c*2
发帖数: 24 | 1 I have been struggling in understanding the results of the supplementary
figure 6 [ http://www.nature.com/nature/journal/v473/n7347/extref/nature09883-s1.pdf ]. The Bcl6 -/- strains was shown to have higher expression of Bcl6 than in the wild type. How could this happen? I kind of think it should be the opposite.
Any clues? | o*****r
发帖数: 156 | 2 someone has mentioned before that in KO, not the whole gene was completely
deleted.
In most cases, just an exon. So depends on which part of the gene been
probed in microarray,
you might see higher level profile because cells tend to increase the gene
expression level trying to
compromise the KO defect, though not effective.
strains was shown to have higher expression of Bcl6 than in the wild type.
How could this happen? I kind of
think it should be the opposite.
【在 c*2 的大作中提到】
: I have been struggling in understanding the results of the supplementary
: figure 6 [ http://www.nature.com/nature/journal/v473/n7347/extref/nature09883-s1.pdf ]. The Bcl6 -/- strains was shown to have higher expression of Bcl6 than in the wild type. How could this happen? I kind of think it should be the opposite.
: Any clues?
| c*2
发帖数: 24 | 3 Hi oranger,
Thanks for the explanation. It is helpful.
I actually downloaded and checked the expression data. Actually there are
two probe sets targeting the Bcl6, one of which as expected has low
expressoin of bcl6 in the mutant strain compared to the wild type.
Interestingly I also noticed that the Trp53 gene has the opposite gene
expression levels as shown in that figure too. It is really confusing.
Thanks.
【在 o*****r 的大作中提到】
: someone has mentioned before that in KO, not the whole gene was completely
: deleted.
: In most cases, just an exon. So depends on which part of the gene been
: probed in microarray,
: you might see higher level profile because cells tend to increase the gene
: expression level trying to
: compromise the KO defect, though not effective.
:
: strains was shown to have higher expression of Bcl6 than in the wild type.
: How could this happen? I kind of
| o*****r
发帖数: 156 | 4 I don't know about that.
You could always email the authors for clarification.
【在 c*2 的大作中提到】
: Hi oranger,
: Thanks for the explanation. It is helpful.
: I actually downloaded and checked the expression data. Actually there are
: two probe sets targeting the Bcl6, one of which as expected has low
: expressoin of bcl6 in the mutant strain compared to the wild type.
: Interestingly I also noticed that the Trp53 gene has the opposite gene
: expression levels as shown in that figure too. It is really confusing.
: Thanks.
| c*2
发帖数: 24 | 5 Just a follow-up on this. In case some of you are interested. I emailed the
author and here is his response.
==
Thanks for your interest and your question. We made the same observation as
you did. Trp53 is represented by multiple probe sets (1438808_at, 1438542_at
, 1459780_at, 1457623_x_at, 1427739_a_at, 1426538_a_at) and only one of them
shows indeed upregulation in Imatinib-treated BCL6-/- leukemia cells (i.e.
the one you can see in Figure S6). Figure S6 shows examples of microarray
probe sets with BCL6-dependent gene expression changes.
However, our conclusion regarding BCL6-dependent regulation of p53 is not
based on these microarray data. Using various ChIP techniques, we could show
that BCL6 is strongly recruited to the BCL6 promoter. More importantly, our
Western blots show that BCL6-/- leukemia cells express extremely high
levels of p53 protein compared to BCL6-wildtype leukemia cells. Likewise,
qRT-PCR data show that mRNA levels of p53 are much higher in BCL6-/- cells.
We often see that microarray data not always correctly predict real gene
expression changes. For this reason, we would not trust microarray data per
se, unless we can verify them by qRT-PCR and/or Western blot or Flow
cytometry.
Please let me know if you have other questions or if we can help otherwise
with your experiments on BCL6/p53.
Kind regards,
Markus
【在 o*****r 的大作中提到】
: I don't know about that.
: You could always email the authors for clarification.
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