Differential ATAC-seq and ChIP-seq peak detection using ROTS

Changes in cellular chromatin states fine-tune transcriptional output and ultimately lead to phenotypic changes. Here we propose a novel application of our reproducibility-optimized test statistics (ROTS) to detect differential chromatin states (ATAC-seq) or differential chromatin modification states (ChIP-seq) between conditions. We compare the performance of ROTS to existing and widely used methods for ATAC-seq and ChIP-seq data using both synthetic and real datasets. Our results show that ROTS outperformed other commonly used methods when analyzing ATAC-seq data. ROTS also displayed the most accurate detection of small differences when modeling with synthetic data. We observed that two-step methods that require the use of a separate peak caller often more accurately called enrichment borders, whereas one-step methods without a separate peak calling step were more versatile in calling sub-peaks. The top ranked differential regions detected by the methods had marked correlation with transcriptional differences of the closest genes. Overall, our study provides evidence that ROTS is a useful addition to the available differential peak detection methods to study chromatin and performs especially well when applied to study differential chromatin states in ATAC-seq data.

Parents' depression and loneliness during pregnancy and respiratory infections in the offspring: A prospective birth cohort study

Background

An association between maternal prenatal stress and increased rates of respiratory tract infections in the offspring has been described earlier. Data regarding the father’s role is lacking. In this study our aim was to evaluate, whether mothers’ and fathers’ depressive symptoms and loneliness during pregnancy predict higher rates of respiratory tract infections in the offspring.

Methods

In this longitudinal cohort study we gathered information on parental psychological risk during gestational week 20 using the BDI-II and UCLA loneliness scale questionnaires for the parents of 929 children. Loneliness was divided into social and emotional components, the former describing patterns of social isolation and the latter a perceived lack of intimate attachments. Episodes of acute otitis media, physician visits due to respiratory tract infections, and antibiotic consumption relating to respiratory tract infections were documented in the infants, excluding twins, from birth until 10 months of age using study diaries. Analyses were carried out by structural equation modeling, which provides dynamic estimates of covariances.

Results

Maternal depressive symptoms during pregnancy predicted higher rates of acute otitis media in the infant and maternal emotional loneliness predicted higher rates of physician visits. Acute otitis media, physician visits and antibiotic consumption in the infant were slightly less frequent for families who reported social loneliness in the father or mother. Associations remained when taking into account confounders.

Conclusions

Maternal prenatal depression and emotional loneliness predicted a higher burden of respiratory tract infections in the offspring. The protective influence of parental social loneliness on the burden of respiratory tract infections in infants was not in line with our study hypothesis, but could be explained by reduced use of healthcare services in these socially isolated families.