Microarrays and the relationship of mRNA variation to protein variation during the cell cycle

Browning formation markers of subcutaneous adipose tissue in relation to resting energy expenditure, physical activity and diet in humans

Background Regular exercise and diet may contribute to white adipose tissue (WAT) conversion into a brown adipose-like phenotype that may increase resting energy expenditure (REE), leading to weight loss. We examined the relationship between REE, physical activity (PA) participation and diet with browning formation markers of subcutaneous WAT in healthy men. Materials and methods We assessed REE, diet and body composition of 32 healthy men [age (years): 36.06 ± 7.36, body mass index (BMI): 27.06 ± 4.62 (kg/m2)]. Participants also underwent measurements of PA [metabolic equivalent (MET)-min/week] using the International Physical Activity Questionnaire (IPAQ), while they undertook a subcutaneous fat biopsy from the abdominal region to assess the mRNA expressions of uncoupling protein 1 (UCP1), peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1α), peroxisome proliferator-activated receptor alpha (PPARα) and peroxisome proliferator-activated receptor gamma (PPARγ). Results We found no associations between the UCP1, PGC-1α, PPARα and PPARγ mRNAs with REE, PA levels and diet (p > 0.05). However, the PGC-1α, PPARα and PPARγ mRNAs were more expressed in individuals displaying moderate rather than low PA levels (p < 0.05). Furthermore, PGC-1α, PPARα and PPARγ mRNAs were negatively correlated with fat mass percentage (p < 0.05). PGC-1α and PPARα mRNAs were also negatively correlated with BMI, while PGC-1α mRNA was inversely associated with waist-to-hip ratio (p < 0.05). Conclusion REE, PA levels and diet are not associated with browning formation indices of subcutaneous adipose tissue in healthy adult men.

Rethinking cell-cycle-dependent gene expression in Schizosaccharomyces pombe

Three studies of gene expression during the division cycle of Schizosaccharomyces pombe led to the proposal that a large number of genes are expressed at particular times during the S. pombe cell cycle. Yet only a small fraction of genes proposed to be expressed in a cell-cycle-dependent manner are reproducible in all three published studies. In addition to reproducibility problems, questions about expression amplitudes, cell-cycle timing of expression, synchronization artifacts, and the problem with methods for synchronizing cells must be considered. These problems and complications prompt the idea that caution should be used before accepting the conclusion that there are a large number of genes expressed in a cell-cycle-dependent manner in S. pombe.

Dynamic proteomics of human protein level and localization across the cell cycle

Regulation of proteins across the cell cycle is a basic process in cell biology. It has been difficult to study this globally in human cells due to lack of methods to accurately follow protein levels and localizations over time. Estimates based on global mRNA measurements suggest that only a few percent of human genes have cell-cycle dependent mRNA levels. Here, we used dynamic proteomics to study the cell-cycle dependence of proteins. We used 495 clones of a human cell line, each with a different protein tagged fluorescently at its endogenous locus. Protein level and localization was quantified in individual cells over 24h of growth using time-lapse microscopy. Instead of standard chemical or mechanical methods for cell synchronization, we employed in-silico synchronization to place protein levels and localization on a time axis between two cell divisions. This non-perturbative synchronization approach, together with the high accuracy of the measurements, allowed a sensitive assay of cell-cycle dependence. We further developed a computational approach that uses texture features to evaluate changes in protein localizations. We find that 40% of the proteins showed cell cycle dependence, of which 11% showed changes in protein level and 35% in localization. This suggests that a broader range of cell-cycle dependent proteins exists in human cells than was previously appreciated. Most of the cell-cycle dependent proteins exhibit changes in cellular localization. Such changes can be a useful tool in the regulation of the cell-cycle being fast and efficient.