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)
