¬Ý
1) ¬ÝPresentation:¬Ý
At the start of class present the paper for no more than
30 min.
¬Ý
2)¬Ý Discussion
after presentation:¬Ý Whole class will talk about the paper
(about 20 min), those auditing are welcome to join in the
discussion.
¬Ý
3)¬Ý Introduction
for the following weeks paper (see below).
¬Ý
¬Ý
Important note:¬Ý
One week BEFORE your presentation.¬Ý Present a short
introduction of the paper, no more than 5 min.¬Ý Also type out a
list of discussion points for people to think about while they
read the paper (print enough copies for everyone).
¬Ý
Week
2-3:¬Ý Introduction to epigenetics.
¬Ý
¬Ý
Park
YD, Papp I, Moscone EA, Iglesias VA, Vaucheret H, Matzke AJ,
Matzke MA.
Gene
silencing mediated by promoter homology occurs at the level of
transcription and results in meiotically heritable alterations in
methylation and gene activity.
Plant J. 1996 Feb;9(2):183-94.
¬Ý
Supplemental material based on class
discussion
¬Ý
Week 5 (30th Sept):¬Ý¬Ý¬Ý
¬Ý
Wassenegger
M, Heimes S, Riedel L, Sanger HL.
RNA-directed
de novo methylation of genomic sequences in plants.
Cell. 1994 Feb 11;76(3):567-76.
¬Ý
¬ÝSupplemental material based on
class discussion
¬Ý
Week 6 (7th Oct):¬Ý¬Ý¬Ý
¬Ý
Metzlaff
M, O'Dell M, Cluster PD, Flavell RB.
RNA-mediated
RNA degradation and chalcone synthase A silencing in petunia.
Cell. 1997 Mar 21;88(6):845-54.
¬Ý
¬Ý
Mette
MF, Aufsatz W, van der Winden J, Matzke MA, Matzke AJ.
Transcriptional
silencing and promoter methylation triggered by double-stranded
RNA.
EMBO J. 2000 Oct 2;19(19):5194-201.
¬Ý
¬ÝSupplemental material based on class
discussion
¬Ý
Week 8 (21st Oct):¬Ý¬Ý¬Ý
¬Ý
Llave
C, Kasschau KD, Rector MA, Carrington JC.
Endogenous
and Silencing-Associated Small RNAs in Plants.
Plant Cell. 2002 Jul;14(7):1605-19.
¬Ý
¬Ý
¬Ý
Kakutani
T, Jeddeloh JA, Flowers SK, Munakata K, Richards EJ.
Developmental
abnormalities and epimutations associated with DNA
hypomethylation mutations.
Proc Natl Acad Sci U S A. 1996 Oct
29;93(22):12406-11.
¬Ý
Jeddeloh
JA, Stokes TL, Richards EJ.
Maintenance
of genomic methylation requires a SWI2/SNF2-like protein.
Nat Genet. 1999 May;22(1):94-7.
¬Ý
¬Ý
Volpe
TA, Kidner C, Hall IM, Teng G, Grewal SIS and Martienssen RA.
Regulation
of Heterochromatic Silencing and Histone H3 Lysine-9 Methylation
by RNAi
¬Ý
Allshire
R
RNAi
and Heterochromatin; a Hushed-Up affair
¬Ý
Week 11 (11th Nov):¬Ý¬Ý¬Ý
¬Ý
Jacobsen
SE et al.
Ectopic
hypermethylation of flower specific genes in Arabidopsis. ¬Ý
Current Biology 2000, 10:179-186.
¬Ý
Week 12 (18th Nov):¬Ý¬Ý
¬Ý
¬Ý
Week 13 (25th Nov):¬Ý¬Ý
¬Ý
Nathan Springer
will focus on chromatin and transcriptional regulation but will
not address PTGS or RNAi except briefly.¬Ý This will cover many
epigenetic phenomena not covered in the course (including
paramutation, imprinting and PcG mediated silencing).¬Ý
¬Ý
Then he will
introduce the NSF Functional Genomics of Chromatin project that
the Kaeppler lab is involved in. Before class have a look at the www.chromdb.org website to
become familiar with what is present in plants.¬Ý Nathan will
talk in more detail about the methyltransferases, methyl-binding
domain proteins and SET domain proteins in regards to their
putative function and their evolution.¬Ý This will lead into a
brief discussion about the histone code hypothesis.¬Ý ¬ÝIn this
regard you should read the two reviews below before coming to
class.
¬Ý
Jenuwein T. and
Allis C.D.
Translating the
Histone Code
¬Ý
Strahl B.D. and
Allis C.D.
The language of
covalent histone modifications
¬Ý
¬Ý
Week 14 (2nd Dec):¬Ý
¬Ý
¬Ý
Chris Pires we
will discuss epigenetics in the context of polyploidy.¬Ý Specifically,
we will discuss allopolyploidy - which involves the union of two
genomes from different species.¬Ý Chris is providing you with two
papers.¬Ý The first paper is mandatory:
¬Ý
Thomas C. Osborn,
J. Chris Pires, James A. Birchler, Donald L. Auger, Z. Jeffery
Chen, Hyeon-Se Lee, Luca Comai, Andreas Madlung, R.W. Doerge,
Vincent Colot, Robert A. Martienssen (in press).¬Ý Understanding
mechanisms of novel gene expression in polyploids.¬Ý Trends in
Genetics.
¬Ý
This is a preprint
of a paper that was accepted on 21 November, 2002 (it was handed
out at class, if you need a copy see Chris or someone who
attended class on Nov 25th)¬Ý Please do not distribute
it to anyone without permission.¬Ý It reviews most of the recent
literature on polyploidy pertaining to gene expression with a
focus on rapid genetic and epigenetic changes that occur
immediately upon polyploidization.¬Ý The authors are members of a
polyploid consortium (see http://polyploid.agronomy.wisc.edu/).
¬Ý
The second paper is
optional but gives nice examples of experimental approaches being
used to examine polyploidy and epigenetics.
¬Ý
A Madlung, RW
Masuelli, B Watson, SH Reynolds, J Davidson, L Comai.
Remodeling of DNA
Methylation and Phenotypic and Transcriptional Changes in
Synthetic Arabidopsis Allotetraploids.
Plant Physiology (2002) 129 (June
issue): 733-746.-
¬Ý
The second paragraph of this paper sets the stage: "a consequence of the union of two genomes, abnormal phenotypes have been reported.¬Ý The causes of these phenotypes are largely unknown. McClintock described similar phenomena as ³ÑÍ߀"genomic shock" -³ÑÈÝ‚ which she defined as a preprogrammed response to an unusual challenge resulting in extensive restructuring of the genome.¬Ý This ³Ñ͵Æ"unusual challenge³ÑÈÝ‚" involve epigenetic gene silencing, which results from homologous DNA-DNA or DNA-RNA interactions.¬Ý The hybridization of redundant and diverged homeolgous sets of genes in allopolyploids might trigger widespread gene silencing and changes in chromatin structure and DNA methylation patterns.³Ñ"
¬Ý
¬Ý
Week 15 (9th Dec):¬Ý¬Ý
¬Ý
Compile timeline and decide who
should win the Nobel prize.¬Ý Timeline will be unraveled based on
the model we discussed in class.¬Ý
Listen for venue change in class.
¬Ý
¬Ý
¬Ý
Vaucheret
H, Fagard M.
Transcriptional
gene silencing in plants: targets, inducers and regulators.
Trends Genet. 2001 Jan;17(1):29-35.
¬Ý
Matzke
M, Matzke AJ, Kooter JM.
RNA:
guiding gene silencing.
Science. 2001 Aug 10;293(5532):1080-3.
¬Ý
Voinnet
O.
RNA
silencing: small RNAs as ubiquitous regulators of gene
expression.
Curr Opin Plant Biol. 2002
Oct;5(5):444.
¬Ý
Martienssen
RA, Colot V.
DNA
methylation and epigenetic inheritance in plants and filamentous
fungi.
Science. 2001 Aug
10;293(5532):1070-4.
¬Ý
Finnegan
EJ.
Epialleles
- a source of random variation in times of stress.
Curr Opin Plant Biol. 2002
Apr;5(2):101-6.
¬Ý
Pikaard
CS.
Genomic
change and gene silencing in polyploids.
