Proposal for GENSTRUCTURE/bionet.genome.gene-structure (moderated) Proposed USENET name: bionet.genome.gene-structure One line Description: Genome and chromatin structure and function Status: Moderated Proposed Moderation address: bionet-genome-gene-structure@net.bio.net (genstruc-moderator@net.bio.net is an alias for bionet-genome-gene-structure@net.bio.net) Moderator: Graham Dellaire Proposed mailing list name: GENSTRUCTURE Proposed e-mail address: genstruc@net.bio.net Charter: The purpose of the GENSTRUCTURE newsgroup is to provide a proper forum for the discussion of issues pertaining and involving genome and/or chromatin structure and function (see _Topics of Discussion_). Primarily it should enable those researchers who work in genome/chromatin structure or related fields to communicate ideas and information, as well as, provide a chance for collaboration among national and international research groups. --------------------------------------------------------------------- Topics of Discussion include: 1. Genome/chromatin accessibility and recombination -recombination hotspots (mieotic and mitotic) -fragile sites -imprinting and recombination rates -ectopic gene targeting and chromatin structure 2. 3D-organization of the nucleus -chromosome territories -nucleoli -nuclear lamina (telomere localization) -tissue or cell cycle dependent positioning of chromosomes -RNA tracking 3. Effect of Superhelicity and DNA topology/structure(Triple strand, Z-DNA, cruciform, bent etc) on biological processes such as: -replication (ex. replication fork barriers, initiation sites) -transcription (ex. promoter function in relation to superhelicity) -recombination (ex. Gin and Hin invertases and superhelicity) 4. Histones and Nucleosomes and chromatin structure/function -H1 repression of transcription -Post translational modification of histones acetylation (H4, H3), phosphorylation (H1, H3) and ubiquitination (H2A, H2B) -Histone variants (ex. H2A.Z in mammals, H5 of chicken) 5. Models of genome structure (Loop Domain Model, Channel Model, MegaBase Giant Loop Model, etc.) 6. Classical chromosome elements and their relationship to gene function -centromeres (constitutive heterochromatin and gene silencing) -telomeres (associated silencing and involvement in position effect) 7. Evolution of the Genome -isochores and base-content (GC vs. AT) -formation of gene clusters and syntenic mapping -repetitive elements (satellites, telomeric and centromeric (alpha) repeats, lines and sines) 8. Biologically important mutants and knockouts that affect genome/chromatin structure -ex. SNF/SWI, TOPO mutants in yeast -RAD 51,52,54 knockout mice -AT, BLM, FA mouse models 9. Techniques for genome/chromatin analysis -cytogenetic techniques (g banding, r and q) -Fluorescent In situ analysis(FISH) -Confocal microscopy -Electron microscopy -Electron microscopy In situ analysis (EMISH) -psoralen, polyamine crosslinking -In vivo nucleosome foot printing -Dnase I/Micrococcal Nuclease sensitivity -VM26 Topoisomerase II site mapping 10. Chromatin/DNA binding proteins and their effects on chromatin structure and/or gene expression -Polycomb proteins -Rap1 (telomere silencing) -alpha2-MCM1 (repression of MAT locus) -CENP A/B/C (centromere structure/function) -XCAP-C/E, SMC1/2 (chromatin Condensation) -remodeling of chromatin by SWI/SNF proteins -H-NS in bacteria (role in nucleoid topology vs. gene function) 11. Nuclear Matrix (NM) and Nuclear Lamina (NL) -cell cycle regulation of formation of NM and NL -transcription and replications factors and the concept of a dynamic NM (ex. tissue and temporal specificity) -role of NM in signal transduction (mechanistic vs. chemical signals) 12. Matrix attatchent regions (MAR's), domain boundaries and locus control regions (LCR's) and their relationship to gene structure and function. -definition of transcription/replication domains -model systems ex. betaglobin (LCR) SCS/SCS' of the Drosophila Heat Shock Locus (HS87a7) 13. Phenomenon of Position Effect and Transvection -in drosophila (HP1, polycomb, heterochromatization) -in mammalian systems (silencing or variegated expression of transgenes) -in fungi 14. Epigenetic effects on gene function -imprinting -methylation -maintenance of early/late replication 15. Dosage compensation mechanisms and X chromosome inactivation -MSL proteins of Drosophila -XIC (Xist RNA) in mammals -CpG methylation 16. Chromatin structure and DNA replication -ORC1 protein of yeast -origins of replication (association with cruciform, bent DNA and MARS) 17. Specialized methods of nuclear packaging -bacterial nucleoid -packaging of DNA in spermatozoa 18. DNA repair and chromatin structure -TFIIH (transcription coupled repair) -p53 -BLM and AT genes -poly-ADP-polymerase (PARP) 19. Mechanisms of genomic instability -during oncogenesis -process of chromosomal aberration (stable and unstable) (ex. role of micronuclei in the process) -chromosomal aberration during aging and mechanisms of instability (ex. telomeres and telomerase) In addition this newsgroup provides: A forum for the exchange of information about future congresses and meetings in areas of molecular biology relating to genome structure/function. A forum for the exchange of information about textbooks, internet resources, visual materials, and computer programs. A source of quick help for last-minute troubleshooting, sources of materials, and practical advice; in areas such as -Specific common resources (ex. primers, antibodies, vectors) -Genome analysis techniques -Transgenic models and mutant cell lines Moderation Policy: Mass-posted commercial messages, chain letters, and similar postings not associated with or pertaining to the study of genome/chromatin structure and function will be deleted without comment. Inappropriate messages posted in good faith will be returned to the sender. Messages not strictly within the charter but likely to be of interest to many subscribers (e.g., messages dealing with transcription and replication factors) will be accepted. Subscribers are welcome from universities or any academic institutions, government agencies, medical institutions, and industrial or commercial organizations. Contributions within the functions outlined above are encouraged. Proposed discussion leaders: *Note: Area of expertise is written in brackets Graham Dellaire, e-mail: dellaire@odyssee.net (gdella@po-box.mcgill.ca) Institut du Cancer de Montreal Centre de Recherche L.C. Simard 1560 Sherbrooke Street East, Montreal, Quebec, Canada H2L 4M1 telephone:1 (514) 876 6936; fax: (514) 876 5476 *(Expertise:chromatin structure and recombination; Recombination Access Mapping (RAM); genome structure analysis) Ronald Hancock, e-mail: ronald.hancock@crhdq.ulaval.ca Professor Laval University Cancer Research Centre 1 rue de l'Arsenal Quebec, Canada G1R 2J6 telephone: 1 (418) 691-5281; fax: 1 (418) 691-5439 *(Expertise:genome organisation in vivo; models of genome structure; topoisomerases; VM26 topoisomerase II site mapping) Eric Milot, e-mail: milot@ch1.fgg.eur.nl Faculty of Medicine Dept. of Cell Biology and Genetics P.O. Box 1738 3000 DR Rotterdam The Netherlands telephone: 3110 4087164; fax: 3110 4360225 *(Expertise:Chromatin context and transcription; Polycomb protein; position effect variegation; chromosome and nuclear organisation; dosage compensation) **Tentative Discussion leader** Peter Cook, e-mail: peter.cook@pathology.oxford.ac.uk Professor of Cell Biology, The Sir William Dunn School of Pathology, South Parks Road, Oxford, OX1 3RE, UK. Telephone (direct line) : +44/0 1865 275528 Telephone (switchboard) : +44/0 1865 275500 Fax : +44/0 1865 275501 http://www.molbiol.ox.ac.uk/www/users/counsell/cook.htm (Expertise:Chromatin/Genome Structure and Function in regard to transcription and replication)