Unknown,Transcriptomics,Genomics,Proteomics

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Nucleosome mapping in Saccharomyces cerevisiae in different conditions


ABSTRACT: This experiment aims to map nucleosome positions and comparison of the same in WT NORMAL GROWTH vs WT-NUTRIENT STARVATION/isw1∆2∆ MUTANT/rsc4-∆4 MUTANT in Saccharomyces cerevisiae using a custom designed tiling array on Agilent plat form. The corresponding platform is submitted to GEO under Geo-ID GPL15842. 60mer probes with variable tiling density were designed for all the genes transcribed by RNA polymerase III. Each gene is tiled along with its 1kb downstream and upstream region with the exceptions of RPR1, SCR1, RDN5(1-6) and SNR52. Mononucleosomal DNA and size matched naked DNA was competitively hybridized to the array. Data was extracted and normalized log ratios were calculated using Agilent sofware. Normalized log2 ratio data was used in MLM to detection nucleosome positions. Equal amount of mono-nucleosomal DNA and sized matched naked DNA prepared from formaldehyde fixed cells (Yuan et al. 2005), was labeled with Cy5 and Cy3 respectively and hybridized to the microarray. Each Hybridization was done in triplicate from three independent biological samples in each condition. Enrichment of mono-nucleosomal DNA over naked genomic DNA is a measure of nucleosome density calculated as Log2(nucDNA/nakedDNA).

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Yatendra Kumar 

PROVIDER: E-GEOD-39802 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

A unique nucleosome arrangement, maintained actively by chromatin remodelers facilitates transcription of yeast tRNA genes.

Kumar Yatendra Y   Bhargava Purnima P  

BMC genomics 20130617


<h4>Background</h4>RNA polymerase (pol) III transcribes a unique class of genes with intra-genic promoters and high transcriptional activity. The major contributors to the pol III transcriptome, tRNAs genes are found scattered on all chromosomes of yeast. A prototype tDNA of <150 bp length, is generally considered nucleosome-free while some pol III-transcribed genes have been shown to have nucleosome-positioning properties.<h4>Results</h4>Using high resolution ChIP-chip and ChIP-seq methods, we  ...[more]

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