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Topic: Nucleosome

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Nucleosome core particle

Organelle

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	Nucleosome
		Dimensions of nucleosome stack 6 X 10 nm figure 20.5 (Genes VIII) and figure a, b, and c.
		nucleosomal ladder - native gel, >90% of DNA is represented figure 20.8 (Genes VIII) b.
		Placement of H1 suggest that it binds to the linker DNA prevalent idea is that H1 seals the DNA in the nucleosome by binding DNA as it enters and leaves 5.
	www.siumed.edu /~bbartholomew/course_material/nucleosome.html (372 words)

	Nucleosome
		Nucleosome: Subunit of chromatin composed of a short length of DNA wrapped around a core of histone proteins.
		A second histone (H1 in the illustration) fastens the DNA to the nucleosome core.
		Nucleosomes are usually packed together, with the aid of a histone (H1,) to form a 30nm large fiber.
	www.accessexcellence.org /AB/GG/nucleosome.html (230 words)

	Optical tweezers used to uncoil DNA strands
		The three stages became apparent when a nucleosome was uncoiled as the DNA was stretched with increasing force, said Brent Brower-Toland, lead author of the article and a research associate in Cornell's Laboratory of Atomic and Solid State Physics.
		Nucleosomes seem to stand in the way of a genetic information-transfer process that happens millions of times a day in the cells of our bodies.
		With one end of a nucleosomal DNA strand fastened to microscope slide and the other end attached to a synthetic microsphere and optically trapped in a laser beam, the researchers could accurately gauge dynamic changes in bond strength and organization as DNA was forced to uncoil from histones.
	www.news.cornell.edu /Chronicle/02/2.28.02/nucleosomes.html (838 words)

	Nucleosome
		A nucleosome is a unit made of DNA and histones in eukaryotes.
		Stacked nucleosomes are called 10-nm-fiber and have a packing rate of ~6, compared to "free" DNA (per nm length).
		A chain of nucleosomes can be arranged in a 30-nm-fiber, a helical structure with a packing rate of ~40.
	www.ebroadcast.com.au /lookup/encyclopedia/nu/Nucleosome.html (133 words)

	[No title] (Site not responding. Last check: 2007-09-10)
		I have developed a model of the nucleosome in which DNA is treated as a negatively charged elastic rod, and the histone core is a positively charged cylinder.
		Experimentally, the nucleosome is unfolded at high salt concentrations, and re-folds as the salt concentration is lowered to about 0.8 M NaCl.
		In the unfolded nucleosome it is non-zero only in a tiny skin layer around the DNA and the core, and the corresponding electrostatic free energy, which is proportional to the volume occupied by the field, is almost zero.
	www.scripps.edu /~onufriev/RESEARCH/nucleosome.html (420 words)

	Catalytic activity of the yeast SWI/SNF complex on reconstituted nucleosome arrays
		Fourth, as a rigorous means to obtain an estimate of the level of nucleosome occupancy of the array templates, reconstituted nucleosome arrays were subjected to a sedimentation velocity analysis in the analytical ultracentrifuge.
		Since compaction of nucleosome arrays is predicted further to occlude factor binding sites, the quantitative restriction endonuclease assay that we have described here may prove invaluable for the functional dissection of histone acetyltransferases and histone deacetylases, and for the development of reagents that influence the biochemical activities of effectors of chromatin remodeling.
		Nucleosome arrays were reconstituted on the DNA templates in a Spectra/Por microdialyzer (Spectrum, Houston, TX), using the salt dialysis protocol of Hansen and Lohr (1993), except that 100 mM NaCl was used as the final dialysis step.
	www.nature.com /emboj/journal/v16/n22/full/7590648a.html (8535 words)

	Karolin Luger
		The nucleosome is the elemental repeating unit in chromatin, consisting of two copies each of the four histone proteins (the histone octamer) around which 146 base pairs of DNA are wrapped in nearly two turns of a tight superhelix.
		Nucleosomal DNA is highly distorted and partially occluded from the solvent because of its tight interaction with the histone octamer.
		NAP-1-dependent histone exchange and nucleosome sliding are independent of ATP and rely on the presence of the carboxyl-terminal acidic domain of yeast NAP-1, even though this region is not required for histone binding and chromatin assembly.
	www.hhmi.org /research/investigators/luger.html (1110 words)

	Low-Resolution Nucleosome Mapping
		Low resolution nucleosome mapping is a technique quite similar to DNA footprinting that employs micrococcal nuclease digestion to localize nucleosomes on a stretch of DNA.
		Microccocal nuclease is an enzyme that makes double strand cuts in DNA between nucleosomes when incubated with cell nuclei or permeabilized cells.
		The quality of MNase analysis is dependent on the integrity of the chromatin substrate and thus use of permeabilized cells is preferable to nuclear isolation.
	www.iscid.org /encyclopedia/Low-Resolution_Nucleosome_Mapping (241 words)

	A critical epitope for substrate recognition by the nucleosome remodeling ATPase ISWI -- Clapier et al. 30 (3): 649 -- ...
		of the H4 tail on the nucleosome is crucial for the activation
		5 Becker,P.B. and Hörz,W. (2002) ATP-dependent nucleosome remodeling.
		26 Luger,K. and Richmond,T.J. (1998) The histone tails of the nucleosome.
	nar.oxfordjournals.org /cgi/content/full/30/3/649 (4731 words)

	Genome Biology \| Full text \| Global nucleosome occupancy in yeast
		For example, the distribution of nucleosomes, the fundamental units of chromatin, is poorly understood on a gene-specific basis, much less a global basis [2].
		High occupancy by nucleosomes is thought to be generally repressive [3], and extensive remodeling (and loss) of nucleosomes occurs in the promoters of genes undergoing activation [4].
		Hence, the nucleosome loss associated with Rap1 recruitment is most likely to require additional proteins, such as Esa1, a histone acetyltransferase recruited by Rap1 under exponential growth conditions but released in stress [30].
	genomebiology.com /2004/5/9/R62 (6067 words)

	Scientists discover a genetic code for organizing DNA within the nucleus
		The bead-like nucleosomes are strung along the entire chromosome, which is itself folded and packaged to fit into the nucleus.
		The precise location of the nucleosomes along the DNA is known to play an important role in the cell's day to day function, since access to DNA wrapped in a nucleosome is blocked for many proteins, including those responsible for some of life's most basic processes.
		To identify this nucleosome positioning code, the research team used probabilistic models to characterize the sequences bound by nucleosomes, and they then developed a computer algorithm to predict the encoded organization of nucleosomes along an entire chromosome.
	www.eurekalert.org /pub_releases/2006-07/acft-sda071906.php (806 words)

	A Theoretical Model for the Prediction of Sequence-Dependent Nucleosome Thermodynamic Stability -- Anselmi et al. 79 ...
		A theoretical model for predicting nucleosome thermodynamic stability in terms of DNA sequence is advanced.
		The nucleosome, the elemental unit of chromatin, is the association complex of DNA with the histone octamer.
		However, in the case of nucleosome, it is reasonable that the presence of the histone core changes the topography of the inner
	www.biophysj.org /cgi/content/full/79/2/601 (5570 words)

	Interactive Fly, Drosophila
		To test whether this binding depends on the unstructured histone tails that extend from the nucleosome core, the nucleosome electrophoretic mobility assay was repeated using trypsinized nucleosomes.
		When the naked DNA and the nucleosome are run side by side in the gel shift assay, the pattern of band shift is different.
		The histone tails are apparently relatively unstructured in the nucleosome core and are thought to extend far enough beyond the core particle to permit contacts with the DNA wrapped on the surface and/or contacts with adjacent nucleosomes.
	www.sdbonline.org /fly/polycomb/hp1.htm (4456 words)

	Sequence-specific Recognition of DNA in the Nucleosome by Pyrrole-Imidazole Polyamides (Site not responding. Last check: 2007-09-10)
		Probing the accessibility of the minor groove of nucleosomal DNA with pyrrole-imidazole polyamides.
		In some instances, polyamides bind to the nucleosome core particle with equal affinity compared to free DNA (polyamides 1, 2, and 3; turquois regions in the figure).
		In the most extreme cases, 25- to 50-fold reduced affinity for the nucleosome relative to the free DNA is observed (5 and 6; magenta regions).
	www.scripps.edu /mb/gottesfeld/Sequence-specific.htm (331 words)

	Both DNA and Histone Fold Sequences Contribute to Archaeal Nucleosome Stability -- Bailey et al. 277 (11): 9293 -- ... (Site not responding. Last check: 2007-09-10)
		Nucleosomes are highly conserved structures that form the primary level of genome compaction and archiving into chromatin
		Archaeal nucleosomes (assembled by incubation of 250 ng of HMfA or HMfB with 100 ng of the (TTTAAAGCCG)
		The sequence of clone 1 DNA protected from MN digestion by HMfB incorporation into an archaeal nucleosome is shown on the DNA strands assembled in the predominant rotational and translational positions established for clone 1 DNA.
	www.jbc.org /cgi/content/full/277/11/9293 (6159 words)

	Supercoiling, Topoisomerases and Nucleosome Structure
		Nucleosomes are subsequently wound into chromatin filaments which can be organised by scaffolding proteins.
		While, on the one hand the nucleosome provides a stable structure that protects DNA, on the other hand enzymes such as DNA or RNA polymerase cannot gain access to the DNA template as long as it is sequestered in the nucleosome.
		The positively charged amino-termini of H2B, H3 and H4 protrude from the core nucleosome structure and are the targets for acetylation.
	www.mun.ca /biochem/courses/3107/Lectures/Topics/supercoiling.html (1919 words)

	De novo nucleosome assembly: new pieces in an old puzzle -- Verreault 14 (12): 1430 -- Genes and Development
		The N-terminal domains of histones H3 and H4 are not necessary for chromatin assembly factor 1-mediated nucleosome assembly onto replicated DNA in vitro.
		Nucleosome assembly by a complex of CAF-1 and acetylated histones H3/H4.
		Nucleosomal DNA regulates the core-histone-binding subunit of the human Hat1 acetyltransferase.
	www.genesdev.org /cgi/content/full/14/12/1430 (5582 words)

	ETH Zurich: Institute for Molecular Biology & Biophysics Nucleosome
		The nucleosome is the fundamental repeating unit of chromatin, and both its internal and higher-order structures are crucial to the functioning of DNA in the nucleus.
		We solved the X-ray structure of the nucleosome core of chromatin originally at 2.8 Å resolution (Figure 1) [1] and ultimately at 1.9 Å resolution (Figure 2) [2-4].
		Currently, we are using robotics to extend the amount of high-resolution structural data available for DNA in the nucleosome.
	www.mol.biol.ethz.ch /groups/richmond/projects/nucleosome (488 words)

	The Daily Transcript: Nucleosome Binding Sites
		By regulating how tight nucleosome binding is (or exactly where nucleosomes bind) the cell can control how active a gene is. Many people are trying to figure out how this nucleosome rearrangement takes place - the field is usually referred to as the chromosome remodelling field.
		So if a piece of DNA contained five nucleosomes the first two being unmodified the next two containing one type of modification and the last nucleosome containing a second type of modification, the histones bound to the two daughter strands would carry five nucleosomes each nucleosome containing the same modification found in the parental DNA.
		This inherited nucleosome state contributes to what is known as epigenetics - the inheritance of information that goes beyond the nucleotide sequence of the genome (in this case the histone modifications present at various positions within a genome).
	scienceblogs.com /transcript/2006/08/nucleosome_binding_sites_1.php (1006 words)

	nucleosome
		nucleosome Spherical sub-units of eukaryotic chromatin that are composed of a core particle consisting of an octamer of histones (two molecules each of histones H
		The protein component of chromatin, which consists of nucleosome octamers for the most part, is much more than a passive packing material--it plays an active...
		This enzyme modifies histones so as to make the wrapped DNA inaccessible to the gene-expression machinery, creating a silenced nucleosome configuration known...
	www.mongabay.com /igapo/biotech/nucleosome.html (111 words)

	Young Lab
		We profiled nucleosome modifications across the yeast genome using chromatin immunoprecipitation coupled with DNA microarrays to produce high-resolution genome-wide maps of histone acetylation and methylation.
		These maps take into account changes in nucleosome occupancy at actively transcribed genes, and in doing so, revise previous assessments of the modifications associated with gene expression.
		Both acetylation and methylation of histones are associated with transcriptional activity, but the former occurs predominantly at the beginning of genes whereas the latter can occur throughout transcribed regions.
	web.wi.mit.edu /young/nucleosome (144 words)

	Nucleosome mobilization and positioning by ISWI-containing chromatin-remodeling factors -- Längst and Becker 114 ...
		the sliding of a nucleosome from the middle of a fragment to
		Spontaneous mobility of nucleosomes is inhibited by binding
		Workman, J. and Kingston, R. Alteration of nucleosome structure as a mechanism of transcriptional regulation.
	jcs.biologists.org /cgi/content/full/114/14/2561 (5353 words)

	Cornell News: Nucleosome uncoiling
		The three stages became apparent when a nucleosome was uncoiled as the DNA was stretched with increasing force, says Brent Brower-Toland, lead author of the article and a research associate in Cornell's Laboratory of Atomic and Solid State Physics.
		But, if we released the fiber before the histones were detached, the nucleosomes were able to reassemble themselves and the whole process could be repeated." "Of course the basic plan -- nucleosomes and higher-order structures condensing DNA into a manageable space -- has been known for some time," Wang says.
		The researchers used optical tweezers to probe the barrier encountered by enzymes like RNA polymerase that prompt DNA in nucleosomes to uncoil from histones.
	www.news.cornell.edu /releases/Feb02/nucleosomes_uncoil.hrs.html (905 words)

	A determining influence for CpG dinucleotides on nucleosome positioning in vitro -- Davey et al. 32 (14): 4322 -- ...
		The ovals depict dominant positions adopted by histone octamers in reconstituted chromatin (3): nucleosomes 4 (–427 to –281), 5A (–354 to –208), 5B (–318 to –172) and 6 (–206 to –62).
		Nucleosome boundaries are labelled as in Figure 1.
		or derivative sequence: the upper of the two bands labelled as nucleosome 4 marks a nucleosome (occupying –447 to –301) whose downstream boundary sits at this element; similarly, the lower of the two bands labelled as 5B marks a nucleosome (occupying –303 to –157) whose upstream boundary sits at this element.
	nar.oxfordjournals.org /cgi/content/full/32/14/4322 (5999 words)

	A genomic code for nucleosome positioning : Abstract : Nature
		Eukaryotic genomes are packaged into nucleosome particles that occlude the DNA from interacting with most DNA binding proteins.
		Nucleosomes have higher affinity for particular DNA sequences, reflecting the ability of the sequence to bend sharply, as required by the nucleosome structure.
		This nucleosome positioning code may facilitate specific chromosome functions including transcription factor binding, transcription initiation, and even remodelling of the nucleosomes themselves.
	www.nature.com /nature/journal/v442/n7104/abs/nature04979.html (267 words)

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