I picked this assignment not because I think I got all the correct answers to the questions.
I think I was very overwhelmed by the paper and I read it 2 or 3 times but I was still confused.
However, I still attempted the questions. That is why I think I decided to put in the assignment. Persistence in reading paper is a great personal achievement
1. What can be said about the chromatin of and around the Xist locus in bimaternal, very early embryos that express Kdm4b and are treated with TSA? How do Kdm4b and TSA affect the levels of chromatin ‘relaxation’? How does this relate to Xist expression and XCI?
In the maternal X chromosome, histone marks are present. Kdm4b encodes for a histone demethylase specific to H3k9me3. TSA is a histone deacetylase inhibitor. When Kdm4b and TSA expression is induced via injection, the chromatin is relaxed and Xm-Xist transcripts can be made. Xist transcripts act in cis to inactivate maternal X chromosome when Xist is activated by RNF12.
2. How do you think Kdm4b and TSA can rescue the lethality of a missing paternal Xist in Xm Xp embryos?
Lethality from Xp-Xist absence is due to dosage imbalance of the X chromosome genes. Kdm4b and TSA can induce X inactivation of the maternal chromosome in all cells such that those embryos will have a balanced dosage of genes encoded on the X chromosome.
3. What can you directly conclude from Figure 5a?
The ratio of cells with Xist transcripts is increased in Kdm4b treated embryos when compared to the ratio of cells in Egfp treated embryos.
4. What are one or two things that are still unclear even after reading the paper a couple of times?
This whole paper is a little difficult for me because it there are so many different factors. I understand what they were did to come up with each conclusion but I am still trying to follow why they chose to do each experiment.