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Towards the visualization of genome activity at nanoscale
Joan C Ritland Politz
Address: Program in Cell Dynamics, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School,
377 Plantation Street, Worcester, MA 01605, USA. Email: firstname.lastname@example.org
Published: I February 2006
Genome Biology 2006, 7:304 (doi: 10.1 186/gb-2006-7- 1-304)
The electronic version of this article is the complete one and can be
found online at http://genomebiology.com/2006/7/1/304
2006 BioMed Central Ltd
A report on the Fifth Annual Nanostructural Genomics
meeting, Bar Harbor, USA, 7-10 September 2005.
It is a rare meeting where one can hear the latest develop-
ments in comparative genome analysis, relate these findings
to advances in understanding both the linear and three-
dimensional organization of the eukaryotic genome, and see it
all beginning to fit into the context of the structure and func-
tion of the nucleus, visualized using state-of-the art labeling
and microscopic techniques. These cross-disciplinary areas of
research have been presented by a diverse group of scientists
for the past five years at the Nanostructural Genomics meeting
at the Jackson Laboratory in Bar Harbor, and the 2005
meeting again gave attendees much food for thought.
In his opening address, Timothy O'Brien (Cornell University,
Ithaca, USA) outlined his view of how genomics, cell biology
and optical physics all work together to create an accurate
picture of nuclear structure and function, which can lead to
important insights into cellular form and function. He dis-
cussed his studies of a several megabase region surrounding
the mouse piebald locus, a genetically defined region named
after a coat-color gene within it. He used comparative
genomics to learn more about the nature of particular dele-
tions in this region that cause neonatal respiratory distress
and death. This information was coupled to high-resolution
visualization of gene-rich and gene-poor sections of this
region in the nucleus, and to the prediction of potential tran-
scription-factor binding sites for specific genes, such as
sprouty2, a gene involved in lung branching morphogenesis.
Chromosome sequence and structure
Considering comparative genomics at the sequence level,
Ross Hardison (Pennsylvania State University, University
Park, USA) discussed new algorithms designed to identify
important genomic regions that may not be coding sequence
but are nevertheless conserved between organisms. These
algorithms, including phastCons and RP (regulatory poten-
tial), use methodology such as alphabet clustering, where
different nucleotide-sequence patterns are each classified as
a letter of the alphabet, to reduce complexity and identify
higher-order sequence patterns that may be conserved 'in
spirit', if not in exact sequence, in the genome. Some algo-
rithms are better than others at identifying particular
sequence features; for example, phastCons identifies poten-
tial microRNA genes better than RP.
Moving to the next organizational level, chromatin, Jason
Lieb (University of North Carolina, Chapel Hill, USA)
described a novel approach to the study of the structure of
active chromatin in yeast. Using chromatin immunoprecipi-
tation (ChIP) he has compared the pattern of sites identified
by binding in vivo of the DNA-binding domain of the tran-
scription factor Leu3 to the pattern obtained by 'DIP ChIP',
in which naked DNA is allowed to bind the Leu3 protein in
vitro and is then crosslinked and immunoprecipitated. By
comparing the two experiments he found that promoters
contain fewer nucleosomes than do other DNA sites. In addi-
tion, Lieb showed that, even at the promoter, nucleosomal
organization is dynamic and influences the type of protein
that binds to a particular site. Evidence of promotor-specific
chromatin structure in the human genome came from Keji
Zhao (National Heart, Lung and Blood Institute, National
Institutes of Health, Bethesda, USA), who used ChIP in com-
bination with serial analysis of gene expression (SAGE) to
show that histone-acetylation islands in the human genome
correlate with active promoter regions but not with the
entire transcriptionally active gene.
The notion that the three-dimensional organization of chro-
matin reflects gene activity is intellectually satisfying but has
Genome Biology 2006, 7:304
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Ritland Politz, Joan C. Meeting Report: Towards the Visualization of Genome Activity at Nanoscale Dimensions, article, February 1, 2006; United States. (digital.library.unt.edu/ark:/67531/metadc931445/m1/1/: accessed November 19, 2018), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT Libraries Government Documents Department.