CALL FOR DISCUSSION: GENSTRUCTURE/bionet.genome.gene-structure (moderated)

BIOSCI Administrator biosci-help at net.bio.net
Thu Oct 31 14:54:01 EST 1996


We have received a proposal below for a new newsgroup,

GENSTRUCTURE/bionet.genome.gene-structure (moderated)

Discussion on the following proposal will now be open through 10 Nov
on BIOFORUM/bionet.general (*not* on BIONEWS/bionet.announce).  For
those who are not on the BIOFORUM/bionet.general newsgroup currently,
either read bionet.general on USENET or contact one of the following
biosci addresses to sign up by e-mail:

Subscription Address                 Location
--------------------                 --------
biosci at daresbury.ac.uk               Europe, Africa, and Central Asia
biosci at net.bio.net                   Americas and the Pacific Rim

One warning, however: BIOFORUM/bionet.general is a "chatty" newsgroup
and many other items will be discussed there besides this newsgroup
proposal.  USENET news access is definitely better than e-mail if you
want to monitor only this discussion.

Discussion Guidelines
---------------------
Please do not post one-line messages saying things like "I am in favor
of such a newsgroup".  We will collect votes later.  The discussion
period is an opportunity for anyone to bring up reservations about the
proposed charter below and to propose modifications prior to the vote.
If the charter is perfect as is, then there is no need for anyone to
say anything!!!

The newsgroup discussion leader may submit a revised proposal in light
of the discussion, and the new charter would be included in the call
for votes which will go out on 11 November (Newsgroup Discussion
leaders - please note this deadline - if no revisions are received
before the deadline, the original charter will be voted on.).

Please be aware that only one vote is counted per e-mail address, so
it is necessary to have your own account in order to vote.  Multiple
votes from the same address are not accepted.  If you are interested
in the following newsgroup, but do not have an e-mail address of your
own, please obtain one from your computer center before the call for
votes is issued.

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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 at net.bio.net
                                (genstruc-moderator at net.bio.net
                                is an alias for
                                bionet-genome-gene-structure at net.bio.net)

Moderator:			Graham Dellaire

Proposed mailing list name:     GENSTRUCTURE

Proposed e-mail addresses:      genstruc at net.bio.net
                                genstruc at daresbury.ac.uk

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.

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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 at odyssee.net (gdella at 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 at 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 at 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 at 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)
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