Gene-L5-Genome III: chromosomes, telomeres and gene silencing

how is the human eukaryotic genome organised on chromosome level?

• 22 autosomes, 2 sex chromosomes

• p arm- short

• q arm- long

what happens to chromosomes during the cell cycle- interphase and M phase

interphase

• DNA is replicated and each chromosome is duplicated- has 2 copies of each homologous chromosome

M phase- mitosis

• chromosome condenses into visible chromosomes

• nuclear envelope breaks down

• chromosomes are captured by mitotic spindles and pulled apart to opposite poles

• nuclear envelope reforms

what are centromeres, what is their structure? how do they function during cell division?

• centromeres-DNA sequences

• function: directs movement of chromosomes into daughter cells during cell division

• this is where the mitotic spindle attaches

• kinetochore- acts as an anchor for spindle microtubules

what features of chromatin are found at the centromere? how do they affect gene activity?

• centromeric chromatin- heterochromatin

• has special H3 variant

• histone deacetylation

• histone methylation

• makes compact and stable chromatin structue

what are the origins of replication- how do they differ in prokaryotes and eukaryotes?

origin of replication: DNA sequence where replication begins

• prokaryotes: one single origin as they have less DNA to replicate

• humans: multiple origins per chromosome. at AT rich regions- easier to unwind due to 2 hydrogen bonds

what are telomeres? where are they located and what is their function?

• telomeres: end structures of eukaryotic chromosomes- not proteins, just DNA sequnces

• composed of repeated sequences

• G-rich sequences- makes a 3’ single stranded overhang of 15 nucleotides

• can be extended by telomerase enzyme

1. chromosome end stability: DNA folds back into itself to make a t loop. prevents the exposure of single stranded DNA and stops activation of DNA damage repair pathways

2. prevention of information loss during replication: compensates for loss of DNA due to primer removal on lagging strand

how does telomerase solve the end replication problem?

• telomerase binds to 3’ end and has an RNA template where it attaches an extra telomere

• now DNA polymerase has somewhere to bind and replicate the information that would have been lost

how does telomere shortening relate to ageing, disease and chromatin silencing?

• somatic cells have little to no telomerase activity and therefore shorten over time

• leads to cellular senescenc

• short telomeres- accelerate ageing dyndrome

• Down syndrome- accelerated telomere loss

how does telomere gene silencing occur in yeast? what do SIR proteins do? what does Rap1 do?

• SIR- silence information regulator

• yeast telomere-bound SIR protein complex recognises underacetlyated (H4) or methylated (H3) N-terminal
  tails of selected histones and keeps
  them deacetylated

• Rap1 recognises telomeric DNA that needs to be silenced and acts as a signal for SIR to be recruited

• SIr assembles and spreads along the chromosome from this site- modifies the N terminal this

how does methylation lead to gene silencing? how is it recognised by the immune system?

• DNA methylation is a gene silencing mechanism

• occurs at cysteine bases- forms 5-methylcytosine

• common at CpG C-G dinucleotides

• in humans: DNA is usually hypermethylated (silenced)

• in bacteria and viruses, DNA is undermethylated and immune system recognises this via TLR9 recognising undermethylated CpG DNA

how are DNA methylation patterns maintained after DNA replication?

• after replication: parental strand is methylated and the new strand is ynmethylated

• DNA is temporarily hemimethylated

• DNA methyltransferase enzymes helps methylate the full DNA by

1. recognition of methylated cytosine on parental strand

2. methylation of the corresponding cytosine on the new strand

characteristics features of eukaryotic genes?

1. promotor region: DNA sequence where RNA polymerase and TFs bind and defines the start of transcription

2. regulatory proteins: have DNA sequences recognised by regulatory proteins to control gene expression levels

3. Exons- coding sequences which are transcribed into RNA and translated into proteins

4. introns: non coding sequences and in between cons and removed by splicing