Discovering effector domains in human transcription factors

Genomic studies are transforming knowledge about the epigenetic, transcription factor, and 3D landscapes of the genome. However, comprehensive information is lacking about the effector domains used by transcription factors to influence gene expression. Addressing this gap, DelRosso et al. developed a high-throughput screen to discover effector domains in human regulatory factors.

Topologically associating domains are disrupted by evolutionary genome rearrangements forming species-specific enhancer connections in mice and humans

Distinguishing between conserved and divergent regulatory mechanisms is essential for translating preclinical research from mice to humans, yet there is a lack of information about how evolutionary genome rearrangements affect the regulation of the immune response, a rapidly evolving system. The current model is topologically associating domains (TADs) are conserved between species, buffering evolutionary rearrangements and conserving long-range interactions within a TAD. However, we find that TADs frequently span evolutionary translocation and inversion breakpoints near genes with species-specific expression in immune cells, creating unique enhancer-promoter interactions exclusive to the mouse or human genomes. This includes TADs encompassing immune-related transcription factors, cytokines, and receptors. For example, we uncover an evolutionary rearrangement that created a shared LPS-inducible regulatory module between OASL and P2RX7 in human macrophages that is absent in mice. Therefore, evolutionary genome rearrangements disrupt TAD boundaries, enabling sequence-conserved enhancer elements from divergent genomic locations between species to create unique regulatory modules.

It is currently unclear how evolutionary genome rearrangements affecting the mouse and human genomes influence the expression of genes important in immunity. Gilbertson et al. report that evolutionary genome rearrangements disrupt topologically associating domain boundaries, enabling sequence-conserved enhancer elements from divergent locations between species to create unique regulatory modules.

Conservation and divergence in gene regulation between mouse and human immune cells deserves equal emphasis

Model organisms such as mice are important for basic research and serve as valuable tools in preclinical translational studies. A challenge with translating findings from mice to humans is identifying and separating evolutionarily conserved mechanisms in the immune system from those diverging between species. A significant emphasis has been placed on defining conserved gene regulation principles, with divergent mechanisms often overlooked. We put forward the perspective that both conserved and divergent mechanisms that regulate gene expression programs are of equal importance. With recent advances and availability of datasets, immunologists should take a closer look at the role for genetic diversity in altering gene expression programs between mouse and human immune cells.

Bcl-6 directly represses the gene program of the glycolysis pathway

Despite our increasing knowledge of the molecular events that induce the glycolysis pathway in effector T cells, very little is known about the transcriptional mechanisms that dampen the glycolysis program in quiescent cell populations such as memory T cells. Here, we show that the transcription factor Bcl-6 directly repressed genes involved in the glycolysis pathway, including Slc2a1, Slc2a3, Pkm2 and Hk2, in T_H1 cells exposed to low amounts of interleukin 2 (IL-2). Thus, Bcl-6 plays an opposing role to the IL-2-sensitive glycolytic transcriptional program that c-Myc and HIF-1α promote in effector T cells. Additionally, the Th1-lineage-specifying factor T-bet functionally antagonized the Bcl-6-dependent repression of genes in the glycolysis pathway, implicating the molecular balance between these two factors in metabolic gene program regulation.