Crossroads between transposons and gene regulation

Abstract

Transposons are mobile genetic elements that have made a large contribution to genome evolution in a largely species-specific manner. A wide variety of different transposons have invaded genomes throughout evolution, acting in a first instance as ‘selfish’ elements, whose success was determined by their ability to self-replicate and expand within the host genome. However, their coevolution with the host has created many crossroads between transposons and the regulation of host gene expression. Transposons are an abundant source of transcriptional modulatory elements, such as gene promoters and enhancers, splicing and termination sites, and regulatory non-coding RNAs. Moreover, transposons have driven the evolution of host defence mechanisms that have been repurposed for gene regulation. However, dissecting the potential functional roles of transposons remains challenging owing to their evolutionary path, as well as their repetitive nature, which requires the development of specialized analytical tools. In this special issue, we present a collection of articles that lay out current paradigms in the field and discuss a vision for future research.

This article is part of a discussion meeting issue ‘Crossroads between transposons and gene regulation’.

1. Introduction

Upon discovering transposable elements (TEs) in maize around 70 years ago, Barbara McClintock proposed that they acted as ‘controlling elements' that regulate development [1]. In the following decades, it became clear that TEs are ubiquitous selfish genetic elements, with the capacity to move and replicate within a genome. However, in the past decade, large-scale genomic studies have revealed that TEs are a surprisingly substantial source of gene regulatory activity in eukaryotic genomes [2]. These findings have sparked renewed interest in McClintock's visionary ideas, and suggest TEs play fundamental roles shaping gene expression in health and disease.

Numerous examples have now been described where TEs appear to regulate whole networks of genes, in contexts such as innate immunity [3], pluripotency [4] and placentation [5,6], among others. Additionally, thanks to the advent of CRISPR-based genetic and epigenetic editing methods, we can now also test for causal relationships between TE insertions, gene regulation and phenotypes [3,7–9]. Such functional studies will be particularly important to assess the impact of TE variants within the human population, such as those involved in cancer [10]. There is potential for TEs to affect virtually any phenotype, but this variation has been ‘hidden’ in genome-wide association studies owing to the requirement of specific assays and/or analysis tools.

The past several years have also seen significant advances in our understanding of how TE activity is controlled by the host. The majority of TEs in any given cell are silenced, but we are only just beginning to elucidate the mechanisms by which TEs are targeted for repression, which include both epigenetic and post-transcriptional mechanisms [11]. A major emerging research focus is on KRAB zinc-finger (KZNF) proteins, which constitute the largest family of transcription factors in mammalian genomes. Recent large-scale functional genomic studies have revealed that KZNFs represent a rapidly evolving defence system against TEs [12]. Additionally, CRISPR-based genome-wide genetic screens [13] for regulators of transposition and other studies continue to uncover novel molecules and pathways involved in TE silencing. These findings pose many new questions about how TEs are controlled and how their interactions with genome defence machinery shape the global landscape of gene expression.

In May 2019, a Royal Society Discussion Meeting was held in a packed Wellcome Trust Lecture Hall to discuss how TE invasions during evolution have shaped the gene regulatory landscape across all kingdoms of life. This special issue of the Philosophical Transactions of the Royal Society B extends that discussion to the wider public, presenting the current state of the art in the field through a mixture of original research articles, reviews and opinion papers.

2. TEs as cis-regulatory elements

It is now widely appreciated that TEs are a major source of cis-regulatory activity in host genomes, and a key challenge is understanding the extent to which their activity affects cell function and host biology [14]. TEs appear to exhibit preferential activity in specific types of gene regulatory networks, such as those underlying early development, responses to environmental stimuli or infection, and diseases like cancer. As reviewed by Torres-Padilla [15], TE transcriptional activation is pronounced during early development and seemingly associated with the totipotent state, which raises the intriguing possibility that some of this activity has been co-opted to regulate proper development. There is also growing evidence that TEs are a common source of inducible regulatory elements that are activated in response to environmental stress or infection, suggesting they may facilitate adaptive evolution of these responses. In this issue, Bourque and colleagues [16] identify TEs that show inducible regulatory activity upon bacterial infection in human cells, and a study by Gonzalez and colleagues [17] identifies TEs with regulatory activity induced by insecticide exposure in Drosophila. Given the pervasive influence of TEs in diverse cell contexts, another key question is the extent to which unfixed transposons contribute to gene regulatory variation within populations. Using data from human lymphoblastoid and induced pluripotent stem cells lines, Feschotte and colleagues [18] find evidence for numerous TE insertion polymorphisms that are linked to changes in gene expression. This suggests that TEs are an underappreciated source of regulatory and phenotypic variation across human individuals. Finally, while most studies examining TE cis-regulatory activity have focused on their potential promoter or enhancer activity, Sundaram & Wysocka [19] review recent findings that indicate that TEs can influence gene regulation through a wide range of other mechanisms, including silencing gene expression and altering three-dimensional genome architecture.

3. Co- and post-transcriptional roles of TEs

While many studies on the impact of TEs on gene regulation focus on the control of transcription initiation, TEs may also affect downstream processes, including splicing, transcriptional termination and mRNA stability [20]. Through these co- and post-transcriptional events, TEs can be used by the host to control tissue-specific transcriptional diversity and steady-state levels. For example, Maquat [21] reviews in this issue how SINE elements located in the 3′ UTR of transcripts promote Staufen-mediated mRNA decay. This strategy to regulate mRNA stability is shared by mice and humans, with some examples of apparent convergent evolution. Post-transcriptional processing of TE transcripts into small RNAs may also impact on genome regulation, as suggested by Panda et al. [22]. They identify TE-derived small interfering RNAs in Arabidopsis that were previously thought to be pollen-specific, and that can participate in RNA-directed DNA methylation, potentially affecting gene expression. Whereas it is tempting to view TE-mediated regulatory events as a result of evolutionary co-option, many may be neutral in effect, and in some contexts even deleterious. In particular, epigenetic alterations occurring during tumourigenesis can unmask the regulatory activity of TEs. Jordan and colleagues [23] explore here how TE-derived splicing isoforms generate transcriptional diversity specifically in cancer. As several of these affect cancer-associated genes, this mechanism could be implicated in the tumourigenic process.

4. Repurposing of TE regulatory mechanisms

TEs can also drive regulatory innovation owing to their mutagenic action. The potentially deleterious consequences of TE mobility place substantial pressure for the evolution of mechanisms that ensure transcriptional silencing of TEs. Such mechanisms can then be repurposed by the host to enact other key epigenetic events. For example, DNA methylation is thought to have arisen to control the expansion of TEs [24], yet it has become an important mark for mammalian gene regulation, essential for processes such as imprinting and X inactivation. In this issue, the Jacobs and Trono labs explore the repurposing of another canonical TE silencing pathway, which involves KZNFs and their co-repressor interacting factor KAP1/TRIM28. Intriguingly, KZNFs remain well-conserved despite that fact that most of the TE families targeted by them are no longer transpositionally competent. Jacobs and colleagues [25] hypothesize that this is because KZNFs have been repurposed for gene regulation. They find that human KZNFs can bind gene promoters independently of the presence of TEs, seemingly regulating time- and tissue-specific expression in the brain. This includes gene activating roles, which contrast with the canonical role of KZNFs as mediators of TE silencing. One possibility is that these KZNFs are no longer bound by KAP1. Another possibility is that KAP1 itself may occasionally act as a positive transcriptional regulator. Trono and colleagues [26] explore this hypothesis, showing that KAP1 interacts with transcription initiation/elongation factors, and that it binds actively transcribed Pol II promoters, with variable effects on gene expression.

5. Specialized tools for TE research

Advances in genomic technologies continue to expand our ability to uncover the regulatory activities of transposons with increasing ease and precision. However, TEs pose a number of unique challenges that have required continued development of specialized experimental and computational approaches [2]. The primary hurdle is their high copy number in host genomes, which can lead to ambiguous mapping assignments of short sequencing reads. This issue affects all assays that rely on high-throughput short read sequencing data, and as discussed in a review by Hammel and colleagues [27], longer read lengths and the development of computational methods are helping to address this issue. Experimental methods have also been developed to track new TE insertions with increasing sensitivity, which is critical for assessing the mutagenic consequences of transposon reactivation in contexts like cancer. Burns and colleagues [28] report one such method to profile new LINE-1 insertions in single cells. Retrotransposition assays in cell culture are useful tools to study transposon replication, and García-Pérez and colleagues [29] now combine this technology with the use of small RNAs to gain new insights into the regulation of retrotransposition. Finally, mutant models with disrupted transposon silencing pathways can be valuable experimental tools for discovering new transposons, and Panaud and colleagues [30] report one such line in rice.

6. Conclusion

We interpreted the success of the Discussion Meeting as a reflection of the emerging awareness for potential functional roles of the repetitive fraction of genomes. Tools are now at our disposal that enable us to differentiate between purely biochemical processes (e.g. post-translational modifications of histones, transcription) at TEs that are inconsequential, and those events that provide cells and the host organism with an adaptive advantage. The next decade will see the roles of TEs clarified to a high level of molecular and functional detail in an increasing variety of contexts, across species, tissues and diseases.

Biographies

Guest editor profiles

Dr Miguel R. Branco. After graduating in Biochemistry from the University of Lisbon, Portugal, Miguel did a PhD at the MRC Clinical Sciences Centre in London, where he studied the spatial organization of the genome. He then joined the Babraham Institute in Cambridge to investigate mechanisms of epigenetic regulation, and in particular the role of DNA hydroxymethylation in embryonic stem cells. In 2011, he was awarded a Next Generation Fellowship from the Centre for Trophoblast Research. He joined the Blizard Institute (QMUL) in 2013 after securing a Sir Henry Dale Fellowship. Miguel's interests revolve around epigenetic mechanisms that regulate genome function and that are implicated in cell identity, development and disease. His work focuses on retrotransposable elements, aiming to functionally dissect the epigenetic influence that these abundant genomic elements exert on the regulation of the host genome.

Dr Edward B. Chuong. Edward Chuong is an assistant professor of molecular cellular and developmental biology at the BioFrontiers Institute at the University of Colorado, Boulder. His laboratory investigates the evolution of vertebrate immune regulatory networks, focusing on the contribution by transposable elements. Dr Chuong received his BS in Bioinformatics from the University of California, San Diego and his PhD in Genetics from Stanford University. He did his postdoctoral training as an HHMI/Jane Coffin Childs Fellow at the University of Utah.

Data accessibility

This article has no additional data.

Authors' contributions

We contributed equally to this piece.

Competing interests

We declare we have no competing interests.

Funding

We received no funding for this study.