The CLAMP GA-binding transcription factor regulates heat stress-induced transcriptional repression by associating with 3D chromatin loops

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 identify the first reported transcription factor (TF) that regulates repression of constitutive genes upon heat stress across species and define direct and indirect mechanisms of action by integrating 3D genomic approaches. We demonstrate that the CLAMP (Chromatin-linked adaptor for MSL complex proteins) GA-binding transcription factor (TF) regulates ∼75% of the HS-induced repression in Drosophila, a well-established model for understanding the mechanisms of HS-induced gene regulation. Using Micro-C, we demonstrate that heat stress induces widespread changes in local 3D chromatin looping, which are significantly associated with HS-induced transcriptional changes. Overall, we identify CLAMP as the first reported TF that induces HS repression, which modulates 3D chromatin looping through both direct mechanisms and indirect mechanisms. Moreover, we present the highest-resolution heat stress 3D genomic dataset available in Drosophila, providing a key resource for generating mechanistic insights into how temperature regulates 3D genomic contacts.