Cardiff University | Prifysgol Caerdydd ORCA
Online Research @ Cardiff 
WelshClear Cookie - decide language by browser settings

Chromatin particle spectrum analysis: A method for comparative chromatin structure analysis using paired-end mode next-generation DNA sequencing

Kent, Nicholas A., Adams, Steffan, Moorhouse, A. and Paszkiewicz, K. 2010. Chromatin particle spectrum analysis: A method for comparative chromatin structure analysis using paired-end mode next-generation DNA sequencing. Nucleic Acids Research 39 (5) , e26. 10.1093/nar/gkq1183

Full text not available from this repository.

Abstract

Microarray and next-generation sequencing techniques which allow whole genome analysis of chromatin structure and sequence-specific protein binding are revolutionizing our view of chromosome architecture and function. However, many current methods in this field rely on biochemical purification of highly specific fractions of DNA prepared from chromatin digested with either micrococcal nuclease or DNaseI and are restricted in the parameters they can measure. Here, we show that a broad size-range of genomic DNA species, produced by partial micrococcal nuclease digestion of chromatin, can be sequenced using paired-end mode next-generation technology. The paired sequence reads, rather than DNA molecules, can then be size-selected and mapped as particle classes to the target genome. Using budding yeast as a model, we show that this approach reveals position and structural information for a spectrum of nuclease resistant complexes ranging from transcription factor-bound DNA elements up to mono- and poly-nucleosomes. We illustrate the utility of this approach in visualizing the MNase digestion landscape of protein-coding gene transcriptional start sites, and demonstrate a comparative analysis which probes the function of the chromatin-remodelling transcription factor Cbf1p.

Item Type: Article
Date Type: Publication
Status: Published
Schools: Biosciences
Subjects: Q Science > Q Science (General)
Additional Information: 12 pp.
Publisher: Oxford University Press
ISSN: 0305-1048
Last Modified: 05 Jun 2017 02:59
URI: http://orca.cf.ac.uk/id/eprint/22763

Citation Data

Cited 35 times in Google Scholar. View in Google Scholar

Cited 64 times in Scopus. View in Scopus. Powered By Scopus® Data

Actions (repository staff only)

Edit Item Edit Item