BUCK LAB

Chromatin architectures at fission yeast transcriptional promoters and replication origins

Robert M. Givens, William K. M. Lai, Jason M. Rizzo, Jonathan E. Bard, Piotr A. Mieczkowski, Janet Leatherwood, Joel A. Huberman and Michael J. Buck

We have used micrococcal nuclease (MNase) digestion followed by deep sequencing in order to obtain a higher-resolution map than previously available of nucleosome positions in the fission yeast, Schizosaccharomyces pombe. With our higher-resolution dataset, we were able to confirm that fission yeast has an unusually short average nucleosome repeat length, ~152 bp, and that transcriptional start sites (TSSs) are associated with nucleosome-depleted regions (NDRs), with downstream nucleosomes in regular arrays and upstream nucleosomes less reproducibly spaced. In addition, we found enrichments for related functions in four of eight groups of genes clustered according to chromatin configurations near TSSs. At replication origins, our data revealed asymmetric localization of Pre-Replication Complex (pre-RC) proteins within large NDRs-a feature that is conserved in fission and budding yeast and is therefore likely to be conserved in other eukaryotic organisms.

Supplemental Data files:

Supplemental Figures S1 - S9

Supplemental Tables S1 - S3

Addional Figure 1. Chromatin and Replication Protein Architecture at 217 Fission Yeast DNA Replication Origins.

Additional Method details available at http://www.biomedcentral.com/1756-0500/4/499

 

Data Files:

Raw Sequence data at NCBI GEO - GSE28071

 

Sample Name File
Log Fixed Narrow Bowtie Alignment file
120bp Extended File
Cuts Files
Template Filtering Results
Log Fixed Broad Bowtie Alignment file
120bp Extended File
Cuts Files
Template Filtering Results
Log Unfixed Narrow Bowtie Alignment file
120bp Extended File
Cuts Files
Template Filtering Results
Stationary Unfixed Narrow Bowtie Alignment file
120bp Extended File
Cuts Files
Template Filtering Results

Igor Pro Chromosome-View Files