Establishment of enhancer landscapes in hematopoietic cells revisited
A study from Patrick Matthias and his group at the FMI challenges a widely accepted model on how epigenome dynamics control the differentiation of hematopoietic cells. The plasticity of pluripotent stem cells was thought to be written in their genome in the form of a reduced heterochromatin prevalence and an abundance of "primed" regulatory regions (promoters and enhancers), from which the active elements to be used in later developmental stages are selected. Here, the authors show that early priming of enhancers and heterochromatin dynamics only play a minor role and that most active enhancers are generated de novo without involvement of these mechanisms. The study thus provides important novel insights into the dynamic regulation of the epigenome during hematopoiesis and possibly other systems.
As different craftsmen with different plans and instructions take over during the construction of a house, different sets of proteins, transcription factors and DNA elements come into play as B cells mature from hematopoietic stem cells (HSCs). For several years scientist have hypothesized that the genome contains an epigenetic master plan that is set up early in differentiation and defines what regions will become active at later stages. Based on a few initial studies, it was proposed that enhancers active in differentiated (hematopoietic) cells are bookmarked or "primed" by histone 3 lysine 4 monomethylation (H3K4me1) during the earliest differentiation stages (HSCs, early progenitors), prior to lineage commitment. Enhancers that become active and initiate or fine-tune gene expression at later differentiation stages are then selected from this initial pool of primed elements. This attractive hypothesis was challenged by recent work from Patrick Matthias' group at the Friedrich Miescher Institute for Biomedical Research, which demonstrates that, while such priming indeed exists, it plays only a minor role in setting up the gene expression patterns required for the control of differentiation.
In a study published today in Nature Communications Amin Choukrallah, a Postdoctoral Fellow in the Matthias group, in close collaboration with Lukas Burger from the FMI computational biology platform, and his colleagues dissected the chronology of epigenetic events taking place during the maturation of B-cells from HSCs. They particularly focused on so-called enhancer regions in the genome. These are DNA cis-regulatory elements that can be located hundreds of kilobases away from their target gene and that control and fine-tune gene expression at every differentiation stage. According to the current classification, enhancers can either be in a primed or in an active state, as can be determined by specific combination of histone modifications. Active enhancers harbor H3K4me1 and acetylation marks (H3K27ac) and are associated with expressed genes, while primed enhancers harbor only H3K4me1, lack acetylation and their target genes are not or only very weakly expressed.
"We were surprised that the vast majority of active enhancers used in mature cells, progenitors or in entire organs were not primed in previous stages," said Choukrallah. "It is remarkable that the enhancer repertoire is dynamically reshaped during maturation of B cells at every stage analyzed." Strikingly, the FMI scientists found similar proportions of primed enhancers in stem cells, progenitor cells and differentiated cells. This challenges the concept that the abundance of primed enhancers reflects cellular plasticity in stem cells and progenitor cells. Matthias comments: "Our results also highlight the role of cell- and stage-specific transcription factors in establishing enhancer repertoires during B cell development."
In addition, the scientists found that heterochromatin and Polycomb-mediated silencing, the two major epigenetic systems that silence lineage-inappropriate genes (such as pluripotency genes) also play only minor roles in regulating enhancer dynamics. "We also found that the distribution and the coverage of heterochromatin does not discriminate pluripotent stem cells from terminally differentiated cells, challenging another widely accepted notion in the field" comments Burger.
"There is one additional interesting finding," adds Matthias: "Enhancer usage discriminates closely related cell stages sharing highly similar gene expression patterns. In the near future, interrogating enhancer repertoires will allow us to define developmental stages with higher granularity. This may also have an impact in other fields, e.g. for diagnosis."