Abstract
To survive exposure to heat stress (HS), organisms activate stress response genes and repress constitutive gene expression, thereby preventing the accumulation of potentially toxic RNA and protein products. Although many studies have elucidated the mechanisms that drive HS-induced activation of stress response genes across species, little is known about the mechanisms that repress constitutively expressed genes. Using nascent RNA-sequencing, we determined that CLAMP (Chromatin-linked adaptor for MSL complex proteins) is a critical GA-binding transcription factor (TF) that drives 75% of the Heat shock (HS) induced repression in Drosophila, a well-established model for understanding the mechanisms of heat stress-regulated gene regulation. Using Micro-C, we demonstrate for the first time that heat stress induces widespread changes in local 3D chromatin organization at chromatin loops, which are significantly associated with HS-induced transcriptional changes. Furthermore, we demonstrate that CLAMP regulates 3D chromatin loop formation and HS-induced repression through both direct and indirect mechanisms. Overall, we demonstrate that CLAMP is the first sequence-specific transcription factor identified that targets HS-dependent transcriptional repression by suppressing 3D chromatin loop anchor formation during HS and also present the highest resolution heat stress 3D genomic dataset available in Drosophila, which provides a key resource for generating mechanistic insight into how temperature regulates 3D genomic contacts.