Temporal dependence of enhancer function

Descripción del proyecto

Momento de las interacciones potenciador-promotor en la regulación génica

La regulación génica en el desarrollo de los vertebrados depende de las interacciones potenciador-promotor. Los cambios aquí pueden causar trastornos del desarrollo y cánceres. Sin embargo, estas interacciones no siempre conducen a la activación de genes, por lo que sus efectos sobre la transcripción pueden no estar claros. El momento es esencial para la activación. El proyecto TimedEnhancer, financiado por el Consejo Europeo de Investigación, analizará cómo el momento de las interacciones potenciador-promotor afecta a la transcripción durante la diferenciación de células madre embrionarias. Descubrirá los mecanismos moleculares que subyacen a la activación transcripcional y la relación entre las interacciones pasadas y presentes, utilizando un enfoque genómico para añadir una dimensión temporal a los métodos unicelulares. Combinar técnicas avanzadas de genómica, unicelulares y de perturbación, el proyecto revelará cómo responden los genes a múltiples potenciadores y el impacto del momento de plegamiento del genoma.

Objetivo

During vertebrate development, genes are regulated by distal regulatory elements, presumably via physical contacts between enhancers and transcription start sites. Alterations in enhancer sequences and/or their interactions with gene promoters can perturb gene expression, leading to developmental disorders and cancers, which argues for their pivotal role in transcription. Conversely, enhancer-promoter contacts can also be uncoupled from gene activation during developmental transitions and in single cells, where they are highly heterogeneous. Thus, the relationship between enhancer-promoter interactions and transcription is frequently indirect and the mechanisms that dictate when promoter-enhancer contacts can result in gene expression differences remain unknown. The core hypothesis of this proposal is that it is the timing of promoter-enhancer communication that instructs gene activation.

Aim1 will examine whether and how the precise timing of enhancer-promoter interactions contributes to transcription. My group will determine which molecular mechanisms during transcriptional activation are regulated by enhancers contacting their target genes at different time points during embryonic stem cell differentiation.

Aim2 will investigate how present and preceding enhancer-promoter contacts relate to transcriptional activity and transcription factor binding in single cells. My group will develop a genomic approach to trace the memory of preceding interactions at gene regulatory elements, thus adding a novel temporal dimension to current single-cell methods.

By longitudinally combining cutting-edge genomic, single-cell and activity perturbation assays, my group will uncover how genes integrate regulatory inputs from several enhancers and assess how the timing of genome folding mechanistically contributes to this process. This research plan will newly elucidate temporality as a powerful feature that shapes the regulatory potential of enhancers and promoters.