7.342: Week 9 Questions

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7.342: Reading the Blueprint of Life: Transcription, Stem Cells, & Differentiation

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Post discussion, questions, or comments about the Week 9 course material here.


Odelberg et al:

It seems strange that they didn't include any in vivo experiments.

Takahashi et al

What is teratoma formation?


Takahashi et al

I know cellpictures can be some what dodgy, but I really like figure 5.

Odelberg et al:

How valid is Figure 1C. Perhaps I cannot recognize proper muscle stucture, but what are the discrepencies between the images?


Takahashi & Yamanaka

Why exactly Klf4 is required for inducing dedifferentiation? They say it represses p53 but this doesn't sound like it's the whole story. Why did they pick Klf4 initially? They tried 24 they tried, maybe they could find more if they try other molecules?

Odelberg et al.

Msx1 is a homeodomain transcirption repressor; what are the known targets of Msx1 and has any work been done with this protein? What's its in vivo function?


Takahashi et al:

Fig 3c shows the methylation of the nanog promoter in iPs-MEFs to be much more similar to MEFs than ES cells. However fig 3a demonstrates that nanog is expressed in the iPS cells. Does this suggest that DNA methylation plays only a minor role in silencing the gene? The pattern of methylation in iPS cells is different to in MEFs - is this just a result of the way the data is presented, or could changes in the pattern (and not the amount) of methylation explain how gene repression can be overcome?

Odelberg et al:

Have the molecular mechanisms of msx-1 induced cellular dedifferentiation now been elucidated? What is the role of msx-1 in humans? (Presumably it doesn't cause dedifferentiation of our cells normally?)


Odelberg: Very cool--although, they mention several times that mice and humans have msx1 as well. If that is the case, how come we can't regenerate limbs? Also, would it be possible to go over how retroviral vectors are used to make stable cell lines? (Isn't it a bit sketchy to put the gene of interest downstream, rather than upstream, of the IRES-neoR?)

Takahashi: How does bisulfite genomic sequencing work? Also, how did they ensure that their gene integrations would integrate into a transcriptionally active section of DNA?


Odelberg et al: I'm not sure if I've understood this right, but I'm really confused by Fig 1 part B. In the right panel, is the C2C12 column a negative control? If so, why has the 28 rRNA hybridized to it?

Takashi et al: Fig 3D - they've shown immunostaining for SSEA-1. What is SSEA-1, and what does it signify?


. Odelberg, et al.:

Do mammals' genomes still contain the msx1 gene because one of our ancestors, like the urodele amphibians of today, used to be able to regenerate body parts? Humans do not regenerate whole limbs or digits, but they can heal and regenerate smaller things. During normal human healing, is the tissue regrowth done exclusively by adult stem cells that had never differentiated before the injury, or is there some dedifferentiation going on?

Takahashi, et al.:

What is G418? What is a "nude mouse," and why are they used?