Alternative splicing (AS) is a major source of biological diversity and a crucial determinant of cell fate and identity. Characterizing the role of AS regulatory networks in physiological and pathological processes remains challenging. The work presented here addresses this challenge using systems biology analyses of AS regulatory networks in programmed cell death and neurological disorders. The first study describes a genome-wide screen based on splicing-sensitive reporters to identify factors that affect the AS of apoptosis regulators Bclx and Mcl1. The screen identified over 150 factors that affect apoptosis through modulating the pro- and anti-apoptotic splicing variants of these apoptosis regulators. This screen revealed a new functional connection between apoptosis regulation and cell-cycle control through an AS network. It also unearthed many disease-associated factors as AS effectors. The second study describes the functions of the Polyglutamine-binding protein 1 (PQBP1)-mediated AS regulatory network in neurological disorders. PQBP1 is a factor linked to intellectual disability and was unexpectedly identified as an AS effector from the screen described above. We found that PQBP1 influences the splicing of many mRNAs and is associated with a wide range of splicing factors. Depletion of PQBP1 in mouse primary cortical neurons caused defects in neurite outgrowth and altered AS of mRNAs enriched for functions in neuron projection regulation. Disease-mutants of PQBP1 lose associations with splicing factors and cannot complement the aberrant AS patterns and neuron morphology defects in PQBP1 depleted-neurons. This study revealed a novel function of PQBP1 in AS regulation associated with neurite outgrowth and indicated that aberrant AS underlies the pathology of PQBP1-related neurological disorders. A final study examines the dynamics of the Drosophila Sex-lethal AS regulation network using a combination of experimental tools and mathematical modeling. This study demonstrates that the features of Sxl AS regulation have great potentials in building synthetic memory circuits in mammalian cells to track cell fate. Collectively, this work describes the landscape of three diverse AS regulatory networks in various biological processes. The results and methods presented here contribute to our rapidly advancing knowledge of AS regulation in biology and human disease.

The aim of this study was to gain insight into the nature of resistance genes and mechanisms of resistance present in different ascochyta blight (AB) resistant genotypes of lentil to efficiently select non-allelic AB resistance genes mediating different mechanisms of resistance for gene pyramiding. Recombinant inbred lines (RILs) from all possible crosses among AB resistant Lens culinaris genotypes CDC Robin, 964a-46, ILL 7537 and ILL 1704 were subjected to allelism tests. Efforts were also made to understand the genetics of resistance in the L. ervoides accession L-01-827A. LR-18, a RIL population from the cross CDC Robin × 964a-46 was subjected to quantitative trait loci (QTL) mapping using a comprehensive genetic linkage map previously developed from polymorphic SNPs, SSRs and phenotypic markers. Results of allelism tests suggested that genes conditioning resistance to ascochyta blight in all lentil genotypes were non-allelic. Two complementary recessive resistance genes in L-01-827A were detected. QTL analysis indicated that CDC Robin and 964a-46 were different at two AB resistance QTLs. Histological tests suggested that cell death inhibition in CDC Robin, and reduced colonization of epidermal cells in 964a-46 might be the mechanisms of resistance in these genotypes. Comparing the expression of key genes in the salicylic acid (SA) and jasmonic acid (JA) signaling pathways of CDC Robin and 964a-46 suggested that the SA pathway was strongly triggered in 964a-46. However, the JA pathway was triggered in both, but at a lower expression level in 964a-46 than in CDC Robin. RNA-seq analysis revealed a number of candidate defense genes differentially expressed among genotypes with hypothetical actions in different layers of the plant defense machinery. The expression levels of the six candidate defense genes measured by quantitative real-time PCR analysis was correlated with those of RNA-seq. In conclusion, 964a-46 and CDC Robin mediated resistance to ascochyta blight through different resistant mechanisms, making them ideal candidates for resistance gene pyramiding. Gene pyramiding can be accelerated using closely linked markers to CDC Robin and 964a-46 resistance genes identified through QTL analysis.