Supplementary Material
Systems biology meets chromatin function
A report on the 4th Elmau conference on nuclear organization
Christophe Lavelle and Alex Sigal
This is a list of additional references (not included in the main text for space convenience)
discussed by the speakers during the workshop. They are all selected from participants’ (in
bold) own recently published work.
Bancaud, A., Conde e Silva, N., Barbi, M., Wagner, G., Allemand, J. F., Mozziconacci, J.,
Lavelle, C., Croquette, V., Victor, J. M., Prunell, A., and Viovy, J. L. (2006). Structural
plasticity of single chromatin fibers revealed by torsional manipulation. Nat Struct Mol
Biol 13, 444-450.
Blais, A., and Dynlacht, B. D. (2005). Devising transcriptional regulatory networks operating
during the cell cycle and differentiation using ChIP-on-chip. Chromosome Res 13, 275288.
Blais, A., Tsikitis, M., Acosta-Alvear, D., Sharan, R., Kluger, Y., and Dynlacht, B. D. (2005).
An initial blueprint for myogenic differentiation. Genes Dev 19, 553-569.
Bystricky, K., Heun, P., Gehlen, L., Langowski, J., and Gasser, S. M. (2004). Long-range
compaction and flexibility of interphase chromatin in budding yeast analyzed by highresolution imaging techniques. Proc Natl Acad Sci U S A 101, 16495-16500.
Chassagnole, C., Jackson, R. C., Hussain, N., Bashir, L., Derow, C., Savin, J., and Fell, D. A.
(2006). Using a mammalian cell cycle simulation to interpret differential kinase
inhibition in anti-tumour pharmaceutical development. Biosystems 83, 91-97.
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Ciliberto, A., Lukacs, A., Toth, A., Tyson, J. J., and Novak, B. (2005). Rewiring the exit from
mitosis. Cell Cycle 4, 1107-1112.
Csikasz-Nagy, A., Battogtokh, D., Chen, K. C., Novak, B., and Tyson, J. J. (2006). Analysis
of a generic model of eukaryotic cell-cycle regulation. Biophys J 90, 4361-4379.
Fakan, S., and van Driel, R. (2004). Where do we go in the nucleus? Biol Cell 96, 553-554.
Fraser, P. (2006). Transcriptional control thrown for a loop. Curr Opin Genet Dev 16, 490495.
Gehlen, L., Rosa, A., Klenin, K., Langowski, J., Gasser, S. M., and Bystricky, K. (2006).
Spatially confined polymer chains: implication of chromatin fiber flexibility and
peripheral anchoring on telomere-telomere interaction. J of Physics: Condens Matter,
245-252.
Gerhardt, J., Jafar, S., Spindler, M. P., Ott, E., and Schepers, A. (2006). Identification of new
human origins of DNA replication by an origin-trapping assay. Mol Cell Biol 26, 77317746.
Hornberg, J. J., Binder, B., Bruggeman, F. J., Schoeberl, B., Heinrich, R., and Westerhoff, H.
V. (2005). Control of MAPK signalling: from complexity to what really matters.
Oncogene 24, 5533-5542.
Huynh, V. A., Robinson, P. J., and Rhodes, D. (2005). A method for the in vitro
reconstitution of a defined "30 nm" chromatin fibre containing stoichiometric amounts
of the linker histone. J Mol Biol 345, 957-968.
Jackson, D. A. (2003). The principles of nuclear structure. Chromosome Res 11, 387-401.
Kepert, J. F., Toth, K. F., Caudron, M., Mucke, N., Langowski, J., and Rippe, K. (2003).
Conformation of reconstituted mononucleosomes and effect of linker histone H1
binding studied by scanning force microscopy. Biophys J 85, 4012-4022.
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Klipp, E., Nordlander, B., Kruger, R., Gennemark, P., and Hohmann, S. (2005). Integrative
model of the response of yeast to osmotic shock. Nat Biotechnol 23, 975-982.
Klipp, E., Nordlander, B., Kruger, R., Gennemark, P., and Hohmann, S. (2006).
Corrigendum: Integrative model of the response of yeast to osmotic shock. Nat
Biotechnol 24, 1293.
Lavelle, C. (2006). Transcription elongation through a chromatin template. Biochimie (in
press).
Lipniacki, T., Paszek, P., Brasier, A. R., Luxon, B., and Kimmel, M. (2004). Mathematical
model of NF-kappaB regulatory module. J Theor Biol 228, 195-215.
Lipniacki, T., Paszek, P., Marciniak-Czochra, A., Brasier, A. R., and Kimmel, M. (2006).
Transcriptional stochasticity in gene expression. J Theor Biol 238, 348-367.
Maske, C. P., Hollinshead, M. S., Higbee, N. C., Bergo, M. O., Young, S. G., and Vaux, D. J.
(2003). A carboxyl-terminal interaction of lamin B1 is dependent on the CAAX
endoprotease Rce1 and carboxymethylation. J Cell Biol 162, 1223-1232.
Mellor, J. (2005). The dynamics of chromatin remodeling at promoters. Mol Cell 19, 147157.
Mellor, J. (2006). Dynamic nucleosomes and gene transcription. Trends Genet 22, 320-329.
Metivier, R., Reid, G., and Gannon, F. (2006). Transcription in four dimensions: nuclear
receptor-directed initiation of gene expression. EMBO Rep 7, 161-167.
Morillon, A., Karabetsou, N., Nair, A., and Mellor, J. (2005). Dynamic lysine methylation on
histone H3 defines the regulatory phase of gene transcription. Mol Cell 18, 723-734.
Mozziconacci, J., Lavelle, C., Barbi, M., Lesne, A., and Victor, J. M. (2006). A physical
model for the condensation and decondensation of eukaryotic chromosomes. FEBS Lett
580, 368-372.
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Osborne, C. S., Chakalova, L., Brown, K. E., Carter, D., Horton, A., Debrand, E.,
Goyenechea, B., Mitchell, J. A., Lopes, S., Reik, W., and Fraser, P. (2004). Active
genes dynamically colocalize to shared sites of ongoing transcription. Nat Genet 36,
1065-1071.
Pickersgill, H., Kalverda, B., de Wit, E., Talhout, W., Fornerod, M., and van Steensel, B.
(2006). Characterization of the Drosophila melanogaster genome at the nuclear lamina.
Nat Genet 38, 1005-1014.
Raz, V., Carlotti, F., Vermolen, B. J., van der Poel, E., Sloos, W. C., Knaan-Shanzer, S., de
Vries, A. A., Hoeben, R. C., Young, I. T., Tanke, H. J., et al. (2006). Changes in lamina
structure are followed by spatial reorganization of heterochromatic regions in caspase-8activated human mesenchymal stem cells. J Cell Sci 119, 4247-4256.
Robinson, P. J., Fairall, L., Huynh, V. A., and Rhodes, D. (2006). EM measurements define
the dimensions of the "30-nm" chromatin fiber: evidence for a compact, interdigitated
structure. Proc Natl Acad Sci U S A 103, 6506-6511.
Robinson, P. J., and Rhodes, D. (2006). Structure of the '30 nm' chromatin fibre: a key role
for the linker histone. Curr Opin Struct Biol 16, 336-343.
Roguev, A., Schaft, D., Shevchenko, A., Aasland, R., Shevchenko, A., and Stewart, A. F.
(2003). High conservation of the Set1/Rad6 axis of histone 3 lysine 4 methylation in
budding and fission yeasts. J Biol Chem 278, 8487-8493.
Shiels, C., Islam, S. A., Vatcheva, R., Sasieni, P., Sternberg, M. J., Freemont, P. S., and
Sheer, D. (2001). PML bodies associate specifically with the MHC gene cluster in
interphase nuclei. J Cell Sci 114, 3705-3716.
Sivolob, A., Lavelle, C., and Prunell, A. (2003). Sequence-dependent nucleosome structural
and dynamic polymorphism. Potential involvement of histone H2B N-terminal tail
proximal domain. J Mol Biol 326, 49-63.
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Taddei, A., Van Houwe, G., Hediger, F., Kalck, V., Cubizolles, F., Schober, H., and Gasser,
S. M. (2006). Nuclear pore association confers optimal expression levels for an
inducible yeast gene. Nature 441, 774-778.
Toth, K., Brun, N., and Langowski, J. (2006). Chromatin compaction at the
mononucleosome level. Biochemistry 45, 1591-1598.
van Driel, R., Fransz, P. F., and Verschure, P. J. (2003). The eukaryotic genome: a system
regulated at different hierarchical levels. J Cell Sci 116, 4067-4075.
van Steensel, B., and Henikoff, S. (2000). Identification of in vivo DNA targets of chromatin
proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-428.
Visser, A. E., Verschure, P. J., Gommans, W. M., Haisma, H. J., and Rots, M. G. (2006).
Step into the groove: engineered transcription factors as modulators of gene expression.
Adv Genet 56, 131-161.
Volpi, E. V., Chevret, E., Jones, T., Vatcheva, R., Williamson, J., Beck, S., Campbell, R. D.,
Goldsworthy, M., Powis, S. H., Ragoussis, J., Trowsdale, J. and Sheer, D. (2000).
Large-scale chromatin organization of the major histocompatibility complex and other
regions of human chromosome 6 and its response to interferon in interphase nuclei. J
Cell Sci 113 (Pt 9), 1565-1576.
Wang, J., Shiels, C., Sasieni, P., Wu, P. J., Islam, S. A., Freemont, P. S., and Sheer, D.
(2004). Promyelocytic leukemia nuclear bodies associate with transcriptionally active
genomic regions. J Cell Biol 164, 515-526.
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