The evolution of new exons from Alu elements in human and primates

1 PhD project in the IPP summer call 2019

Scientific Background

Alu elements are primate-specific retrotransposons that frequently integrate in introns. Mutations in Alu elements can lead to the evolution of new exons, a process called Alu exonisation, known to profoundly affect human gene regulation and expression (Tajik et al, 2015; Attig et al, 2016). Alu exonisation requires tight control, as the spurious incorporation into mature transcripts is often deleterious (Zarnack et al, 2013). To which extent selective processes promoted Alu exonisation during primate evolution remains poorly understood.

PhD project proposal: High-throughput investigation of Alu exonisation in evolution

In this project, we aim to combine phylogenetic inference with high-throughput splicing measurements to trace the differentiation and evolution of Alu exons across primates. We will pursue the following questions: Which mutations promote Alu exonisation? Which RNA-binding proteins (RBPs) are involved in Alu exonisation? In order to address these questions, we will employ an experimental high-throughput screening approach that we recently developed to measure the effects of mutations on splicing (Braun et al, 2018). Starting from 1,000 Alu exons in the human genome, we will search for sequence variants in the human population as well as in the orthologous Alu elements in Old World and New World monkeys that will be introduced into splicing reporter constructs (so-called minigenes). High-throughput splicing measurements with these reporter constructs will identify mutations that significantly change Alu exon splicing and allow to trace these back to their phylogenetic origin. We will further integrate public RNA-seq data to correlate the expression of trans-acting RBPs with the inclusion level of the 1,000 Alu exons across species. In summary, we will employ a high-throughput screen to investigate the splicing-regulatory mutations and trans-acting factors that promoted the evolution of Alu exons in primates.

Publications relevant to these projects

Braun, S*, Enculescu, M*, Setty, ST*, Cortés-López, M, de Almeida, BP, Sutandy, FXR, Schulz, L, Busch, A, Seiler, M, Ebersberger, S, Barbosa-Morais, NL, Legewie, S$, König, J$ and Zarnack, K$ (2018) Decoding a cancer-relevant splicing decision in the RON proto-oncogene using high-throughput mutagenesis. Nat Commun 9, 3315.

Attig, J, Ruiz de los Mozos, I, Haberman ,N, Wang, Z, Emmett, W, Zarnack, K, König, J$ and Ule, J$ (2016) Splicing repression allows the gradual emergence of new Alu-exons in primate evolution. eLife, doi: 10.7554/eLife.19545.

Tajnik, M*, Vigilante, A*, Braun, S, Hänel, H, Luscombe, NM, Ule, J, Zarnack, K$ and König, J$ (2015). Intergenic Alu exonisation facilitates the evolution of tissue-specific transcript ends. Nucleic Acids, Res 43, 10492-505.

Zarnack, K*, König, J*, Tajnik, M, Martincorena, I, Eustermann, S, Stevant, I, Reyes, A, Anders, S, Luscombe, NM and Ule, J (2013). Direct competition between hnRNP C and U2AF65 protects the transcriptome from the exonization of Alu elements. Cell 152, 453-466.


Dr Julian König