| The enormous complexity of messenger RNA (mRNA) architecture and function is a major source of biological diversity in eukaryotes. However, defining the landscape of post-transcriptional networks in physiological and disease processes remains formidable. The work presented here addresses this ongoing challenge with systems biological analyses of post-transcriptional networks in cell differentiation and programmed cell death.;The first study establishes genomic binding profiles of Saccharomyces cerevisiae spliceosome components, thus mapping global coupling of transcription and spliceosome assembly. These profiles revealed that most splicing catalytic events occur post-transcriptionally in yeast and that differentially processed mRNAs recruit distinct nuclear export factors. Moreover, the recruitment patterns of various mRNA processing regulators defined new components of a splicing regulon controlling spore development.;The second study explores alternative splicing in apoptosis regulation with novel splicing-sensitive reporters for Bcl2-like factors Bcl-x and Mcl1. A whole-genome siRNA screen in human cells identified >150 factors that modulate the balance of pro- versus anti-apoptotic splice variants, including novel functional connections with signal transduction, disease genes, and, most strikingly, cell cycle control. Specifically, inhibition of aurora kinase A and related cell cycle factors promoted pro-apoptotic splicing of Bcl-x, Mcl1, and caspase-9, and altered splicing of other apoptotic transcripts. This response preceded mitotic arrest, indicating coordinated upregulation of pro-death splice variants that promotes apoptosis in arrested cells. These shifts were coupled to caspase-dependent turnover of ASF/SF2, which directly binds and regulates these mRNAs, revealing an alternative splicing network linking cell-cycle control to apoptosis.;A final study examines stress-responsive cross-regulatory dynamics of RNA-binding protein (RBP) paralogs in mammalian hematopoietic cells. Specifically, amino acid starvation triggered autophagic turnover of polypyrimidine tract binding protein-1 (PTBP1) and heterogeneous ribonucleoprotein-L (hnRNP-L), and upregulation of their respective T-cell-enriched paralogs, regulator of differentiation 1 (ROD1) and hnRNP-LL. These findings identify selective autophagic turnover of RBP paralogs as a novel mechanism for post-transcriptional switches in RBP expression.;Collectively, this work describes the regulatory and mechanistic landscape of three diverse post-transcriptional networks in eukaryotic cells. The insights and methods presented here contribute to our rapidly evolving understanding of post-transcriptional networks in biology and disease. |
