of Histones and DNA
Xic of inactive X transcribes lncRNA XIst–>covers the entire chromosome and silences gene expression via Epigenetic modification of Histones and DNA
What represses Xist and how?
Tsix
Both Xist and Tsix produce ncRNA transcripts; Tsix RNA transcript is antisense to Xist
Tsix can bind to the Xist sequence and inhibit its action, preventing X-inactivation
Depends on who produces what? When 2 X”s coming together, exchanging factors which determines who’s making more of what ( hypothesis)
How is XIC (X-inactivation center) established?
Pre-XIC: both chromosomes have low conc of Xist
Establishment of XIC: one X will make a lot of Tsix —> there will be reduction of Xist in the area around this X chromosome
Therefore, X inactivation is inhibited, and this chromosome will be the active X chromosome
Phenotypic plasticity
Ability of one genotype to produce more than one phenotype when exposed to different environments
(As the modification of developmental events by environment, or as the ability of an individual organism to alter its phenotype in response to change in environmental conditions
What can cause phenotypic plasticity
Environmental effects (ex: hunger winter) may involve Epigenetic changes in gene function that get passed down
Adult neuronal plasticity and neurogenic is; changes in chromatin marks & transcriptional networks associated with sustained neuronal activity, mood disorders, addiction
Not methylated agouti gene
Continuously active, producing mRNA across lifespan
Mouse with yellow fur
Develops obesity and diabetes during adulthood
Methylated agouti gene
Agouti mRNA made briefly during development
Agouti gene silenced remainder of mouse life
Healthy mouse, brown fur
Are fat yellow mice and skinny brown mice genetically identical
Yes
Methylation or lack of determines weight and whether prone to disease or not
What happened when fat yellow mouse (agouti gene unmethylated and active) had diet supplement during pregnancy and nursing with additional methyl groups?
Offspring mostly brown and healthy; agouti gene methylated and silenced
No dietary supplementation? Offspring yellow and unhealthy
Bisulfide conversion of DNA
- method to study changes in epigenome
- bisulfide converts C to U if C is NOT METHYLATED
- use reverse transcriptase, PCR, DNA sequencing, or methylation specific restriction enzyme digestion to determine methylation status of specific strand
Methylated cytokines don’t react with bisulfide; allows us to determine methylation status of different genes
How to detect DNA methylation with methylation sensitive restriction enzymes?
Methylation insensitive (MspI) cuts enzyme; methylation sensitive (HpaIIdoes NOT cut DNA where it is methylated !!!
(Both restriction enzymes cut same sequence aka isoschizomer)
Methylation insensitive is insensitive and CUTS
