GMS6061 The Nucleus
Format
Short (“chalk”) talk and discussion.
Your grades will be based on your participation in the review and research paper
discussion.
For reviews:
Point of greatest interest
What point/paradigm/model/finding/observation is of most interest to you?
For original research papers:
Hypothesis
What hypothesis do the authors test?
Method
What method is of most interest to you?
Result
Which result is of most interest to you? Does it support the hypothesis and
conclusions of the authors?
Opinion
Form an opinion about the conclusion(s) of the paper.
Your experiment
Propose one (or more) experiment to extend or further support the conclusions of the
paper.
Faculty
Brian Burke, Professor, Anatomy and Cell Biology bburke@ufl.edu
Edward K.L. Chan, Professor, Department of Oral Biology echan@ufl.edu
Jianhong Hu, Postdoctoral Fellow, Renne lab, jhhu@ufl.edu
Alexander Ishov, Assistant Professor, Anatomy and Cell Biology ishov@ufl.edu
Cory Lindsay, Graduate Student, Ishov lab, clindsay@ufl.edu
Viacheslav Morozov, Postdoctoral Fellow, Ishov lab, morozov@ufl.edu
Michael Kladde, Associate Professor, Biochemistry & Molecular Biology kladde@ufl.edu
Kyle Roux, Postdoctoral Fellow, Burke lab kroux@ufl.edu
Date
3-27
3-29
4-3
4-5
4-10
4-12
4-17
Topic
Nuclear domains
ND10/PML body
Nuclear proteins with roles outside of the nucleus
Nuclear microRNA processing
Chromatin modification and DNA damage
Latency of DNA tumor viruses: How herpes viral
proteins hijack the host cellular replication machinery
during latency
DNA methylation and chromatin structure
Faculty
Ishov
Ishov
Lindsay
Chan
Morozov
Hu
Kladde
4-19
4-24
4-26
Nuclear pore complex
Nuclear lamina and disease
Nuclear dynamics and genome organization
Burke
Roux
Ishov
1. Tuesday, March 27
Topic:
Nuclear domains
Review:
Dundr M, Misteli T.
Functional architecture in the cell nucleus.
Biochem J. 2001 Jun 1;356(Pt 2):297-310.
Matera AG.
Cajal bodies.
Curr Biol. 2003 Jul 1;13(13):R503.
Paper:
Schmidt U, Richter K, Berger AB, Lichter P. In vivo BiFC analysis of Y14 and NXF1
mRNA export complexes: preferential localization within and around SC35 domains.
J Cell Biol. 2006 Jan 30;172(3):373-81.
Optional:
Bubulya PA, Spector DL.
"On the move"ments of nuclear components in living cells.
Exp Cell Res. 2004 May 15;296(1):4-11.
2. Thursday, March 29
Topic:
ND10 or PML bodies
Review:
Borden KL. Pondering the promyelocytic leukemia protein (PML) puzzle: possible
functions for PML nuclear bodies.
Mol Cell Biol. 2002 Aug;22(15):5259-69.
Everett RD, Chelbi-Alix MK. PML and PML nuclear bodies: Implications in antiviral
defense. Biochimie. 2007 Jan 27
Paper:
Lin DY, Huang YS, Jeng JC, Kuo HY, Chang CC, Chao TT, Ho CC, Chen YC, Lin TP,
Fang HI, Hung CC, Suen CS, Hwang MJ, Chang KS, Maul GG, Shih HM. Role of
SUMO-interacting motif in Daxx SUMO modification, subnuclear localization, and
repression of sumoylated transcription factors. Mol Cell. 2006 Nov 3;24(3):341-54.
Shen TH, Lin HK, Scaglioni PP, Yung TM, Pandolfi PP. The mechanisms of PMLnuclear body formation. Mol Cell. 2006 Nov 3;24(3):331-9.
Optional:
Takahashi Y, Lallemand-Breitenbach V, Zhu J, de The H.
PML nuclear bodies and apoptosis.
Oncogene. 2004 Apr 12;23(16):2819-24. Review.
3. Tuesday, April 3:
Topic:
Nuclear Proteins with Roles Outside of the Nucleus
Review:
The Mitotic Spindle Matrix: A Fibro-membranous Lamin Connection. (2006) Zheng, Y.,
Tsai, M.Y. Cell Cycle 5 (20): 2345-2347.
Paper:
A mitotic lamin B matrix induced by RanGTP required for spindle assembly. (2006) Tsai
MY, Wang S, Heidinger JM, Shumaker DK, Adam SA, Goldman RD, Zheng Y. Science
(5769): 1887-93.
4. Thursday, April 5:
Topic:
Nuclear microRNA processing
Paper:
Kim, Y.K. and V.N. Kim. 2007. Processing of intronic microRNAs. EMBO J. 26:775783.
5. Tuesday, Aptil 10:
Topic:
Chromatin modification and DNA damage
Review:
Squatrito M, Gorrini C, Amati B. Abstract Tip60 in DNA damage response and growth
control: many tricks in one HAT. Trends Cell Biol. 2006 Sep;16(9):433-42.
Paper:
Tang Y, Luo J, Zhang W, Gu W. Tip60-dependent acetylation of p53 modulates the
decision between cell-cycle arrest and apoptosis. Mol Cell. 2006 Dec 28;24(6):827-39.
Sykes SM, Mellert HS, Holbert MA, Li K, Marmorstein R, Lane WS, McMahon SB.
Acetylation of the p53 DNA-binding domain regulates apoptosis induction. Mol Cell.
2006 Dec 28;24(6):841-51.
6. Thursday, April 12:
Topic:
Latency of DNA tumor viruses: How herpes viral proteins hijack the host cellular
replication machinery during latency
Review:
Sugden B.
In the beginning: a viral origin exploits the cell.
Trends Biochem Sci. 2002 Jan;27(1):1-3.
Hammerschmidt W, Sugden B.
Epstein-Barr virus sustains Burkitt's lymphomas and Hodgkin's disease.
Trends Mol Med. 2004 Jul;10(7):331-6.
Paper:
1.Barbera AJ et al. The nucleosomal surface as a docking station for Kaposi's sarcoma
herpesvirus LANA. Science. 2006 Feb 10;311(5762):856-61
2.You J et al. Kaposi's sarcoma-associated herpesvirus latency-associated nuclear antigen
interacts with bromodomain protein Brd4 on host mitotic chromosomes. J Virol. 2006
Sep;80(18):8909-19.
7. Tuesday, April 17:
Topic:
DNA methylation and chromatin structure
Review:
Feinberg AP, Tycko B.
The history of cancer epigenetics.
Nat Rev Cancer. 2004 Feb;4(2):143-53.
Paper:
Lorincz MC, Dickerson DR, Schmitt M, Groudine M.
Intragenic DNA methylation alters chromatin structure and elongation efficiency in
mammalian cells.
Nat Struct Mol Biol. 2004 Nov;11(11):1068-75
8. Thursday, April 19:
Topic:
Nuclear pore complex
Review:
Tran EJ, Wente SR. Dynamic nuclear pore complexes: life on the edge.
Cell. 2006 Jun 16;125(6):1041-53.
Paper:
Frey S, Richter RP, Gorlich D. FG-rich repeats of nuclear pore proteins form a threedimensional meshwork with hydrogel-like properties. Science. 2006 Nov
3;314(5800):815-7.
9. Tuesday, April 24:
Topic:
Nuclear lamina and disease
Review:
Yosef Gruenbaum, Ayelet Margalit, Robert D. Goldman, Dale K. Shumaker &
Katherine L. Wilson
The nuclear lamina comes of age.
Nature Reviews Molecular Cell Biology 2005 6, 21-31.
Paper:
Lammerding J, Schulze PC, Takahashi T, Kozlov S, Sullivan T, Kamm RD,
Stewart CL, Lee RT.
Lamin A/C deficiency causes defective nuclear mechanics and mechanotransduction.
J Clin Invest. 2004 Feb;113(3):370-8.
Lammerding J, Hsiao J, Schulze PC, Kozlov S, Stewart CL, Lee RT.
Abnormal nuclear shape and impaired mechanotransduction in
emerin-deficient cells.
J Cell Biol. 2005 Aug 29;170(5):781-91. Epub 2005 Aug 22.
10. Thursday, April 26:
Topic:
Nuclear dynamics and genome organization
Review:
Misteli T. Beyond the sequence: cellular organization of genome function. Cell. 2007 Feb
23;128(4):787-800.
Paper:
Janicki SM, Tsukamoto T, Salghetti SE, Tansey WP, Sachidanandam R, Prasanth KV,
Ried T, Shav-Tal Y, Bertrand E, Singer RH, Spector DL.
From silencing to gene expression: real-time analysis in single cells.
Cell. 2004 Mar 5;116(5):683-98.
Optional:
Taddei A, Hediger F, Neumann FR, Gasser SM.
The function of nuclear architecture: a genetic approach.
Annu Rev Genet. 2004;38:305-45.