Cross-Sectional and Longitudinal Associations between Household Food Security and Child Anthropometry at Ages 5 and 8 Years in Ethiopia, India, Peru, and Vietnam

En: Journal of Nutrition, No. 145, pp. 1924-1933. doi:10.3945/jn.115.210229Background: Poor childhood nutritional status has lifetime effects and food insecurity is associated with dietary practices that can impair nutritional status. Objectives: We assessed concurrent and subsequent associations between food insecurity and height-for-age z scores (HAZs) and body mass index–for-age z scores (BMI-Zs); evaluated associations with transitory and chronic food insecurity; and tested whether dietary diversity mediates associations between food insecurity and nutritional status. Methods: We used data from the Young Lives younger cohort composed of children in Ethiopia (n = 1757), India (n =1825), Peru (n = 1844), and Vietnam (n = 1828) recruited in 2002 (round 1) at ;1 y old, with subsequent data collection at 5 y in 2006 (round 2) and 8 y in 2009 (round 3). Results: Children from food-insecure households had significantly lower HAZs in all countries at 5 y (Ethiopia, 20.33; India, 20.53; Peru, 20.31; and Vietnam, 20.68 HAZ; all P < 0.001), although results were attenuated after controlling for potential confounders (Ethiopia, 20.21; India, 20.32; Peru, 20.14; and Vietnam, 20.27 HAZ; P < 0.01). Age 5 y food insecurity predicted the age 8 y HAZ, but did not add predictive power beyond HAZ at age 5 y in Ethiopia, India, or Peru. Age 5 y food insecurity predicted the age 8 y BMI-Z even after controlling for the 5 y BMI-Z, although associations were not significant after the inclusion of additional confounding variables (Ethiopia, P = 0.12; India, P = 0.29; Peru, P = 0.16; and Vietnam, P = 0.51). Chronically food-insecure households had significantly lower HAZs than households that were consistently food-secure, although BMI-Zs did not differ by chronic food-insecurity status. Dietary diversity mediated 18.8–30.5% of the association between food security and anthropometry in Vietnam, but mediated to a lesser degree (8.4–19.3%) in other countries. Conclusions: In 4 countries, food insecurity at 5 y of age was associated with both HAZ and BMI-Z at age 8 y, although the association was attenuated after adjusting for other household factors and anthropometry at age 5 y, and remained significant only for the HAZ in Vietnam

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers. Here, we probe these unassigned TSSs and show that, in all species studied, a significant fraction of CAGE peaks initiate at microsatellites, also called short tandem repeats (STRs). To confirm this transcription, we develop Cap Trap RNA-seq, a technology which combines cap trapping and long read MinION sequencing. We train sequence-based deep learning models able to predict CAGE signal at STRs with high accuracy. These models unveil the importance of STR surrounding sequences not only to distinguish STR classes, but also to predict the level of transcription initiation. Importantly, genetic variants linked to human diseases are preferentially found at STRs with high transcription initiation level, supporting the biological and clinical relevance of transcription initiation at STRs. Together, our results extend the repertoire of non-coding transcription associated with DNA tandem repeats and complexify STR polymorphism