Independent and complementary methods for large-scale structural analysis of mammalian chromatin.

Independent and complementary methods for large-scale structural analysis of mammalian chromatin. Research Abstract Details 

Research Abstract Table of Contents

Jump to the:

Independent and complementary methods for large-scale structural analysis of mammalian chromatin. Abstract Text:

Jonathan H Dennis,Hua-Ying Fan,Sheila M Reynolds,Guocheng Yuan,James C Meldrim,Daniel J Richter,Daniel G Peterson,Oliver J Rando,William S Noble,Robert E Kingston,

The fundamental building block of chromatin, the nucleosome, occupies 150 bp of DNA in a spaced arrangement that is a primary determinant in regulation of the genome. The nucleosomal organization of some regions of the human genome has been described, but mapping of these regions has been limited to a few kilobases. We have explored two independent and complementary methods for the high-throughput analysis of mammalian chromatin structure. Through adaptations to a protocol used to map yeast chromatin structure, we determined sites of nucleosomal protection over large regions of the mammalian genome using a tiling microarray. By modifying classical primer extension methods, we localized specific internucleosomally cleaved mammalian genomic sequences using a capillary electrophoresis sequencer in a manner that allows high-throughput nucleotide-resolution characterization of nucleosome protection patterns. We developed algorithms for the automated and unbiased analysis of the resulting data, a necessary step toward large-scale analysis. We validated these assays using the known positions of nucleosomes on the mouse mammary tumor virus LTR, and additionally, we characterized the previously unreported chromatin structure of the LCMT2 gene. These results demonstrate the effectiveness of the combined methods for reliable analysis of mammalian chromatin structure in a high-throughput manner.

Independent and complementary methods for large-scale structural analysis of mammalian chromatin. Publishing Authors By Initials

JH Dennis,HY Fan,SM Reynolds,G Yuan,JC Meldrim,DJ Richter,DG Peterson,OJ Rando,WS Noble,RE Kingston,

For similar investigative techniques: genetic techniques: sequence analysis: sequence analysis, dna research abstracts see: investigative techniques: genetic techniques: sequence analysis: sequence analysis, dna research

PUBMED ID PMID:

MEDLINE DATE:

Independent and complementary methods for large-scale structural analysis of mammalian chromatin. Journal Published:

PUBLICATION TYPE: Research Support, U.S. Gov't,

Journal: Genome research

VOLUME: 17

Page Numbers: 928-39

Journal Abbreviation: Genome Res.

ISSN: 1088-9051

DAY: 3

MONTH: Jun

YEAR: 2007

Independent and complementary methods for large-scale structural analysis of mammalian chromatin. Information

Number of References:

LANGUAGE: eng

NlmUniqueID: 9518021

Independent and complementary methods for large-scale structural analysis of mammalian chromatin. Keywords Mesh Terms:

KEYWORDS: Sequence Analysis, DNA

MESH TERMS: genetics

Chemical & Substance for Abstract: Independent and complementary methods for large-scale structural analysis of mammalian chromatin. Information

Substance Name: Nucleosomes

Registry Number: 0

Grant and Affiliation Information for Independent and complementary methods for large-scale structural analysis of mammalian chromatin.

AFFILIATION: Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.

Country: United States

AGENCY: United States NHGRI

GRANT: HG003161

ACRONYM: HG

MEDLINETA: Genome Res

REFSOURCE:

DATABASENAME:

ACCESSION NUMBER:

Number Hits: 0

Independent and complementary methods for large-scale structural analysis of mammalian chromatin Related Publications

• A clinical trial of an antidepressant, tranylcy-promine ("Parnate").
• A not so Pacific voyage: the 'floating laboratory' of Nicolas Baudin.
• Antiplasmodial activity of compounds from Sloanea rhodantha (Baker) Capuron var. rhodantha from the Madagascar rain forest.
• Antiproliferative Cassane Diterpenoids of Cordyla madagascariensis ssp. madagascariensis from the Madagascar Rainforest(1).
• Antiproliferative cardenolides of an Elaeodendron sp. from the Madagascar rain forest(1).
• Antiproliferative prenylated stilbenes and flavonoids from Macaranga alnifolia from the Madagascar rainforest.
• Antiproliferative xanthones of Terminalia calcicola from the Madagascar rain forest.
• Bridging converts a noncytotoxic nor-paclitaxel derivative to a cytotoxic analogue by constraining it to the T-Taxol conformation.
• Cytotoxic Cardenolide Glycosides of Roupellina (Strophanthus) boivinii from the Madagascar Rainforest.
• Cytotoxic clerodane diterpenoids and their hydrolysis products from Casearia nigrescens from the rainforest of Madagascar.
• Cytotoxic compounds of Physena madagascariensis from the Madagascar rain forest paragraph sign.
• Cytotoxic compounds of Schizolaena hystrix from the Madagascar rainforest.
• Cytotoxic triterpenoid saponins of Albizia gummifera from the Madagascar rain forest.
• DNase I Footprint Analysis of Protein-DNA Binding.
• Direct analysis of RNA after transfection.
• Effectiveness of chiropractic treatment for infantile colic.
• Evaluation of the tubulin-bound paclitaxel conformation: synthesis, biology, and SAR studies of C-4 to C-3' bridged paclitaxel analogues.
• Fund raising: innovative fund raising brings art to a hospital.
• Furoquinoline alkaloids of Ertela (Monnieria) trifolia (L.) Kuntze from the Suriname rainforest.
• Gene regulation in the postgenomic era: technology takes the wheel.
• Guttiferones K and L, antiproliferative compounds of Rheedia calcicola from the Madagascar rain forest.
• Homology-driven chromatin remodeling by human RAD54.
• Human ACF1 alters the remodeling strategy of SNF2h.
• Independent and complementary methods for large-scale structural analysis of mammalian chromatin.
• Ipomoeassin F, a new cytotoxic macrocyclic glycoresin from the leaves of Ipomoea squamosa from the Suriname rainforest.
• Preparation of poly(a)(+) RNA.
• Rotational-echo double-resonance NMR distance measurements for the tubulin-bound Paclitaxel conformation.
• Shifting adaptive landscapes: progress and challenges in reconstructing early hominid environments.
• Tambouranolide, a new cytotoxic hydroxybutanolide from a Tambourissa sp. (Monimiaceae).
• The shape of things to come: structural and synthetic studies of taxol and related compounds.