GLOBAL INVESTIGATION OF POLY(A) TAIL LENGTH DYNAMICS DURING MACROPHAGE ACTIVATION

Abstract

Post-transcriptional regulation plays important roles in spatial-temporal dynamics of gene expression by controlling mRNA stability, translation efficiency, and mRNA localization. In metazoans, poly(A) tail length control plays crucial roles in almost every aspect of post-transcriptional mRNA regulation, and underlies development, normal homeostasis, and diseases. Most systematic, genome-wide investigations of poly(A) tail length control have been limited to specific biological contexts, such as oocyte fertilization. The absence of zygotic transcription makes oocytes a tractable system to examine changes in poly(A) tail lengths without the confounding influence of new transcripts. However, somatic systems are more challenging to monitor post-transcriptional poly(A) tail length regulation, since new transcripts with longer tails continuously enter the mRNA pool. Therefore, most examples of poly(A) tail length regulation in non-developmental systems have only been shown with a handful of genes in some specific biological contexts. The complexity, relevance and widespread nature of poly(A) tail dynamics are largely unknown for post-embryonic cellular processes.In this thesis, I integrated multiple transcriptomic approaches for exploring post-transcriptional poly(A) tail dynamics in post-embryonic systems. By examining mRNA abundance, nascent transcription, and poly(A) tail length across a time course of macrophage activation, a period of widespread and dynamic changes in the gene expression program, I found that a large fraction of the transcriptome underwent changes in poly(A) tail length, including transient increases for pro-inflammatory genes, with distinct patterns of changes in other sets of genes. Increases in tail length correlated with an increase in mRNA levels regardless of transcriptional activity, and many mRNAs that underwent tail extension encode proteins necessary for immune function and post-transcriptional regulation. Our analyses indicate that many mRNAs undergoing tail lengthening are, in turn, degraded by elevated levels of ZFP36, constituting a post-transcriptional feedback loop that ensures transient regulation of transcripts integral to macrophage activation. Collectively, my thesis work introduces an analytic framework to study post-transcriptional control of poly(A) tail length in transcriptionally active, cellular processes and provides evidence that readenylation can be widely used, exerting a profound effect on gene expression in a non-developmental context.