Structural basis of Ty3 retrotransposon integration at RNA Polymerase III-transcribed genes

Guillermo Abascal-Palacios,Laura Jochem,Fabienne Beuron,Alessandro Vannini,Carlos Pla-Prats

doi:10.1038/s41467-021-27338-w

Abstract

Retrotransposons are endogenous elements that have the ability to mobilise their DNA between different locations in the host genome. The Ty3 retrotransposon integrates with an exquisite specificity in a narrow window upstream of RNA Polymerase (Pol) III-transcribed genes, representing a paradigm for harmless targeted integration. Here we present the cryo-EM reconstruction at 4.0 Å of an active Ty3 strand transfer complex bound to TFIIIB transcription factor and a tRNA gene. The structure unravels the molecular mechanisms underlying Ty3 targeting specificity at Pol III-transcribed genes and sheds light into the architecture of retrotransposon machinery during integration. Ty3 intasome contacts a region of TBP, a subunit of TFIIIB, which is blocked by NC2 transcription regulator in RNA Pol II-transcribed genes. A newly-identified chromodomain on Ty3 integrase interacts with TFIIIB and the tRNA gene, defining with extreme precision the integration site position.

Highlights

Retrotransposons are endogenous elements that have the ability to mobilise their DNA between different locations in the host genome
The minimal factors required for Ty3 targeting at Pol III genes are the TFIIIB subunits, Brf[1] and TATA-box binding protein (TBP), whereas TFIIIC is essential for directionality of integration, which occurs in a narrow window of 2–3 base pairs upstream the transcriptional start site (TSS)[30,31,32]
After step-wise binding of the TFIIIC and TFIIIB transcription factors to the tD(GUC)K gene promoter (Fig. 1b, lanes 2–4), a pre-assembled Ty3 intasome was added to the reaction

Summary

Introduction

Retrotransposons are endogenous elements that have the ability to mobilise their DNA between different locations in the host genome. The Ty3 retrotransposon integrates with an exquisite specificity in a narrow window upstream of RNA Polymerase (Pol) III-transcribed genes, representing a paradigm for harmless targeted integration. Tethering of transposable elements and retroviruses to host factors, in order to integrate at specific genomic location, is not confined only to Ty3/Gypsy TEs8–11. Ty1/Copia retrotransposon interacts directly with subunits of RNA Pol III12–15, S. pombe Tf1 element interacts with the Atf1p protein[8] and the human immunodeficiency virus (HIV) integrase binds to the transcriptional co-activator lens epithelium-derived growth factor (LEDGF/p75)[16,17,18]. The minimal factors required for Ty3 targeting at Pol III genes are the TFIIIB subunits, Brf[1] and TBP, whereas TFIIIC is essential for directionality of integration, which occurs in a narrow window of 2–3 base pairs (bp) upstream the transcriptional start site (TSS)[30,31,32]. Despite recent advances[39,40], the structural analysis of host-retroelement targeting has been restricted to cryo-electron-microscopy (cryo-EM) structures of histone-integrase interactions in nucleosomal context[41,42] and to crystal structures of HIV integrase domains bound to LEDGF/p7516

Methods

Results

Conclusion