Cookies on this website

We use cookies to ensure that we give you the best experience on our website. If you click 'Accept all cookies' we'll assume that you are happy to receive all cookies and you won't see this message again. If you click 'Reject all non-essential cookies' only necessary cookies providing core functionality such as security, network management, and accessibility will be enabled. Click 'Find out more' for information on how to change your cookie settings.

Gene transcription occurs via a cycle of linked events, including initiation, promoter-proximal pausing, and elongation of RNA polymerase II (Pol II). A key question is how transcriptional enhancers influence these events to control gene expression. Here, we present an approach that evaluates the level and change in promoter-proximal transcription (initiation and pausing) in the context of differential gene expression, genome-wide. This combinatorial approach shows that in primary cells, control of gene expression during differentiation is achieved predominantly via changes in transcription initiation rather than via release of Pol II pausing. Using genetically engineered mouse models, deleted for functionally validated enhancers of the α- and β-globin loci, we confirm that these elements regulate Pol II recruitment and/or initiation to modulate gene expression. Together, our data show that gene expression during differentiation is regulated predominantly at the level of initiation and that enhancers are key effectors of this process.

Original publication




Journal article


Mol Cell

Publication Date





983 - 997.e7


Poll II recruitment, enhancers, gene regulation, promoter proximal pausing, transcription, Animals, Cell Differentiation, Enhancer Elements, Genetic, Exons, Fetus, Gene Expression Regulation, Gene Library, HSP70 Heat-Shock Proteins, Humans, Introns, K562 Cells, Liver, Mice, Mice, Knockout, Promoter Regions, Genetic, Proto-Oncogene Proteins c-myc, RNA Polymerase II, Signal Transduction, Transcription Initiation, Genetic, alpha-Globins, beta-Globins