Epigenetics Flashcards
Implications of DNA Methylation and Where it Occurs
- inhibits transcription
- usually found around transcription start sites
- methylation occurs on CpG islands on cytosine
- CpG islands attract transcriptional repressors
- correct expression of tissue-specific gene and X activation relies on DNA methylation
Bisulfite-Mediated Conversion of DNA
- upon separation and treatment with bisulfite, umethylated Cs become Us
- can use PCR to amplify
- DNA pol turns U into T on OT strand, and complementary to that will be A
- All of the Ts that you will see will show that they are unmethylated Cs and all of the Cs that remain in the OT strand represent methylated Cs
- Can use this to map the methylation of the promoter
Isoschizomer
Restriction enzymes that recognize the same sequence
dMTase
Demethyltransferase
DNMT
Uses SAM to add methyl groups to DNA
DNA Methylation Patterns in Development
Paternal genes are actively demethylated immediately upon fertilization
Maternal methylation is passively diluted
This occurs to make cells totipotent during cleavage, so this differentiation is ‘written’ by CpG islands
Methylation occurs during implantation
Denovo methylation occurs rarely after gastrulation, but this phenomenon is seen frequently in cancer
Rett Syndrome
- progressive neurologic developmental disorder
- X-linked dominant
- period of apparently normal development 6-18 mo
- life expectancy ~40 yrs
- MECP2 gene mutations are the cause of most cases of Rett syndrome
MECP2
- capable of binding specifically to methylated DNA
- represses transcription from methylated promoters
- ubiquitously present, most expressed in brain
- loss of function in differentiated post-mitotic neurons likely results in inappropriate overexpression of gene with potentially damaging effects during CNS maturation
- MECP2 is like a nucleus for repression, it becomes a scaffold for other proteins to bind
Genomic Imprinting
While most autosomal genes are expressed roughly equally from the two parental alleles, imprinted genes are expressed preferentially or completely from only one allele (paternal or maternal) depending on the specific imprinted gene under consideration.
Imprinted genes play vital role in embryonic growth, neonatal behavior, tissue/developmental-stage specific monoallelic expression patterns
Methylated imprinted genes DO NOT become demethylated during methylation reprogramming in preimplantation
Prader-Willi and Angelman Syndromes***
IGF2
Growth promoting hormone during gestation
Exerts its effects by binding to IGF-1 receptor
IGF2 may also bind to IGF-2 receptor (maternal gene), which acts as signaling ANTAGONIST
-This gene was imprinted by paternal line
-can bind many receptors
- deleting mother’s IGF2 receptor gene results on large offspring
- deleting father’s IGF-2 ligand gene produces dwarf offspring
- deleting mother’s receptor gene and father’s ligand gene produces normally sized offspring
Beckwith-Wiedermann Syndrome
Activation of maternal IGF2 ligand gene causes larger offspring
What can be done to N-termini of histone tails?
Acetylation of K
Phosphorylation of ser
Methylation of K and R
Sumoylation
Long ncRNA
Function in
- chromatin remodeling
- transcriptional regulation
- post-transcriptional regulation
- precursors for siRNA
- X-inactivation
- Xist
- Tsix (negative regulator of Xist)
Xist
LncRNA that is transcribed fromm Xic on inactive chromosome (Xi)
-Xist RNA covers the entire chromosome and silences gene expression via epigenetic modification of histones and DNA
Establishment of XIC
- Pre-Xic
- both chromosomes will express Xist in low []s - Establishment of XIC
- one X chromosome will begin to express Tsix in high levels. This leads to huge reduction in Xist in this chromosome, making this the active X chromosome.
