What Is Enhancer Hijacking, And How Can I Detect It?

Active gene expression requires the coordinated interaction between gene promoters and genetic elements called enhancers. Enhancers are DNA sequences that are often located at great distances in linear sequence from the genes they regulate, but physically interact with the gene’s promoter region. This interaction is mediated through the looping of chromatin, bringing transcription factors, bound to the enhancer sequence, into physical contact with the transcription complex assembled on the gene promoter.

Cellular machinery exists to control the ability of chromatin to form loops, involving both cis- and trans-acting factors thereby limiting gene promoters to a small enhancer subset. As a result, enhancers play a crucial role in determining when and where genes are turned on or off during development and in response to various environmental signals.

The phenomenon of enhancer hijacking occurs when promoters co-opt or “hijack” alternative enhancer elements enabling the gene to escape normal gene regulatory mechanisms. One well-known example of enhancer hijacking is observed in certain types of cancer, such as some forms of leukemia.^1,2 As a result of a chromosomal translocation, a piece of DNA containing an enhancer sequence is relocated to a region near a different gene. The result Is an enhancer element that activates the expression of the neighboring gene in an abnormal context or at inappropriate levels, leading to uncontrolled cell division and the formation of cancerous cells. A lesser-known cause of enhancer hijacking involves mutations in the machinery controlling the 3D organization of the chromatin itself. For example, mutations impacting TAD boundary formation (TADs represent insulated genomic regions that promote intra-region chromatin looping but minimize looping between neighboring regions) remove a crucial limiter to loop formation.³

Irrespective of the underlying etiology for enhancer hijacking, changes in 3D chromatin architecture can be observed (these changes can be global or highly localized). Detection of 3D chromatin architecture is best achieved using chromatin conformation capture (3C) approaches, the most widely used being Hi-C.

3D genome topology relates to enhancer hijacking in several ways:

Chromatin Folding:

The DNA in the nucleus is not randomly arranged but forms loops and domains that bring enhancers and promoters closer together. These structural elements are facilitated by the looping interactions between DNA regions. Enhancers can physically contact their target genes through these loops, enabling the appropriate regulation of gene expression. Alterations in chromatin folding can disrupt these interactions and result in the hijacking of enhancers by other genes.

Chromosomal Rearrangements:

Chromosomal rearrangements, such as translocations or inversions, can directly impact the 3D genome topology. When enhancers or regulatory elements are relocated due to these rearrangements, they may be close to genes they do not normally regulate. As a result, the hijacked enhancers can activate or silence the expression of the nearby gene in an aberrant manner, contributing to oncogenic processes.

Super Enhancers:

Super enhancers are clusters of enhancers that have a high density of transcription factor binding and are associated with the regulation of critical genes, including oncogenes. These super enhancers are often found in specific regions of the genome, and alterations in the 3D genome structure can affect their activity. Changes in the organization of super enhancers can lead to the hijacking of their regulatory function by nearby genes, resulting in dysregulated gene expression and the development of diseases such as cancer.

A few examples of enhancer hijacking in cancer:

Chronic Myeloid Leukemia (CML): In CML, a chromosomal translocation occurs between chromosomes 9 and 22, resulting in the formation of the Philadelphia chromosome. This translocation fuses the BCR (breakpoint cluster region) gene from chromosome 22 with the ABL1 (Abelson tyrosine kinase 1) gene on chromosome 9. As a result, the BCR-ABL fusion gene is formed, which contains an enhancer from the BCR gene that inappropriately activates the ABL1 gene. This leads to uncontrolled cell division and the development of CML.⁴

Ewing Sarcoma: Ewing sarcoma is a rare bone and soft tissue cancer primarily affecting children and young adults. It is characterized by a chromosomal translocation between chromosomes 11 and 22, resulting in a fusion between the EWSR1 (Ewing sarcoma breakpoint region 1) gene on chromosome 22 and an ETS family transcription factor gene (such as FLI1) on chromosome 11. The resulting fusion protein acts as an abnormal transcription factor and hijacks enhancer elements, leading to the dysregulation of various target genes involved in cell growth and differentiation.⁵

Neuroblastoma: Neuroblastoma is a childhood cancer that originates from developing nerve cells. In a subset of neuroblastoma cases, there is a rearrangement involving the MYCN gene, which encodes a transcription factor involved in normal neural development. The rearrangement results in the MYCN gene being placed under the control of enhancers from other genes, such as the TERT (telomerase reverse transcriptase) gene. This enhancer hijacking leads to the overexpression of MYCN, promoting uncontrolled cell proliferation and tumor growth.⁶

These are just a few examples, and enhancer hijacking can occur in various other types of cancer as well. Understanding the specific genetic alterations and the resulting dysregulation of gene expression is crucial for developing targeted therapies to counteract the effects of enhancer hijacking in cancer.

The 3D genome topology, or the three-dimensional organization of DNA within the nucleus, plays a significant role in enhancer hijacking. The spatial arrangement of the genome can bring distant enhancer elements in proximity to target genes, allowing for their regulatory interactions. Enhancer hijacking often involves alterations in the three-dimensional structure of the genome, which can lead to aberrant enhancer-gene interactions and subsequent dysregulation of gene expression.

By studying the 3D genome architecture and the interactions between enhancers and target genes, researchers can gain insights into the mechanisms of enhancer hijacking. Advances in technologies like chromosome conformation capture (such as Hi-C) and imaging techniques allow for the investigation of these spatial interactions, aiding in our understanding of how alterations in 3D genome topology contribute to the dysregulation of gene expression in diseases, including enhancer hijacking in cancer.

In summary, enhancer hijacking remains an active area of research, as scientists aim to understand the underlying mechanisms and identify potential therapeutic targets. By elucidating the specific genetic alterations that lead to enhancer hijacking, researchers may be able to develop strategies to disrupt these aberrant interactions and restore normal gene regulation, potentially offering new avenues for treating diseases associated with enhancer hijacking.

References:

1 Bhagwat et al (2018)

2 Ottema et al (2021)

3 Yang et al (2021)

4 Laurent et al (2001)

5 Marchetto et al (2020)

6 Helmsauer et al (2020)