Cohesin alters immune response gene expression primarily by transcriptional burst frequency modulation

Abstract

Transcription is an intermittent process that occurs in bursts. The frequency and the number of messenger RNAs (mRNAs) produced by these bursts determine expression levels and shape cell-to-cell variability. Burst dynamics are modulated by productive encounters between enhancers and promoters, which can be facilitated by the cohesin complex through loop ex-trusion. In experimental systems, cohesin deficiency disrupts cell-type-specific expression pro-grams more severely than constitutive gene expression. Cohesin loss of function increases the self-renewal of hematopoietic progenitor stem cells (HPSCs), and cohesin-related mutations are frequent in cancers, such as AML. Cohesin defects in human AML, mouse HSPC and mature myeloid cells lead to a transcriptional state characterised by the reduced expression of inducible inflammatory genes and the elevated expression ofMyctargets and oxidative phosphorylation (OXPHOS) genes. In this thesis, I combine RNAseq, GROseq, scRNAseq, and smFISH to explore how cohesin depletion affects transcriptional parameters at steady-state and during cell-state transitions. Using primary macrophages as a model system, I find that loss of cohesin alters the dynamics of transcriptional bursts without measurably increasing cell-to-cell variability in scRNAseq. I show that expression changes triggered by LPS are primarily orchestrated through the modulation of burst frequencies, and this modulation is blunted in cohesin-deficient macrophages. An increase in burst frequency can have consequences not just for individual cells, but also for their neighbours. Specifically, the frequency of transcriptionalIfnb1bursts determines the number of cells that produceIfnb1-encoded type I interferon (IFN), which through paracrine signalling can alter IFN-dependent expression in neighbouring cells. Co-culture with cohesin-deficient macrophages reduces LPS-induced gene expression in wildtype (WT) macrophages, indicating that cohesin defects can buffer inflammatory responses and impair cell-state transitions due to the defective control of burst frequencies. I speculate that these features contribute to the somatic selection of cohesin mutations in cancer.