E-GEOD-5649 - Genomewide demarcation of RNA PolII transcription units by physical fractionation of chromatin- ORF enrichment

Status
Submitted on 27 August 2006, released on 30 August 2006, last updated on 10 June 2011
Organism
Saccharomyces cerevisiae
Samples (10)
Array (1)
Protocols (2)
Description
Epigenetic modifications of chromatin serve an important role in regulating the expression and accessibility of genomic DNA. We report here a genomewide approach for fractionating yeast chromatin into two functionally distinct parts, one containing RNA polymerase II transcribed sequences, and the other comprising noncoding sequences and genes transcribed by RNA polymerases I and III. Noncoding regions could be further fractionated into promoters and segments lacking promoters. The observed separations were apparently based on differential crosslinking efficiency of chromatin in different genomic regions. The results reveal a genomewide molecular mechanism for marking promoters and genomic regions that have a license to be transcribed by RNA polymerase II, a previously unrecognized level of genomic complexity that may exist in all eukaryotes. Our approach has broad potential use as a tool for genome annotation and for the characterization of global changes in chromatin structure that accompany different genetic, environmental, and disease states. Keywords: Genomewide mapping of regulatory elements through differential fractionation of crosslinked chromatin based on nucleosome occupancy. ORF enrichment- Cells were crosslinked and nuclei isolated to prepare solubilized chromatin. Crosslinks were then reversed by incubation at 65°C, and DNA was prepared. In initial experiments, immunoprecipitation using antimethyl-lysine histone H3 antibody was performed before the crosslinks were reversed. However, the IPs were not required for ORF enrichment.
Experiment type
other 
Contacts
Jason D Lieb <jlieb@bio.unc.edu>, Michael L Cleary, Patrick O Brown, Peter L Nagy
Citation
Genomewide demarcation of RNA polymerase II transcription units revealed by physical fractionation of chromatin. Nagy PL, Cleary ML, Brown PO, Lieb JD.
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-5649.idf.txt
Sample and data relationshipE-GEOD-5649.sdrf.txt
Processed data (1)E-GEOD-5649.processed.1.zip
Array designA-GEOD-4184.adf.txt
Links