DOSTIE - LECTURE 2 Flashcards
DNA methylation and gene regulation
what do PCR1 and PCR2 do
synergise to repress many genes by adding H3K27me3 and H2AK119ub
what do polycomb group proteins (PcGs) do
facultative heterochromatin is usually located within euchromatin (gene rich regions that are either transcriptionally active or not actively repressed and which are not compacted)
what is the marker for obligatory heterochromatin
marked by H3K9me3
usually encodes repetitive DNA sequences
what do trithorax and polycomb do
regulation of HOX genes by Trx and PcG
conserved through evolution
really important
what does the Antp gene do and what happens when it is mutated
homeotic transformation
in which organisms does DNA methylation happen
happens in both prokaryotes and eukaryotes
occurs after bases are incorporated into the DNA
which bases are methylated in prokaryotes
A and C can be methylated
A is more important
what is the hsd system of prokaryotes and how is DNA methylation involved
how is DNA methylation in prokaryotes used in DNA replication and mismatch repair
how does mismatch repair work
how does methylation affect mutation rates in bacteria
how does DNA methylation regulate the segregation of daughter chromosomes
what does SeqA do
activation of the pap operon by DNA methylation
what turns the papBA gene on vs off
how does the Dcm system work
methylation is not essential
deletion of either or both methylase systems are still viable
methylation in eukaryotes
unlike prokaryotes methylation in eukaryotes is essential
5-methylcytosine is very abundant
what are the functions of DNA methylation in mammals
which enzymes mediate cytosine methylation
in which context of the genome does cytosine methylation happen
which DNMTs are encoded by mammals
DNMT1, DNMT3a and DNMT3b are essential for viability
what does NMT1 do
involved in the maintenance of DNA methylation
recruited at replication forks during S phase by UHRF1
UHRF1 specifically binds to hemimethylated and DNMT1 only methylates hemimethylated DNA
mice deficient in Dnmt1 lose 90% of their 5-methylcytosine and die early in embryogenesis
what do DNMT3a and DNMT3b do
involved in de novo DNA methylation
each essential for proper development, but also have non overlapping functions
what are the two types of demethylations
passive or active
what is passive DNA demethylation
5-aza as a treatment for cancer
what is active DNA methylation
occurs independently from DNA replication via direct removal of the methyl group by TET enzymes
how is DNA demethylated by Tet enzymes
what is an example of when natural DNA demethylation occurs
how are CpG distributed in euchromatin
what are unmethylated CGIs recognised by
how are unmethylated CGIs recognised at active promoters
how can long term gene silencing be achieved
can be achieved by CGI methylation
methylation of CpG always leads to transcriptional repression
what are the proteins that bind methyl-CpG
what are the three ways in which DNA methylation can cause transcriptional repression
- direct interference with transcription activator factor binding
- specific transcriptional repressors
- inactive chromatin structure formaiton
how does direct interference with transcription activator factor binding work
how does DNA methylation repress transcription by specific transcriptional repressors
how does DNA methylation repress transcription by inactive chromatin structure formation
