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Neu
221: Genetics and Epigenetics in Brain Development
(Winter 2006)
Michael G.
Rosenfeld
Kristen
Jepsen
Victoria Lunyak
Bob McEvilly
Course
Syllabus
[Download
Course Syllabus]
[Download
Reading List PDFs for the Course]
1/10/06:
Course
Organization/Discussion Topic Assignments
Opening
remarks “Introduction to Epigenetics” - Victoria
Lunyak
[Download MS PowerPoint
Handout]
Background
resources
Epigenetic
regulation by histone methylation and histone variants.
Cheung P, Lau P. Mol Endocrinol. 2005 19(3):563-73.
DNA methylation and
histone modifications: teaming up to silence genes.
Fuks F. Curr Opin Genet Dev. 2005 15(5):490-5
Genomic views of
chromatin.
Huebert DJ, Bernstein BE. Curr Opin Genet Dev.
2005 15(5):476-81.
The key to
development: interpreting the histone code?
Margueron R, Trojer P, Reinberg D. Curr Opin Genet
Dev. 2005 15(2):163-76.
The dynamics of
chromatin remodeling at promoters.
Mellor J.Mol Cell. 2005 19(2):147-57.
Methylation of
histones: playing memory with DNA.
Peters AH, Schubeler
D.
Curr Opin Cell Biol.
2005 17(2):230-8. Erratum in: Curr Opin Cell Biol.
2005 17(3):341.
Epigenetic silencing
mechanisms in budding yeast and fruit fly: different
paths, same destinations.
Pirrotta V, Gross
DS. Mol Cell. 2005 18(4):395-8.
Histone variants meet their match.
Sarma K, Reinberg D. Nat
Rev Mol Cell Biol. 2005 6(2):139-49.
Taking LSD 1 to a
new high.
Wysocka J, Milne TA, Allis CD. Cell 2005 122(5):654-8
Histone variants,
nucleosome assembly and epigenetic inheritance.
Henikoff S, Furuyama T, Ahmad K. Trends Genet.
2004 20(7):320-6. Erratum in: Trends Genet.
2005
21(1):36.
SWRred not shaken;
mixing the histones.
Korber P, Horz W.
Cell. 2004 117(1):5-7.
A crack in histone
lysine methylation.
Kubicek S, Jenuwein
T. Cell. 2004 119(7):903-6.
Polycomb complexes
and silencing mechanisms.
Lund AH, van
Lohuizen M. Curr Opin Cell Biol. 2004
16(3):239-46.
Cracking the histone
code: one, two, three methyls, you're out!
Dutnall RN. Mol Cell. 2003 Jul;12(1):3-4.
Histone and
chromatin cross-talk.
Fischle W, Wang Y, Allis CD.
Curr Opin Cell Biol.
2003 15(2):172-83.
1/17/06:
Lecture by
Michael G. Rosenfeld, followed by group discussion of
the following paper:
Chromosome-wide
mapping of estrogen receptor binding reveals long-range
regulation requiring the forkhead protein FoxA1.
Carroll JS,
Liu XS,
Brodsky AS,
Li W,
Meyer CA,
Szary AJ,
Eeckhoute J,
Shao W,
Hestermann EV,
Geistlinger TR,
Fox EA,
Silver PA,
Brown M. Cell 2005 122:33-43.
Additional
background resources:
Strategies for
dissecting epigenetic mechanisms in the mouse.
Mager J, Bartolomei MS. Nat Genet.
2005
37(11):1194-200.
Mapping of genetic
and epigenetic regulatory networks using microarrays.
van Steensel B. Nat Genet. 2005 37 Suppl:S18-24.
1/24/06: Paper
Discussion: STAT3 methylation, NSC
Discussion Moderator: Kristen Jepsen
1.
FGF2-induced chromatin remodeling regulates
CNTF-mediated gene expression and astrocyte differentiation.
Song MR, Ghosh A. Nat Neurosci 2004, 7:229-235.*
Developmental stage
dependent regulation of DNA methylation and chromatin
modification in a immature astrocyte specific gene
promoter.
Masakazu Namihira, Kinichi Nakashima, Tetsuya Taga
FEBS Letters 2004, 572:184–188*
*additional
background reading for discussion
DNA methylation is a
critical cell-intrinsic determinant of astrocyte
differentiation in the fetal brain.
Takizawa T,
Nakashima K, Namihira M, Ochiai W, Uemura A, Yanagisawa
M, Fujita N, Nakao M, Taga T. Dev Cell. 2001
1(6):749-58.
2.
Neural induction promotes large-scale chromatin
reorganisation of the Mash1 locus
Ruth R. E. Williams,
Véronique Azuara, Pascale Perry, Stephan Sauer, Maria
Dvorkina,
Helle
Jørgensen, Jeffery Roix, Philip McQueen, Tom Misteli,
Matthias Merkenschlager and
Amanda G. Fisher.
J
Cell Sci. 2006 119:132-40.
1/31/06: Paper
Discussion: RNAi, REST &
Notch
Discussion Moderator: Victoria Lunyak
3. A
small modulatory dsRNA specifies the fate of adult
neural stem cells.
Kuwabara T, Hsieh J, Nakashima K, Taira K, Gage FH:
Cell 2004, 116:779-793.
Additional reading
for discussion purposes:
REST and Its
Corepressors Mediate Plasticity of Neuronal Gene
Chromatin throughout Neurogenesis
Nurit Ballas, Christopher Grunseich, Diane D. Lu, Joan
C. Speh and Gail Mandel. Cell 2005, 121:645-657
4.
MicroRNA function in animal development.
Wienholds E, Plasterk RH. FEBS Lett. 2005
579(26):5911-22.
LIN-12/Notch
activation leads to microRNA-mediated down-regulation of
Vav in C. elegans.
Yoo AS, Greenwald I. Science. 2005 310(5752):1330-3.
Additional
background resources:
RNA meets chromatin.
Bernstein E, Allis CD. Genes Dev. 2005
19(14):1635-55.
Stem cells: from
epigenetics to microRNAs.
Cheng LC, Tavazoie M, Doetsch F. Neuron.
2005 46(3):363-7.
Encountering
microRNAs in cell fate signaling.
Karp X, Ambros V. Science. 2005 310(5752):1288-9.
Chromatin
remodelling and epigenetic features of germ cells.
Kimmins
S, Sassone-Corsi P. Nature. 2005 434(7033):583-9.
Regulation of
heterochromatin by histone methylation and small RNAs.
Grewal SI,
Rice JC. Curr Opin Cell Biol. 2004 16(3):230-8.
Epigenetic control
of neural stem cell fate.
Hsieh J, Gage FH. Curr Opin Genet Dev. 2004
14(5):461-9.
2/7/06: Paper
Discussion: DNA Methylation and
MECP2
Discussion
Moderator: Bob McEvilly
5.
Derepression of BDNF Transcription involves
calcium-dependent phosphorylation of MeCP2.
Chen WG, Chang Q, Lin Y, Meissner A, West AE, Griffith
EC, Jaenisch R, Greenberg ME Science 2003,
302:885-889.
6. DNA
methylation-related chromatin remodeling in
activity-dependent BDNF gene regulation.
Martinowich K, Hattori D, Wu H, Fouse S, He F, Hu Y, Fan
G, Sun YE. Science 2003, 302:890-893.
2/14/06: Paper
Discussion: Chromatin Looping
Discussion Moderator: Victoria Lunyak
7.
Looping and interaction between hypersensitive sites in
the active beta-globin locus.
Tolhuis B,
Palstra RJ,
Splinter E,
Grosveld F,
de Laat W.
Mol Cell.
2002, 10:1453-65.
8. Loss
of silent-chromatin looping and impaired imprinting of
DLX5 in Rett syndrome.
Horike S,
Cai S,
Miyano M,
Cheng JF,
Kohwi-Shigematsu T.
Nat Genet. 2005, 37:31-40.
Additional reading for discussion purposes:
The three 'C' s of
chromosome conformation capture: controls, controls,
controls.
Dekker J. Nat Methods. 2006 3(1):17-21.
2/21/05: Paper
Discussion: X
Inactivation
Discussion Moderator: Bob McEvilly
9.
Epigenetic Dynamics of Imprinted X Inactivation During
Early Mouse Development.
Ikuhiro Okamoto, Arie P. Otte, C. David Allis, Danny
Reinberg, Edith Heard. Science 2004 303:644-9
10.
Reactivation of the Paternal X Chromosome in Early Mouse
Embryos.
Winifred Mak, Tatyana B. Nesterova, Mariana de Napoles,
Ruth Appanah, Shinya Yamanaka, Arie P. Otte, Neil
Brockdorff. Science 2004 303:666-9
Additional reading
for discussion purposes:
X-linked genes and mental functioning.
David H. Skuse. Human
Molecular Genetics 2005, 14: R27–R32
Additional
background resources:
Mechanisms of
X-chromosome inactivation.
Chang SC, Tucker T,
Thorogood NP, Brown CJ. Front Biosci. 2006
11:852-66.
Delving into the
diversity of facultative heterochromatin: the
epigenetics of the inactive X chromosome.
Heard E. Curr
Opin Genet Dev. 2005 15(5):482-9.
Epigenetic
regulation of mammalian genomic imprinting.
Delaval K, Feil R. Curr Opin Genet Dev. 2004
14(2):188-95.
Imprinted X
inactivation and reprogramming in the preimplantation
mouse embryo.
Sado T,
Ferguson-Smith AC. Hum Mol Genet. 2005 14 Spec No
1:R59-64.
2/28/06: Paper
Discussion: Maternal
Programming
Discussion Moderator: Kristen Jepsen
11.
Epigenetic programming by
maternal behavior.
Ian C G Weaver, Nadia Cervoni, Frances A Champagne, Ana
C D’Alessio, Shakti Sharma, Jonathan R Seckl, Sergiy
Dymov,Moshe Szyf & Michael J Meaney  Nature
Neuroscience 2004 7, 847 – 854.
12.
Transposable Elements: Targets for Early Nutritional
Effects on Epigenetic Gene Regulation Robert A.
Waterland and Randy L. Jirtle. Mol Cell Bio 2003,
23:5293-5300.
Additional reading
for discussion purposes:
A pregnant mother’s
diet may turn the genes around.
Sandra Blakeslee. NY Times
Oct 7 2003.
Additional
background resources:
Epigenetic
reprogramming in mammals.
Morgan HD, Santos F, Green K, Dean W, Reik W. Hum Mol
Genet. 2005 14 Spec No 1:R47-58.
Epigenetic
Programming of Stress Responses through Variations in
Maternal Care.
Fish EW, Shahrokh D,
Bagot R, Caldji C, Bredy T, Szyf M, Meaney MJ. Ann N
Y Acad Sci. 2004 1036:167-80.
3/7/06: Paper
Discussion: Reprogramming in Somatic Cell Nuclear
Transfer -
Discussion
Moderator: Bob McEvilly
13. Mice
cloned from olfactory sensory neurons.
Kevin Eggan, Kristin
Baldwin, Michael Tackett, Joseph Osborne, Joseph Gogos,
Andrew Chess, Richard Axel & Rudolf Jaenisch. Nature
2004 428: 44-49
Odorant receptor
gene choice is reset by nuclear transfer from mouse
olfactory sensory neurons.
Jinsong Li, Tomohiro Ishii, Paul Feinstein & Peter
Mombaerts. Nature 2004 428:393-399
14.
Nuclear reprogramming of somatic cells after fusion
with human embryonic stem cells. Cowan CA, Atienza
J, Melton DA, Eggan K. Science. 2005
309(5739):1369-73.
Additional reading
for discussion purposes:
Patient-Specific
Embryonic Stem Cells Derived from Human SCNT Blastocysts.
Woo Suk Hwang, Sung Il Roh, Byeong Chun Lee, Sung Keun
Kang, Dae Kee Kwon, Sue Kim, Sun Jong Kim, Sun Woo Park,
Hee Sun Kwon, Chang Kyu Lee, Jung Bok Lee, Jin Mee Kim,
Curie Ahn, Sun Ha Paek, Sang Sik Chang, Jung Jin Koo,
Hyun Soo Yoon, Jung Hye Hwang, Youn Young Hwang, Ye Soo
Park, Sun Kyung Oh, Hee Sun Kim, Jong Hyuk Park, Shin
Yong Moon, Gerald Schatten. Science 2005, 17:1777-83
Additional background resources:
Nuclear reprogramming by human embryonic stem cells.
Surani MA. Cell. 2005 122(5):653-4.
Genetic and
epigenetic aspects of cloning and potential effects on
offspring of cloned mammals.
Smith LC, Murphy BD.
Cloning Stem Cells. 2004;6(2):126-32
3/14/06: Epigenetics and Memory
Discussion Moderator: Kristen Jepsen
15. Long-term memory requires
polyADP-ribosylation.Cohen-Armon
M, Visochek L, Katzoff A, Levitan D, Susswein AJ, Klein
R, Valbrun M, Schwartz JH. Science 2004,
304:1820-1822.
16. CBP histone acetyltransferase activity is
a critical component of memory
consolidation.Korzus
E, Rosenfeld MG, Mayford M. Neuron 2004, 42:961-972.
Additional reading for discussion purposes:
Chromatin acetylation, memory, and LTP are impaired in
CBP+/S mice: a model for the cognitive
deficit in Rubinstein–Taybi syndrome and its
amelioration.
Alarcon JM, Malleret G, Touzani K, Vronskaya S, Ishii S,
Kandel ER, Barco A. Neuron 2004, 42:947-959.
Additional background resources:
Chromatin
architecture and functions: the role(s) of poly(ADP-RIBOSE)
polymerase and poly(ADPribosyl)ation of nuclear
proteins.
Faraone-Mennella MR.
Biochem Cell Biol. 2005 83(3):396-404.
Transcriptional
control of cognitive development.
Hong EJ, West AE, Greenberg ME. Curr Opin Neurobiol.
2005 15(1):21-8.
Chromatin remodeling
in neural development and plasticity.
Hsieh J, Gage FH. Curr Opin Cell Biol. 2005
17(6):664-71.
Epigenetic
mechanisms in memory formation.
Levenson JM, Sweatt JD. Nat Rev Neurosci. 2005
6(2):108-18.
Dynamic and
reversibility of heterochromatic gene silencing in human
disease.
Zardo G, Fazi F, Travaglini L, Nervi C.
Cell Res.
2005 15(9):679-90.
Advances in
chromatin remodeling and human disease.
Cho KS, Elizondo LI,
Boerkoel CF. Curr Opin Genet Dev. 2004
14(3):308-15.
http://physiologyonline.physiology.org/cgi/content/full/19/5/253
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