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Genome Biology
 
February 25 - 27
Isabel Carreira
Biologia Médica, Piso 2, Subunidade 1, Faculdade de Medicina, Pólo 3
(edifício contíguo ao IBILI)
COORDINATOR: Isabel Marques Carreira, Laboratório de Citogenética, Faculdade de Medicina da Universidade de Coimbra; Portugal; Tel: +351 239480027; i_marques@hotmail.com

LECTURERS:
Ana Pombo Nuclear Organisation Group, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, United Kingdomana.pombo@csc.mrc.ac.uk;tel: +442083838232;
Isabel Marques Carreira
Laboratório de Citogenética, Faculdade de Medicina da Universidade de Coimbra, Portugal; Tel: +351 239480027; i_marques@hotmail.com
Joana Barbosa de Melo
Laboratório de Citogenética, Faculdade de Medicina da Universidade de Coimbra, Portugal; Tel: +351 239480027; jbmelo@cnc.cj.uc.pt
Thomas Liehr
Institut für Humangenetik und Anthropologie, Postfach D-07740 Jena, Germany; Tel: 49 3641 9355-35; i8lith@mti.uni-jena.de

COURSE SCHEDULE:

Monday, 25/02/2008Morning
9.30 – Methodologies in the study of chromosomes.
Isabel Marques Carreira
10.00 –Chromosomal behaviour and mechanisms of errors in meiosis and mitosis. Implications in fertility and mental retardation.
Isabel Marques Carreira
11.30 – Coffee break
12.00 - Numerical, balanced and unbalanced structural chromosomal abnormalities and their clinical implications.
Isabel Marques Carreira
Afternoon
14.30 – Resolution of practical problems.
Isabel Marques Carreira
16.00– End of session

Tuesday, 26/02/2008Morning
09.30 – Basics of molecular cytogenetics
Thomas Liehr
10.30 – Coffee break
11.00 – Recent developments in molecular cytogenetics.
Thomas Liehr
12.00 – Interphase FISH
Thomas Liehr
Afternoon
14.30 – Molecular Cytogenetic in Tumor Cells
Thomas Liehr
15.30 – Array CGH – New boundaries of molecular cytogenetics
Joana B Melo
16.30 – End of session

Wednesday, 27/02/2008Afternoon
14.30 – Analysis and discussion of papers I
Chaired by Thomas Liehr, Joana B Melo and Isabel M Carreira
Schmidt S, Claussen U, Liehr T, Weise A. Evolution versus constitution: Differences in chromosomal inversion. Hum Genet 2005, 117: 213-219.
Students presenting: Ana Sofia Azevedo, Filipe Leal and Susana Ribeiro
Balikova I, Martens K, Melotte C, Amyere M, Van Vooren S, Moreau Y, Vetrie D, Fiegler H, Carter NP, Liehr T, Vikkula M, Matthijs G, Fryns JP, Casteels I, Devriendt K, Vermeesch JR. Autosomal-dominant microtia linked to five tandem copies of a copy-number-variable region at chromosome 4p16. Am J Hum Genet 2008, 82:181-187.
Students presenting: Ana Sofia Cabral, João Noutel Santos and Manuel Afonso Barroso
17.00– Social Brainstorming over a cheese and wine

Thursday, 28/02/2008Morning
09.30 –Functional organization of the genome in the interphase cell nucleus I. Chromosomes in interphase, Position, Translocations, Gene expression. Long-range chromatin interactions. Functional organization.
Ana Pombo
11.00 – Coffee break
11.30 –Functional organization of the genome in the interphase cell nucleus I. Chromosomes in interphase, Position, Translocations, Gene expression. Long-range chromatin interactions. Functional organization. (cont)
Ana Pombo
Afternoon
14.30 - Methodologies for fluorescence in situ hybridization (FISH) and chromosome conformation capture (3Cs). FISH, 3D-FISH, immuno-FISH, cryo-FISH, 3Cs, 4C, chromatin immunoprecipitation (ChIP).
Ana Pombo
16.00 – End of session

Friday, 29/02/2008Morning
09.30 - Functional organization of the genome in the interphase cell nucleus II.
Nuclear compartmentalization, Gene expression, Transcription factories.
Ana Pombo
Afternoon
14.30 – Quiz (two broad conceptual questions)
16.00 - Seminar: Poised RNA polymerase II complexes in epigenetics and genome architecture. Ana Pombo, MRC, Imperial College, London
REFERENCES:
A. Supplemental Reading for Thomas Liehr’ sessions
Zoo-FISH
1. K Mrasek, et al. Reconstruction of the female Gorilla gorilla karyotype by Zoo-FISH using 25-color FISH and multicolor banding (MCB). Cytogenet Cell Genet 2001, Vol. 93, pp 242-248.
2. K Mrasek, et al. Detailed Hylobates lar karyotype defined by 25-color FISH and multicolor banding. Int J Mol Med, Int J Mol Med 2003, Vol 12, pp 139-146
3. M Gross, et al. A molecular cytogenetic study of chromosome evolution in chimpanzee. Cytogenet Genome Res 2006, Vol 112, pp67-75.
Chromosome 9 pericentric region heteromorphisms
1. H Starke, et al. Homologous sequences at human chromosome 9 bands p12 and q13-21.1 are involved in different patterns of pericentric rearrangements. Eur J Hum Genet 2002, Vol. 10, pp 790-800.
2. S Schmidt, U Claussen, T Liehr, A Weise. Evolution versus constitution: Differences in chromosomal inversion. Hum Genet 2005, Vol 117, pp 213-219.
Acrocentric chromosome polymorphisms and hidden euchromatic
translocations
1. V Trifonov, et al. Enlarged chromosome 13 p-arm hiding a cryptic partial trisomy 6p22.2-pter. Prenat Diagn, Vol 23, pp 427-430.
2. H Starke, et al. 3 cases with enlarged acrocentric p-arms * 2 cases with cryptic partial trisomies. J Histochem Cytochem, 2005, Vol. 53, pp 359-360.
Small supernumerary marker chromosomes
1. T Liehr, et al. Small supernumerary marker chromosomes (sSMC) in humans. Cytogenet Genome Res, Vol 107, pp 55-67.
2. T Liehr. Familial small supernumerary marker chromosomes are predominantly inherited via the maternal line. Genet Med 2006, Vol 8, pp 459-462.
3. T Liehr, et al. Small supernumerary marker chromosomes - progress towards a genotype-phenotype correlation. Cytogenet Genome Res 2006, Vol 112, pp 23-34.
4. T Felka, et al. U Claussen. DNA degradation during maturation of erythrocytes- molecular cytogenetic characterization of Howell-Jolly bodies. Cytogenet Genome Res 2007, vol 119, pp 2-8.
5. T Liehr, A Weise. Frequency of small supernumerary marker hromosomes in prenatal, newborn, developmentally retarded and nfertility diagnostics. Int J Mol Med 2007, Vol 19, pp 719-731.
Chromosome structure
1. A Kuechler, et al. Detection of microdeletions in the short arm of the X chromosome by chromosome stretching. Cytogenet Cell Genet. 2001, Vol. 95, pp 12-16.
2. H Lehrer, et al. The hierarchically organized splitting of chromosomal bands into sub-bands analyzed by multicolor banding (MCB). Cytogenet Genome Res 2004, Vol 105, pp 25-28.
3. A Weise, et al. Evidence for interphase DNA decondensation transverse to the chromosome axis - a multicolor banding (MCB) analysis. Int J Mol Med 2002, Vol 9, pp 359-361.
Case report as example for combination of different approaches
I Balikova, et al. Autosomal-dominant microtia linked to five tandem copies of a copy-number-variable region at chromosome 4p16. Am J Hum Genet 2008, 82:181-187.

B. Supplemental Reading for Ana Pombo’ sessions:
Reviews:
1. Pombo A., Branco M.R. Functional organization of the genome during interphase. Current Opinion in Genetics and Development 2007 17: 451-455.
2. Misteli, T, Beyond sequence: cellular organization of genome function. Cell 2007 128: 787-800.
Paper describing:
Cryo-FISH and chromosome intermingling
Branco, M.R. and A. Pombo, Intermingling of chromosome territories in interphase suggests role in translocations and transcription-dependent associations. PLoS Biol, 2006. 4(5): p. e138.
Chromosome Conformation Capture (3Cs)
Dekker, J., Rippe, K., Dekker, M., and Kleckner, N. (2002). Capturing chromosome conformation. Science 295, 1306-1311.
3Cs in mammalian cells, b-globin locus
Tolhuis, B., et al., Looping and interaction between hypersensitive sites in the active beta-globin locus. Mol Cell, 2002. 10(6): p. 1453-65.
RNA-TRAP
Carter, D., et al., Long-range chromatin regulatory interactions in vivo. Nat Genet 2002 32: 623-6.
Interchromosomal interactions Th2-IFNg in naïve cells
Spilianakis, C.G., et al., Interchromosomal associations between alternatively expressed loci. Nature, 2005. 435(7042): p. 637-45.
Interchromosomal interactions H element and OR genes
1. Lomvardas, S., et al., Interchromosomal interactions and olfactory receptor choice. Cell, 2006. 126(2): p. 403-13.
2. Fuss SH, et al., Local and cis effects of the H element on expression of odorant receptor genes in mouse. Cell 2007 130: 373-84.
4Cs
3. Simonis, M., et al., Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat Genet, 2006. 38: 1348-54.
Chromatin organization at the nuclear lamina
Pickersgill, H., et al., Characterization of the Drosophila melanogaster genome at the nuclear lamina. Nat Genet, 2006. 38: 1005-1014.

Other relevant papers:
Chromosome arrangements in mammalian nuclei
1. Parada, L.A., et al., Conservation of relative chromosome positioning in normal and cancer cells. Curr Biol, 2002. 12: 1692-7.
2. Croft, J.A., et al., Differences in the localization and morphology of chromosomes in the human nucleus. J Cell Biol, 1999. 145: 1119-31.
3. Bridger, J.M., et al., Re-modelling of nuclear architecture in quiescent and senescent human fibroblasts. Current Biology, 2000. 10: 149-152.
4. Tanabe, H., et al., Evolutionary conservation of chromosome territory arrangements in cell nuclei from higher primates. Proc Natl Acad Sci U S A, 2002. 99: 4424-9.
Transcription factories and stochastic gene activity
1. Muller, W.G., et al. Organization of chromatin and histone modifications at a transcription site. J Cell Biol 2007, 177: 957-67.
2. Osborne, C.S., et al., Active genes dynamically colocalize to shared sites of ongoing transcription. Nat Genet, 2004. 36: 1065-71.
3. Levsky, J. M., et al., Single-cell gene expression profiling. Science, 2002 297: 836-840.
4. Pombo, A., et al., Regional specialization in human nuclei: visualization of discrete sites of transcription by RNA polymerase III. EMBO J., 1999. 18: 2241-53.
5. Osborne, C.S., et al., Myc dynamically and preferentially relocates to a transcription factory occupied by IgH. PLoS Biol 2007, 5: e630.
More inter-chromosomal interactions
2. Augui, S., et al., Sensing X Chromosome Pairs Before X Inactivation via a Novel X-Pairing Region of the Xic, Science, 2007, 318: 1632-1636.
3. Zhao, Z., et al., Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions. Nat Genet, 2006, 38: 1341-1347.
4. Bacher, C.P., et al., Transient colocalization of X-inactivation centres accompanies the initiation of X inactivation. Nat Cell Biol, 2006. 8: 293-9.
5. Ling, J.Q., et al., CTCF mediates interchromosomal colocalization between Igf2/H19 and Wsb1/Nf1. Science, 2006. 312: 269-72.
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