Gene expression regulation from the nucleus to the mitochondria

Abstract

Gene expression links genotype to phenotype; it is the fundamental mechanism by which genomic information stored in DNA is functionalized into RNA and, eventually, protein. Gene expression is a complex process, tightly regulated at many levels: transcription is controlled by transcription factors, chromatin topology, and the architecture of the genome itself. RNA processing and degradation are regulated by RNA-binding proteins and non-coding RNAs. All this occurs before an RNA reaches ribosomes to be translated into protein. Understanding the complex network and dynamics that regulate transcription elongation requires a quantitative analysis of RNA polymerase II (Pol II) behavior in a wide variety of regulatory environments. We performed native elongating transcript sequencing (NET-seq) in 42 strains of S. cerevisiae lacking known elongation regulators and found that wild-type elongation dynamics are determined by a balance between the opposing effects of many factors. To better understand the genome-wide effects of these perturbations on nascent transcription, we developed and applied a novel algorithm, PFinder, which highlighted regions of the yeast genome significantly impacted by loss of key regulatory factors. This orchestrated dance of gene regulation occurs not only in the nucleus of all eukaryotic cells, but also in mitochondria. These organelles, responsible for generating cellular energy, house thousands of copies of their own distinct genome, expressed by orthogonal regulatory machinery. While the architecture of nuclear genomes has been well characterized, the structural organization of the mitochondrial genome and its role in the regulation of mitochondrial function are largely unexplored. We probed the architecture of mitochondrial genomes by adapting Fiber-seq for the mitochondria (mtFiber-seq), which revealed the vast majority of mitochondrial genomes to be inaccessible, with few genomes expressing genes. Human mitochondrial genes are expressed as two polycistronic transcripts, so apart from genomic accessibility, mitochondrial RNA abundance is likely regulated through degradation rather than production. Indeed, we can account for nearly 70% of mitochondrial mRNA abundance by measuring and modeling RNA degradation kinetics. This work explores the many mechanisms of gene expression regulation in the nucleus and the mitochondria, illuminating the complex network controlling gene expression from genomic architecture to transcription elongation to RNA degradation.