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Background: Quiescent cells have a low level of gene activity compared to growing cells. Using a yeast model for cellular quiescence, we defined the genome-wide profiles of three species of histone methylation associated with active transcription between growing and quiescent cells, and correlated these profiles with the presence of RNA polymerase II and transcripts., Results: Quiescent cells retained histone methylations normally associated with transcriptionally active chromatin and had many transcripts in common with growing cells. Quiescent cells also contained significant levels of RNA polymerase II, but only low levels of the canonical initiating and elongating forms of the polymerase. The RNA polymerase II associated with genes in quiescent cells displayed a distinct occupancy profile compared to its pattern of occupancy across genes in actively growing cells. Although transcription is generally repressed in quiescent cells, analysis of individual genes identified a period of active transcription during the development of quiescence., Conclusions: The data suggest that the transcript profile and histone methylation marks in quiescent cells were established both in growing cells and during the development of quiescence and then retained in these cells. Together, this might ensure that quiescent cells can rapidly adapt to a changing environment to resume growth.

Background: Epistasis (synergistic interaction) among SNPs governing gene expression is likely to arise within transcriptional networks. However, the power to detect it is limited by the large number of combinations to be tested and the modest sample sizes of most datasets. By limiting the interaction search space firstly to cis-trans and then cis-cis SNP pairs where both SNPs had an independent effect on the expression of the most variable transcripts in the liver and brain, we greatly reduced the size of the search space., Results: Within the cis-trans search space we discovered three transcripts with significant epistasis. Surprisingly, all interacting SNP pairs were located nearby each other on the chromosome (within 290 kb-2.16 Mb). Despite their proximity, the interacting SNPs were outside the range of linkage disequilibrium (LD), which was absent between the pairs (r(2) < 0.01). Accordingly, we redefined the search space to detect cis-cis interactions, where a cis-SNP was located within 10 Mb of the target transcript. The results of this show evidence for the epistatic regulation of 50 transcripts across the tissues studied. Three transcripts, namely, HLA-G, PSORS1C1 and HLA-DRB5 share common regulatory SNPs in the pre-frontal cortex and their expression is significantly correlated. This pattern of epistasis is consistent with mediation via long-range chromatin structures rather than the binding of transcription factors in trans. Accordingly, some of the interactions map to regions of the genome known to physically interact in lymphoblastoid cell lines while others map to known promoter and enhancer elements. SNPs involved in interactions appear to be enriched for promoter markers., Conclusions: In the context of gene expression and its regulation, our analysis indicates that the study of cis-cis or local epistatic interactions may have a more important role than interchromosomal interactions.