From Trigger to Transition

QC 2026-05-13

Abstract

Throughout life, cells undergo cell-state transitions, such as changing cell identities or adapting to environmental stress. Because cells in an organism contain the same set of genes, distinct cell-state transitions arise from differences in gene expression. Gene expression is primarily regulated at the level of transcription, a complex process driven by RNA Polymerase II (Pol II). Beyond Pol II, transcription is coordinated by numerous transcription factors and at regulatory genomic regions, such as promoters and enhancers. By tracking transcription and its regulation upon cell-state transitions, basic biological principles can be identified and leveraged when studying diseases.

The papers presented in this thesis trigger and track transcriptional responses upon two types of cell-state transitions: stress and differentiation. Differentiation is a slow, controlled process that permanently alters the transcriptional program. In contrast, stress induces rapid, transient changes to the transcriptional program, keeping the cell alive and enabling recovery once the stress ends. A classic example of a stress response is the heat shock response (HSR), which is activated by elevated temperatures and other stressors that cause protein misfolding. The HSR represses thousands and activates hundreds of genes, some of which encode chaperones that assist in the correct folding of other proteins.

Across the papers, cell-state transitions are triggered mainly by elevated temperatures or chemical components. After a trigger, the transitions are explored primarily with mRNA-seq and PRO-seq, two genome-wide sequencing techniques. mRNA-seq tracks steady-state levels of mature mRNA, while PRO-seq tracks transcription of nascent RNAs. Paper I provides a computational workflow to generate maps of functional genomic regions, such as promoters and enhancers, from mapped PRO-seq reads. Such maps are central to studying transcriptional responses, and the workflow was used to generate results in Papers II–IV. In Paper II, transcriptional responses and master regulators that drive differentiation in human erythroid cells are explored. A brief signal causes slowly propagating and long-lasting transcriptional changes that prepare cells for future tasks involving oxygen transport. The paper also provides the first direct comparison between induced differentiation and stress in a cell model, revealing drastically distinct coordination of transcriptional responses.

Paper III–V focus on transcriptional responses upon stress. In Paper III, transcription in golden retriever macrophages is tracked under normal conditions and upon heat stress. The first complete transcriptional profiling of the dog genome and characterization of the HSR in dog are provided. In Paper IV, transcription is tracked in fly, mouse, dog, and human upon heat stress. The paper uncovers that intron length is an evolutionarily conserved regulatory mechanism that times the production of heat-induced chaperones. This finding addresses the broader question of why any genome has introns that span hundreds of kilonucleotides. In Paper V, transcriptional programs of three distinct forms of protein-damaging stressors are compared: heat shock (HS), HSP90 inhibition, and polyglutamine (polyQ) aggregation. PolyQ aggregation is a feature of Huntington’s disease (HD), for which no cure exists. The paper reveals that transcriptional responses are fundamentally different for the three stressors. PolyQ aggregation is linked to impaired acute stress responses, which could explain why previous attempts to ameliorate the disease by inducing the HSR have not been successful. There is also a lack of commonly induced or repressed genes across mouse brain tissues under polyQ stress, which suggests that therapeutics targeting pathways rather than specific genes should be explored. Overall, this thesis expands current knowledge of transcriptional responses upon cell-state transitions in health and disease.

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