Ontology highlight
ABSTRACT:
PROVIDER: PRJNA719855 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14146515_1.fastq.gz | Fastqsanger.gz | |||
| SRR14146515_2.fastq.gz | Fastqsanger.gz |
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Project description:We have combined standard micrococcal (MNase) digestion of nuclei with a modified protocol for construction paired-end DNA sequencing libraries to map both nucleosomes and subnucleosome-sized particles at single base-pair resolution throughout the budding yeast genome. We found that partially unwrapped nucleosomes and subnucleosome-sized particles can occupy the same position within a cell population, suggesting dynamic behavior. By varying the time of MNase digestion, we have been able to observe changes that reflect differential sensitivity of particles, including eviction of nucleosomes. Our protocol and mapping method provide a general strategy for characterizing full epigenomes. We used micrococcal nuclease mapping, chromatin immunoprecipitation and paired-end sequencing to determine the structure of yeast centromeres at single base-pair resolution.
2011-10-26 | E-GEOD-30551 | biostudies-arrayexpress
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Project description:“Biological noise” is defined as functionally insignificant events that occur in living cells due to imperfect fidelity of biological processes. Distinguishing between biological function and biological noise is often difficult, and experiments to measure biological noise have not been performed. Here, we measure biological noise in yeast cells by analyzing chromatin structure and transcription of an 18 kb region of DNA whose sequence was randomly generated and hence is functionally irrelevant. Nucleosome occupancy on random-sequence DNA is comparable to that on yeast genomic DNA. However, nucleosome-depleted regions are much less frequent, and there are fewer well-positioned nucleosomes and shorter nucleosome arrays. Steady-state levels of RNAs expressed from random-sequence DNA are comparable to those of yeast mRNAs, although transcription and mRNA decay rates are at higher levels. Transcriptional initiation (5’ ends) from random-sequence DNA occurs at numerous sites at low levels, indicating very low intrinsic specificity of the Pol II machinery. In contrast, poly(A) profiles (relative levels and clustering of 3’ isoforms) of random-sequence RNAs are roughly comparable to those of endogenous yeast RNAs, which are restricted to 3’ untranslated regions. RNAs expressed from random-sequence DNA show higher cell-to-cell variability than RNAs expressed from yeast genomic DNA, suggesting that functional elements limit the variability among individual cells within a population. These observations indicate that transcriptional noise occurs at high levels in yeast, and they provide insight into how chromatin and transcription patterns arise from the evolved yeast genome.
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Project description:GwAAP: A Genome-wide Amino Acid coding-decoding quantitative Proteomic system was designed in which each protein could be assigned with a distinct code. Using synthetic biology technology, the amino acids codes were coded in N terminal of the corresponding proteins in the genome of yeast (Saccharomyces cerevisiae), so that the copy number of the code sequences were identical with the targeted proteins in yeast. The code sequences were enriched by HA antibody and decoded and quantified by mass spectrometry strategy. In general, this method increased the detection sensitivity by peptide enrichment, which reduced the dynamic range and the complexity of proteomics. In addition, coding sequence with similar physical and chemical properties resulted in the comparable linear signal response of the mass spectrum, which significantly improve the accuracy of proteomic quantification.
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