Promote the enhancer to enhance the promoter

Now maybe it’s my biased selection of papers, but the frequency of chromatin conformation and DNA dynamics studies seem to be ever increasing. This is definitely due to the fantastic techniques available to study them but also because chromatin is cool and understanding the regulation of gene expression and how chromatin structure and composition reflect it is actually really fascinating. Two papers, recently published in Cell have examined components responsible for the dynamics and regulation of promoter-enhancer interactions.

Varying gene expression

Heterogeneity. A word that currently fills many biologists with excitement. In a cellular context, it refers to the phenomenon whereby a homogeneous population of cells can vary in the levels of gene expression. It brings with it a host of questions; why is there noise in gene expression levels, how is it achieved, is it just a side effect and how does it change depending on external conditions?

With the ability to perform genome-wide studies of RNA expression and chromatin conformation on single cells, these questions have started to be tackled. Ren et al. have recently studied CTCF and its contribution to noise in gene expression in mammalian cells (1).

CTCF, as discussed previously ( (3)), is known to mediate and regulate looping of chromatin in cells by binding specific DNA sequences. This looping can be important for aiding interactions between enhancers and promoters that are far away in sequence (Figure 1).

By using a combination of techniques including single-molecule RNA-FISH and fluorescence-activated cell sorting (FACS), the authors saw an increased variation in gene expression levels when CTCF was depleted. The same was observed when CTCF binding sites, which can be found interwoven with enhancers, were deleted.

Ren’s team used a variant of Hi-C ((3 enzyme) 3eHi-C) as part of their data collection as it analyses the frequency of chromatin contacts. For example between an enhancer and a promoter. With this information that could then identify genes with the most enhancer-promoter interactions – a subset of these genes are known to be involved in T-cell activation.

Making a T-cell

Our bodies are composed of around 200 cell types. Since they all contain the same genetic information they become different through distinct expression of genes. This cellular differentiation occurs for T-cells in the thymus. An important gene that needs expressing is Bcl11b that aids developmental progression.

Expression of Bcl11b can be enhanced by a DNA element known as an enhancer (hence the name). Enhancer elements consist of a dense array of sequences where various transcription factors can bind, which can then promote transcription. One Bcl11b enhancer is known as Major Peak which resides around 850kb downstream from the Bcl11b promoter.

The expanse of DNA between Major Peak and Bcl11b gene raises a problem – how can the two regions interact? Looping of course. However, the looping and movement of Major Peak needs to be tightly regulated so that Blc11b expression is only activated during T-cell development.

Journey to the centre of the nuclei

Isoda et al. have recently published in Cell (2) how the repositioning of Major Peak is achieved. They found that the enhancer moves from a position at the nuclear lamina (a region known to be less transcriptionally active) to the interior of the nucleus. The factor responsible – ThymoD (Figure 1).


Figure 1: Modified from (2) showing the location of Bcl11b (red) and its enhancer (green)


ThymoD, or thymocyte differentiation factor in full, is a non-coding RNA, that is able to achieve this repositioning. The team found that ThymoD promoted demethylation of DNA sites allowing the protein CTCF to bind. CTCF binding activated cohesin-dependent looping allowing for the enhancer and promoter sequences to come into contact (3). Identifying this change in interaction was achieved through Hi-C and was backed up with 3D-FISH experiments using probes for Bcl11b.

ThymoD is expressed from the Bcl11b enhancer. But if the enhancer is initially in a transcriptionally repressive environment (the nuclear lamina) how is it transcribed to promote re-localisation? Well, you will have to wait to find out – an enhancer associated with the ThymoD locus has yet to be identified. It is also still not certain how demethylases (Tet proteins) are recruited.

Further Reading

(1)  Ren et al. CTCF-mediated enhancer-promoter interaction is a critical regulator of cell-to-cell variation of gene expression Molecular Cell, 6, 1049-1058

(2)  Isoda et al. Non-coding transcription instructs chromatin folding and compartmentalisation to dictate enhancer-promoter communication and T cell fate. Cell 1, 108-119 (2017)


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