Nucleosome alterations caused by mutations at modifiable histone residues in Saccharomyces cerevisiae

A genetic analysis reveals novel histone residues required for transcriptional reprogramming upon stress

Cells have the ability to sense, respond and adapt to environmental fluctuations. Stress causes a massive reorganization of the transcriptional program. Many examples of histone post-translational modifications (PTMs) have been associated with transcriptional activation or repression under steady-state growth conditions. Comparatively less is known about the role of histone PTMs in the cellular adaptive response to stress. Here, we performed high-throughput genetic screenings that provide a novel global map of the histone residues required for transcriptional reprogramming in response to heat and osmotic stress. Of note, we observed that the histone residues needed depend on the type of gene and/or stress, thereby suggesting a 'personalized', rather than general, subset of histone requirements for each chromatin context. In addition, we identified a number of new residues that unexpectedly serve to regulate transcription. As a proof of concept, we characterized the function of the histone residues H4-S47 and H4-T30 in response to osmotic and heat stress, respectively. Our results uncover novel roles for the kinases Cla4 and Ste20, yeast homologs of the mammalian PAK2 family, and the Ste11 MAPK as regulators of H4-S47 and H4-T30, respectively. This study provides new insights into the role of histone residues in transcriptional regulation under stress conditions.

An approach of identifying differential nucleosome regions in multiple samples

Background

Nucleosome plays a role in transcriptional regulation through occluding the binding of proteins to DNA sites. Nucleosome occupancy varies among different cell types. Identification of such variation will help to understand regulation mechanism. The previous researches focused on the methods for two-sample comparison. However, a multiple-sample comparison (n ≥ 3) is necessary, especially in studying development and cancer.

Methods

Here, we proposed a Chi-squared test-based approach, named as Dimnp, to identify differential nucleosome regions (DNRs) in multiple samples. Dimnp is designed for sequenced reads data and includes the modules of both calling nucleosome occupancy and identifying DNRs.

Results

We validated Dimnp on dataset of the mutant strains in which the modifiable histone residues are mutated into alanine in Saccharomyces cerevisiae. Dimnp shows a good capacity (area under the curve > 0.87) compared with the manually identified DNRs. Just by one time, Dimnp is able to identify all the DNRs identified by two-sample method Danpos. Under a deviation of 40 bp, the matched DNRs are above 60% between Dimnp and Danpos. With Dimnp, we found that promoters and telomeres are highly dynamic upon mutating the modifiable histone residues.

Conclusions

We developed a tool of identifying the DNRs in multiple samples and cell types. The tool can be applied in studying nucleosome variation in gradual change in development and cancer.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3541-9) contains supplementary material, which is available to authorized users.