Spt5-mediated enhancer transcription directly couples enhancer activation with physical promoter interaction

• Published in: Nature genetics Vol. 52; no. 5; pp. 505 - 515
• Main Authors: Fitz, Johanna, Neumann, Tobias, Steininger, Monika, Wiedemann, Eva-Maria, Garcia, Adriana Cantoran, Athanasiadis, Alexander, Schoeberl, Ursula E., Pavri, Rushad
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.05.2020; Nature Publishing Group
• Subjects: 631/208/191; 631/208/200; 631/337/2019; Acetylation; Agriculture; Animal Genetics and Genomics; Animals; Antibodies; B cells; Biomedical and Life Sciences; Biomedicine; Cancer Research; Cell Cycle Proteins - genetics; Chromatin; Chromatin - genetics; Chromatin Assembly and Disassembly - genetics; Chromosomal Proteins, Non-Histone - genetics; Class switching; Cohesin; Cohesins; Depletion; DNA-directed RNA polymerase; Elongation; Enhancer Elements, Genetic - genetics; Enhancers; Gene expression; Gene Expression - genetics; Gene Function; Gene Rearrangement - genetics; Genes; Genetic aspects; Genetic transcription; Genomes; Heavy chains; Histone H3; Human Genetics; Immunoglobulin Class Switching - genetics; Immunoglobulins; Lymphocytes B; Lysine; Mice; Mice, Inbred C57BL; Mice, Transgenic; Nuclear Proteins - genetics; Occupancy; Physiological aspects; Promoter Regions, Genetic - genetics; Recombination; Recruitment; RNA; RNA polymerase; RNA polymerase II; Transcription activation; Transcription factors; Transcription, Genetic - genetics; Viral antibodies
• ISSN: 1061-4036; 1546-1718
• DOI: 10.1038/s41588-020-0605-6

Active enhancers are frequently transcribed, yet the regulatory role of enhancer transcription remains debated. Here, we depleted the RNA polymerase II pausing and elongation factor Spt5 in activated mouse B cells and found that approximately 50% of enhancer–gene pairs showed co-regulated transcription, consistent with a potential functional requirement for enhancer transcription. In particular, Spt5 depletion led to loss of super-enhancer–promoter physical interaction and gene expression at the immunoglobulin heavy-chain locus ( Igh ), abrogating antibody class switch recombination. This defect correlated strictly with loss of enhancer transcription but did not affect acetylation of histone H3 at lysine 27, chromatin accessibility and occupancy of Mediator and cohesin at the enhancer. Strikingly, CRISPRa-mediated rescue of enhancer transcription in Spt5-depleted cells restored Igh gene expression. Our work suggests that Spt5-mediated enhancer transcription underlies the physical and functional interaction between a subset of active enhancers and their target promoters. Depletion of RNA polymerase II pausing and elongation factor Spt5 in B cells indicates that ~50% of enhancer–gene pairs show co-regulated transcription. CRISPRa-mediated rescue of enhancer transcription in Spt5-depleted cells restores Igh gene expression.