Genome structure/function...new news group

Graham Dellaire dellaire at ODYSSEE.NET
Sat Oct 12 22:58:19 EST 1996


Dear Bionet readers,

I am posting this note to ask for comments and suggestions for 
a new news group on genome/chromatin structure and function:

tentatively called bionet.genome.structure

The importance of chromatin/genomes structure for the processes of
replication, transcription and recombination is becoming more and more
apparent.  Chromatin context can affects the expression and replication
timing of a gene domain. Such interelationship between gene function and
changes in chromatin structure have been demonstrated through an
evolution of techniques from Dnase I sensitivity mapping to fluorescent
in situ hybridization (FISH.  I believe with such far reaching affects
on many areas of molecular biology, it is time we devoted a news group
to the study of genome structure and function. 
  

The following is a list of "possible" topics.  If you feel we should
include others or have suggestions as to the format of the news group
please reply via e-mail to: dellaire at odyssee.net

In addition to myself three tentative discussion leaders have already
been contacted and wish to encourage the formation of such a group.

They are:

Dr. Eric Milot (Erasmus, Neatherlands)
Dr. Ronald Hancock (U of Laval, Quebec, Canada)
Dr. Peter Cook (Oxford, England)

Here is the list of topics so far.


1. Genome/chromatin accessibility and recombination
                    -recombination hotspots (mieotic and mitotic)
                    -fragile sites 
                    -imprinting and recombination rates
		    -ectopic gene targeting and chromatin structure

3. Effect of DNA topology/structure(Triple strand, Z-DNA, cruciform,
bent etc)
   on biological processes such as:
                    -replication
                    -transcription
                    -recombination
                                              
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. 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)

7. 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
 
8. Techniques for genome/chromatin analysis
                    -Fluorescent Insitu Analysis
                    -psoralen, polyamine crosslinking
                    -In vivo nucleosome foot printing
                    -Dnase I/Micrococcal Nuclease sensitivity 
                    -VM26 Topoisomerase II site mapping
                    
9. 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

10. 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)

11. Phenomenon of Position Effect and Transvection
                    -in drosophila (HP1, polycomb, heterochromatization)
                    -in mammalian systems (silencing or variegated
                     expression of transgenes)

12. Epigenetic effects on gene function 
                    -imprinting
                    -methylation
                    -maintenance of early/late replication

13. Dosage compensation mechanisms and X chromosome inactivation
                    -MSL proteins of Drosophila
                    -XIC (Xist RNA) in mammals
                    -CpG methylation 
                    
14. Chromatin structure and DNA replication
                    -ORC1 protein of yeast 

15. DNA repair and chromatin structure
                    -TFIIH (transcription coupled repair)
                    -p53 
                    -BLM and AT genes
                    -poly-ADP-polymerase (PARP)



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