BIOL 7800 (Section 3), Epigenetics, Fall 2014
Class: LSA663, 9:00-10:20 pm (Tuesday & Thursday)
Textbook: Epigenetics by C. David Allis et al, CSHL Press
Instructor: Dr. Joomyeong Kim, LSB room 644, 578-7692, jkim@lsu.edu
Office hours: By appointment.
Date
August 26
August 28
September 2
September 4
September 9
September 11
September 16
September 18
September 23
September 25
September 30
October 2
October 7
October 9
October 14
October 16
October 21
October 23
October 28
October 30
November 4
November 6
November 11
November 13
November 18
November 20
November 25
November 27
Lecture Topics (Chapter Nos*)
Overview of course
DNA Methylation I (Ch 18, 6, 9)
DNA Methylation II (Ch 18, 6, 9)
Paper Discussion 1- Renee, Gapp et al (2014)
(Writing Break)
(Writing Break)
Paper Discussion 2 – Joo Kim
Histone Modification I (Ch 11)
Histone Modification II (Ch 12)
Histone Modification III (Ch 5)
Paper Discussion 3 – Fabian, Lomniczi et al (2013)
(Fall Break)
Paper Discussion 4 – Jonathan, Jiang et al (2013)
RNAi and Heterochromatin formation (Ch 8)
Dosage Compensation (Ch 17, 16, 15)
Genomic Imprinting (Ch 19)
Paper Discussion 5 – Cody, Gregory Hannum et al. (2013)
Paper Discussion 6 – Hannah, Martha Susiarjo et al. (2013),
Amanda, Peter Lewis et al 2013
Paper Discussion 7 – Samantha, Jenkins et al (2014),
Germ cells and Pluripotent Stem Cells (Ch 20, 22)
Paper Discussion 8 - Vallmer, Ryan Lister et al. (2013)
Paper Discussion 9 – Dong, Smith ZD et al (2014)
Epigenetics and Cancers (Ch 24)
(Discussion and review of Proposals)
(Discussion and review of Proposals)
No class
(Thanksgiving)
(Thanksgiving)
*The students are required to read the textbook chapters in Bold-typed;
**The papers to be discussed during the Paper Discussion are accessible through the
Pubmed.
During the beginning phase of the class, this course will cover three main mechanisms
for epigenetics, DNA methylation, Histone Modification, RNAi-mediated
heterochromatin formation. During the second phase of the class, this course will cover
two main phenomena, X chromosome-related dosage compensation and Genomic
imprinting as well as two closely related fields, Regenerative Medicine and Cancers.
Each topic will be followed by the Discussion session covering recent breakthrough
papers, which are listed below. For each discussion session, one or two students will
present the main observation of each paper for the class. Each presentation will be
evaluated by the other students (50% of the final score). For this class, the students also
need to write one NIH-format proposal (5 -10 pages) covering their own research with
possible epigenetic connection. There are two due dates for this proposal writing: the
submission of the abstract will be Oct. 1st and the entire proposal will be Oct. 31st. Each
written proposal will be distributed to three other students for the initial review, and later
discussed and scored during the regular class (Nov 13&18). The evaluation score from
the proposal will make up the remaining 50% of the final grade. The students are
encouraged to discuss this writing with their advisors. This proposal could be used for
potential submission to any fellowship award (NIH F31, NSF and private foundations).
The papers to be discussed in this course.
(2014 class)
Jenkins TG et al. (2014) Age-associated sperm DNA methylation alterations: possible
implications in offspring disease susceptibility. PLoS Genet 10(7): e1004458.
(DNA methylation versus age)
Smith ZD et al. (2014) DNA methylation dynamics of the human preimplantation
embryo. Nature 511: 611–615.
(DNA methylation in humans)
Smith ZD et al. (2012) A unique regulatory phase of DNA methylation in the early
mammalian embryo. Nature 484(7394): 339-344.
(DNA methylation in mice)
Guo H et al. (2014) The DNA methylation landscape of human early embryos. Nature
511: 606–610.
(DNA methylation)
Radford et al. (2014) In utero undernourishment perturbs the adult sperm methylome and
intergenerational metabolism. Science 345(6198) DOI: 10.1126/science.125590
(DNA methylation versus nutrition)
Gapp K et al. (2014) Implication of sperm RNAs in transgenerational inheritance of the
effects of early trauma in mice. Nature Neuroscience 17: 667–669.
(Transgenerational inheritance of stress through small non-coding RNAs)
Kiskins E et al. (2014) Pathways disrupted in human ALS motor neurons identified
through genetic correction of mutant SOD1. Cell Stem Cell 14(6): 781-195.
(Regenerative medicine and iPSC)
Jiang J et al. Translating dosage compensation to trisomy 21. (2013) Nature 500(7462):
296-300.
(Dosage compensation versus its application to the treatment of human genetic disorders)
(2013 class)
Ryan Lister et al. (2013) Global epigenomic reconfiguration during mammalian brain
development. Science 341: 1237905.
(DNA methylation)***
Kathryn Blaschke et al. (2013) Vitamin C induces Tet-dependent DNA demethylation
and a blastocyst-like state in ES cells. Nature 500: 222-226.
(DNA methylation and Stem cells and Environmental intervention)***
Gabriella Ficz et al. (2013) FGF signaling inhibition in ESCs drives rapid genome-wide
demethylation to the epigenetic ground state of pluripotency. Cell Stem Cell 13: 1-9.
(DNA demethylation and Regeneration medicine)***
Gregory Hannum et al. (2013) Genome-wide methylation profiles reveal quantitative
views of human aging rates. Mol Cell 49: 359-367.
(DNA methylation and aging)***
Diane I. Schroeder et al. (2013) The human placenta methylome. PNAS 110: 6037-6042.
(DNA methylation)
Mingchao Xie et al. (2013) DNA hypomethylation within specific transposable element
families associates with tissue-specific enhancer landscape. Nat Genet 45: 836-841.
(DNA methylation)
Lavinia Gordon et al. (2012) Neonatal DNA methylation profile in human twins is
specified by complex interplay between intrauterine environmental and genetic factors,
subject to tissue-specific influence. Genome Res 22: 1395-1406.
(DNA methylation variations)
Martha Susiarjo et al. (2013) Bisphenol A exposure disrupts genomic imprinting in the
mouse. Plos Genet 9: e1003401.
(DNA methylation and environmental intervention)
Agnes Yu et al. (2013) Dynamic and biological relevance of DNA demethylatin in
Arabidopsis antibacterial defense. PNAS 110: 2389-2394.
(DNA methylation and non-mammalian system)
Fei Gao et al. (2012) Differential DNA methylation in discrete developmental stages of
the parasitic nematode Trichinella spirallis. Genome Biology 13: R100.
(DNA methylation and non-mammalian system)
Magdalena E. Potok et al. (2013) Reprogramming the maternal zebrafish genome after
fertilization to match the paternal methylation pattern. Cell 153: 759-772.
(DNA methylation reprogramming in zebrafish)
Yosef Bulganium et al. (2013) Single-cell expression analyses during cellular
reprogramming reveal an early stochastic and a late hierarchic phase. Cell 150: 12091222.
(Regenerative medicine and cell reprogramming)
Jiang Zhu et al. (2013) Genome-wide chromatin state transitions associated with
developmental and environmental cues. Cell 152: 642-654.
(Histone modification versus development)***
Svetlana Petruck et al. (2013) TrxG and PcG proteins but not methylated histones remain
associated with DNA through replication. Cell 150: 922-933.
(Histone modifications)***
Alejandro Lomniczi et al. (2013) Epigenetic control of female puberty. Nat Neurosci 16:
281-289.
(Histone modification and DNA methylation)
Peter W. Lewis et al. (2013) Inhibition of PRC2 activity by a gain-of-function H3
mutation found in pediatric glioblastoma. Science 340: 857-861.
(Histone modification and Cancer)***
Andrzej T. Wierrzbicki et al. (2012) Spatial and functional relationships among Pol Vassociated loci, Pol IV-dependent siRNAs, and cytosine methylation in the Arabidopsis
epigenome. Genes Dev 26: 1825-1836.
(siRNA-mediated DNA methylation)
Cathy C. Laurie et al. (2012) Detectable clonal mosaicism from birth to old age and its
relationship to cancer. Nat Genet 44: 642-650.
(Cancer)
Szilvia Solyom et al. (2012) Extensive somatic L1 retrotransposition in colorectal tumors.
Genome Res 22: 2328-2338.
(Cancer)
Alasdair J.E. Gordon et al. (2013) Heritable change caused by transient transcription
errors. Plos Genet 9: e1003595.
(Epigenetics in E coli)
Jafar Kiani et al. (2013) RNA-mediated epigenetic heredity requires the cytosine
methyltransferase Dnmt2. Plos Genet 9: e1003498.
(RNAi-mediated transgenerational inheritance in mice)***
Peter A. Jones (2012) Functions of DNA methylation: islands, start sites, gene bodies and
beyond. Nat Review Genet 13: 484-492.
(Review)***
Li Shen and Yi Zhang (2013) 5-Hydroxymethycytosine: generation, fate, and genomic
distribution. Curr Opin Cell Biol 25: 289-296.
(review)***
Li Tan and Yujiang Geno Shi (2012) Tet family proteins and 5-hydroxymethylcytosine in
development and disease. Development 139: 1895-1902.
(review)***
Marianne Terndrup Pedersen and Kristian Helin (2010) Histone demethylation in
development and disease. Trends Cell Biol 20: 662-671.
(review)***
Agger et al. (2008) The emrging functions of histone demethylases. Curr Opin Genet
Dev 18: 159-168.
(review)***
Kathrin Plath and William E. Lowry (2011) Progress in understanding reprogramming to
the induced pluripotent state. Nat Review Genet 12: 253-265.
(Review)
Karen Adelman and John T. Lis (2012) Promoter-proximal pausing of RNA polymerase
II: emerging roles in metazoans. Nat Review Genet 13: 720-731.
(Review)
(2010 Class)
Boyer LA, Plath K, Zeitlinger J, Brambrink T, Medeiros LA, Lee TI, Levine SS, Wernig
M, Tajonar A, Ray MK, Bell GW, Otte AP, Vidal M, Gifford DK, Young RA, Jaenisch
R. (2006). Polycomb complexes repress developmental regulators in murine embryonic
stem cells. Nature 441, 349-353.
Cedar H, Bergman Y. (2009). Linking DNA methylation and histone modification:
patterns and paradigms. Nat Rev Genet. 10, 295-304.
Ciccone, D.N., Su, H., Hevi, S., Gay, F., Lei, H., Bakjo, J., Xu, G., Li, E., and Chen, T.
(2009). KDM1B is a histone H3K4 demethylase required to establish maternal genomic
imprints. Nature 461, 415-418.
Guttman M, Amit I, Garber M, French C, Lin MF, Feldser D, Huarte M, Zuk O, Carey
BW, Cassady JP, Cabili MN, Jaenisch R, Mikkelsen TS, Jacks T, Hacohen N, Bernstein
BE, Kellis M, Regev A, Rinn JL, Lander ES. (2009). Chromatin signature reveals over a
thousand highly conserved large non-coding RNAs in mammals. Nature 458, 223-227.
Hark AT, Schoenherr CJ, Katz DJ, Ingram RS, Levorse JM, Tilghman SM. (2000).
CTCF mediates methylation-sensitive enhancer-blocking activity at the H19/Igf2 locus.
Nature 405, 486-489.
Keshet I, Schlesinger Y, Farkash S, Rand E, Hecht M, Segal E, Pikarski E, Young RA,
Niveleau A, Cedar H, Simon I. (2006). Evidence for an instructive mechanism of de novo
methylation in cancer cells. Nat Genet. 38, 149-153.
Kim MS, Kondo T, Takada I, Youn MY, Yamamoto Y, Takahashi S, Matsumoto T,
Fujiyama S, Shirode Y, Yamaoka I, Kitagawa H, Takeyama K, Shibuya H, Ohtake F,
Kato S. (2009). DNA demethylation in hormone-induced transcriptional derepression.
Nature 461, 1007-1012.
Kono T, Obata Y, Wu Q, Niwa K, Ono Y, Yamamoto Y, Park ES, Seo JS, Ogawa H.
(2004). Birth of parthenogenetic mice that can develop to adulthood. Nature 428, 860864.
Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee
L, Ye Z, Ngo QM, Edsall L, Antosiewicz-Bourget J, Stewart R, Ruotti V, Millar AH,
Thomson JA, Ren B, Ecker JR. (2009). Human DNA methylomes at base resolution
show widespread epigenomic differences. Nature 462, 315-322.
Meissner A, Mikkelsen TS, Gu H, Wernig M, Hanna J, Sivachenko A, Zhang X,
Bernstein BE, Nusbaum C, Jaffe DB, Gnirke A, Jaenisch R, Lander ES. (2008). Genomescale DNA methylation maps of pluripotent and differentiated cells. Nature 454, 766770.
Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G et al. (2007).
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature
448, 553-560.
Ooi, S.K., Qiu, C., Bernstein, E., Li, K., Jia, D., Yang, Z., Erdjument-Bromage, H.,
Tempst, P., Lin, S.P., Allis, C.D., Cheng, X., and Bestor, T.H. (2007). DNMT3L
connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA. Nature
448, 714-717.
Schlesinger Y, Straussman R, Keshet I, Farkash S, Hecht M, Zimmerman J, Eden E,
Yakhini Z, Ben-Shushan E, Reubinoff BE, Bergman Y, Simon I, Cedar H. (2007).
Polycomb-mediated methylation on Lys27 of histone H3 pre-marks genes for de novo
methylation in cancer. Nat Genet. 39, 232-236.
Straussman R, Nejman D, Roberts D, Steinfeld I, Blum B, Benvenisty N, Simon I,
Yakhini Z, Cedar H. (2009). Developmental programming of CpG island methylation
profiles in the human genome. Nat Struct Mol Biol. 16, 564-571.
Takahashi K, Yamanaka S. (2006). Induction of pluripotent stem cells from mouse
embryonic and adult fibroblast cultures by defined factors. Cell 126, 663-676.
Tilghman SM. (1999). The sins of the fathers and mothers: genomic imprinting in
mammalian development. Cell 96,185-193.