Fei Sang

Alternative splicing of mRNA precursors is an important step in gene regulation and a major mechanism by which genetic variants cause human disease. However, changes in splicing have only been quantified for a tiny fraction of possible variants in the human genome, limiting our ability to interpret clinical variants, evaluate and develop machine learning models, and understand the splicing regulatory code. Here, to address this data gap, we present OpenSplice, a well-calibrated experimental dataset that quantifies the impact of >590,000 variants on the splicing of >600 human alternatively spliced exons. OpenSplice increases the number of exons with site saturation mutagenesis data ∼28-fold, quantifying the impact of all possible exonic and proximal intronic single nucleotide (nt) substitutions, as well as all 1, 3, 6 and 21nt deletions. Hundreds of thousands of variants affect splicing and we use the data to evaluate machine learning models, to interpret clinical variants, and to map splicing regulatory architectures. Exons and introns exhibit a broad spectrum of regulatory landscapes, including configurations dominated by enhancers or silencers, checkerboard-like patterns with interleaved enhancers and silencers, and sparse architectures with minimal regulatory content. Silencers are particularly important for determining inclusion levels. OpenSplice provides a complete atlas of variants that impact splicing, a rich testing and training dataset for machine learning models, and a comprehensive map of regulatory elements for mechanistic studies.

Pregnancy represents a stage during which maternal physiology and homeostatic regulation undergo dramatic change and adaptation. The fundamental purpose of these adaptations is to ensure the survival of her offspring through adequate nutrient provision and an environment that is tolerant to the semi-allogenic foetus. While poor maternal diet during pregnancy is associated with perturbed maternal adaptations during pregnancy, the influence of paternal diet on maternal well-being is less clearly defined. We fed C57BL/6 male mice either a control (CD), low protein diet (LPD), a high fat/sugar Western diet (WD) or the LPD or WD supplemented with methyl donors (MD-LPD and MD-WD, respectively) for a minimum of 8 weeks prior to mating with C57BL/6 females. Mated females were culled at day 17 of gestation for the analysis of maternal metabolic, gut, cardiac and bone health. Paternal diet had minimal influences on maternal serum and hepatic metabolite levels or gut microbiota diversity. However, analysis of the maternal hepatic transcriptome revealed distinct profiles of differential gene expression in response to the diet of the father. Paternal LPD and MD-LPD resulted in differential expression of genes associated with lipid metabolism, transcription, ubiquitin conjugation and immunity in dams, while paternal WD and MD-WD modified the expression of genes associated with ubiquitin conjugation and cardiac morphology. Finally, we observed changes in maternal femur length, volume of trabecular bone, trabecular connectivity, volume of the cortical medullar cavity and thickness of the cortical bone in response to the father’s diets. Our current study demonstrates that poor paternal diet at the time of mating can influence the patterns of maternal metabolism and gestation-associated adaptations to her physiology.

A sustainable supply of plant protein is critical for future generations and needs to be achieved while reducing green house gas emissions from agriculture and increasing agricultural resilience in the face of climate volatility. Agricultural diversification with more nutrient-rich and stress tolerant crops could provide the solution. However, this is often hampered by the limited availability of genomic resources and the lack of understanding of the genetic structure of breeding germplasm and the inheritance of important traits. One such crop with potential is winged bean (Psophocarpus tetragonolobus), a high seed protein tropical legume which has been termed ‘the soybean for the tropics’. Here, we present a chromosome level winged bean genome assembly, an investigation of the genetic diversity of 130 worldwide accessions, together with two linked genetic maps and a trait QTL analysis (and expression studies) for regions of the genome with desirable ideotype traits for breeding, namely architecture, protein content and phytonutrients.

The underlying mechanisms driving paternally-programmed metabolic disease in offspring remain poorly defined. We fed male C57BL/6 mice either a control normal protein diet (NPD; 18% protein) or an isocaloric low protein diet (LPD; 9% protein) for a minimum of 8 weeks. Using artificial insemination, in combination with vasectomised male mating, we generated offspring using either NPD or LPD sperm but in the presence of NPD or LPD seminal plasma. Offspring from either LPD sperm or seminal fluid display elevated body weight and tissue dyslipidaemia from just 3 weeks of age. These changes become more pronounced in adulthood, occurring in conjunction with altered hepatic metabolic and inflammatory pathway gene expression. Second generation offspring also display differential tissue lipid abundance, with profiles similar to those of first generation adults. These findings demonstrate that offspring metabolic homeostasis is perturbed in response to a suboptimal paternal diet with the effects still evident within a second generation.

A sustainable supply of plant protein is critical for future generations. We also need to reduce carbon emissions from agriculture, while increasing resilience in the face of elevated temperatures and climate volatility. Agricultural diversification with more crop options is hampered by limited available genomic resources, lack of understanding of the genetic structure of breeding germplasm and important trait inheritance- needed to breed desired ideotypes. Winged bean (Psophocarpus tetragonolobus), a high protein seed tropical legume, has been termed ‘the soybean for the tropics’ with potential to help reduce soybean imports in many tropical and semi-tropical countries. Here we present the first chromosome level winged bean genome assembly (98.9% of 536.1MB scaffolds are assigned), an investigation of genetic diversity of 136 worldwide accessions for breeding, together with the first two genetic maps and a trait QTL analysis for genomic regions with desirable ideotype traits for breeding; namely architecture, protein content and phytonutrients.