Download IG Workshop 2007 - Genetic Mysteries

IG Workshop 2007 - Genetic Mysteries: how do we distinguish new discovery from bad science?
SUSAN LOLLE, Associate Professor, Department of Biology, University of Waterloo, Ontario
Research: Dr. Lolle published a high-profile and controversial paper: "Genome-wide non-Mendelian
inheritance of extra-genomic information in Arabidopsis" in Nature in March 2005. She suggested that
we read and discuss several papers that provide additional examples of non-Mendelian inheritance,
including one report of RNA-mediated non-Mendelian inheritance in mouse and three reports of
environmentally-induced genomic "dynamics" in different plant species. In our discussion next week, we
will review the original report of Lolle et al., discuss several alternative hypotheses that have been
proposed to explain the observed results, and finally discuss the significance of this study in the broader
context of epigenetic phenomena.
Important Note: I have added 2 additional papers to the assigned list:
1) Lolle et al, 2005 Nature - the "key" paper that not was included in the original list from Lolle
2) Krishnaswamy & Peterson, Plant Biology, 2007 - a recent & very relevant brief article
Please be sure to read these papers! On Friday, March 2, all students will receive copies of these articles
as pdf attachments to email. These papers will be posted on the IG Workshop site (or at another URL, to
be announced) on Friday afternoon
Discussion Session: 3 – 4 PM, Wed Mar 5 in 277 Science I
Seminar:
The Paradox of Gene Restoration: Is the Proof in the Pollen?
4:10 PM, Tues April 10 in 1414 MBB
Chalk Talk:
Noon, Wed April 18 in 1102 MBB
Publications: All students are expected to have read all assigned papers prior to the Discussion Session.
Because this is a lot of reading, please focus on the paper assigned to your group, but be sure to read
through the papers and related questions assigned to other groups - they are all related and very
interesting!
Agenda for Mar 5 Discussion Session
3:10-3:20
Discussion within Groups (if possible, try to be early - don't be late!!)
3:20-3:55
5' presentations by Recorders from each group
3:55-4:00
Wrap-up: 2 most important questions to ask Lolle?
Discussion Leaders: Keep the discussion on track.
Recorders: Record the discussion and present a summary to the class.
New: Question Keeper: Another student volunteer (not the discussion leader or recorder) should each
record two questions as described below. Question Keeper is responsible for turning in a written copy of
these questions to the instructor at the end of class (include the Date, Group # & Question Keeper's name,
in addition to the questions, Thanks!)
Each group should write two questions that can be ready for asking Susan at the chalk talk. One should
be a technical research question based on the experimental data in one of the papers; the other question
should address a topic in the larger area of how we conduct scientific research.
Group
7
Source
Especially these parts (Questions for discussion are bulleted)
Lolle Nature 05
pp. 505-506; Figure 1, Table 1; Table 2
"Here we show that Arabidopsis plants homozygous for recessive mutant alleles of the organ fusion gene
HOTHEAD 5 (HTH) can inherit allele-specific DNA sequence information that was not present in the
chromosomal genome of their parents but was present in previous generations."
• What is the experimental evidence for this statement?
• What two "trivial" alternative explanations for this finding did the authors consider, but rule out?
6
Lolle Nature 2005
pp. 506-507, Figure 2, Table 3
"We postulate that these genetic restoration events are the result of a template directed process that
makes use of an ancestral RNA-sequence cache."
• Outline three "conventional explanations" for the genetic instability observed at HTH locus.
• Explain why the authors eliminated these possibilities and why they proposed an RNA-mediated
mechanism instead.
5
Peng et al. Nature 2005
Table 1
"This tendency to outcross may provide an alternative explanation for the apparent genetic instability of
hothead mutants."
•
What evidence do Peng et al. present to support their suggestion that a "tendency to outcross"
could explain the results of Lolle et al?
Pruitt et al., Nature 2005
"Ultimately, we discarded this explanation because it was inconsistent with many of our experimental
results"
• Do you think the response of Pruitt et al. sufficiently addresses the Peng's concern?
4
Chen, New Phytologist 2005; Roth, Genetics 1989
• Briefly explain why (in your opinion) Susan Lolle included each of these papers in her list of
suggested readings?
• What potential mechanism(s) for non-Mendelian inheritance are proposed in these papers?
3
Rassoulzadegan Nature 2006
Figure 2, Figure 5
In their analysis of the inheritance of Kit mutations in mouse, Rassoulzadegan et al. report "efficient
paternal and maternal inheritance of the paramutated state..." and conclude that: "Our results identify an
unexpected mode of epigenetic inheritance associated with the zygotic transfer of RNA molecules."
• Briefly describe what is meant by paramutation (in the context of this paper).
• What evidence do the authors present for their proposal that "the paramutated state was induced by
a partial degradation product of Kit RNA"?
2
Molinier, Nature 2006
On the basis of their results in Arabidopsis, Molinier et al. conclude that an epigenetic trait "could be
transmitted through both the maternal and the paternal crossing partner, and proved to be dominant."
• What epigenetic trait analyzed in this paper?
• Suggest several potential molecular mechanisms that could mediate transmission of this trait
(Hint: consider possibilities suggested by Lolle, Chen/Roth, and Rassoulzadegan)
1 Krishnaswamy & Peterson, Plant Biology, 2007
"Our hypothesis is based on a relatively straightforward developmental aberration in which maternal
cells (“Legacy cells”) fuse with the developing embryo, resulting in a chimera, which could then give rise
to the aberrant genetic segregations reported by Lolle et al."
• The Krishnaswamy article summarizes 4 different mechanisms that had been proposed to explain the
high frequency of genomic changes in HTH locus reported by Lolle et al., in Nature 2005 paper.
Briefly outline these.
• Briefly summarize the new and testable (5th) alternative model is proposed in this article.