Transposable Elements Drive Reorganisation of 3D Chromatin

bioRxiv preprint doi: https://doi.org/10.1101/523712; this version posted January 17, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. Transposable elements drive reorganisation of 3D chromatin during early embryogenesis Kai Kruse1, Noelia Díaz1, §, Rocio Enriquez-Gasca1, §, Xavier Gaume2, 4, Maria-Elena Torres-Padilla2, 3 and Juan M. Vaquerizas1, * 1. Max Planck Institute for Molecular Biomedicine, Roentgenstrasse 20, 48149 Muenster, Germany. 2. Institute of Epigenetics and Stem Cells (IES), Helmholtz Zentrum München, Marchioninistraße 25, 81377 Munich, Germany. 3. Faculty of Biology, Ludwig Maximilians Universität, Großhaderner Str. 2, 82152 Planegg-Martinsried, Germany. 4. Present address: Cancer Research Center of Lyon, 28 Rue Laennec, Lyon 69008, France. §. These authors have contributed equally to this work. *. Correspondence to J.M.V. ([email protected], @vaquerizasjm) Keywords: Chromosome conformation capture; low-input Hi-C; early embryonic development; totipotency; transposable elements; MERVL; TAds; 2-cell embryo; 2-cell-like cells; zygotic genome activation; CAF-1; dux. Transposable elements are abundant genetic components of eukaryotic genomes with important regulatory features affecting transcription, splicing, and recombination, among others. Here we demonstrate that the Murine Endogenous Retroviral Element (MuERV-L/MERVL) family of transposable elements drives the 3D reorganisation of the genome in the early mouse embryo. By generating Hi-C data in 2-cell-like cells, we show that MERLV elements promote the formation of insulating domain boundaries throughout the genome in vivo and in vitro. The formation of these boundaries is coupled to the upregulation of directional transcription from MERVL, which results in the activation of a subset of the gene expression programme of the 2-cell stage embryo. Domain boundaries in the 2-cell stage embryo are transient and can be remodelled without undergoing cell division. Remarkably, we find extensive inter-strain MERVL variation, suggesting multiple non-overlapping rounds of recent genome invasion and a high regulatory plasticity of genome organisation. Our results demonstrate that MERVL drive chromatin organisation during early embryonic development shedding light into how nuclear organisation emerges during zygotic genome activation in mammals. INTRODUCTION topology has been reported, highlighting the role of these elements for healthy cellular function Mammalian genomes are characterised by the (Sun et al. 2018). However, despite their func- presence of a high amount of transposable ele- tional relevance, the establishment of a causal re- ments (TEs) with increasingly recognized regula- lationship between TE genomic location and tory features for genome function such as tran- three-dimensional chromatin organisation has scription, splicing, and recombination, among been hindered by the lack of observations in a dy- others (Feschotte 2008; Bourque et al. 2008; namic system that would allow the examination Friedli and Trono 2015; Thompson et al. 2016). of changes in chromatin conformation related to In recent years, TEs have also been associated TEs. with the three-dimensional organisation of chro- Interestingly, specific families of TEs display matin in the nucleus, such as the inter-chromoso- dynamic transcriptional changes during develop- mal colocalisation of similar repetitive elements mental stages around mammalian preimplantation (Cournac et al. 2016), or the occurrence of TEs in development, allowing the examination of their domains or at domain boundaries (Dixon et al. transcriptional regulatory relevance (Rodriguez- 2012; Pope et al. 2014; Darrow et al. 2016; Terrones and Torres-Padilla 2018). This develop- Giorgetti et al. 2016; Winter et al. 2018). This is mental transition involves a remarkably intricate complemented by evidence for insulator function system of tightly orchestrated epigenetic changes of specific TE families (Wang et al. 2015; that ensure the reprogramming of the terminally Schmidt et al. 2012). More recently, an associa- differentiated gametes to enable the formation of tion between the expansion of disease-associated a totipotent zygote (Burton and Torres-Padilla tandem repeats and three-dimensional chromatin 2014; Xu and Xie 2018). The characterisation of 1 bioRxiv preprint doi: https://doi.org/10.1101/523712; this version posted January 17, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. 2-cell-embryo-like cells (2CLC), derived from with their upregulation. Overall our study pro- mouse embryonic stem cells (mESC), has made it vides evidence for a role of repetitive elements in possible to investigate the regulatory mechanisms shaping the three-dimensional organisation of the associated with molecular features of totipotency genome and their co-option in regulating key bio- (Peaston et al. 2004; Macfarlan et al. 2012; logical functions during early mammalian devel- Ishiuchi et al. 2015). In particular, recent exami- opment. nations of 2CLC have hinted at a role for the Mu- rine Endogenous Retroviral Element with a leu- RESULTS cine tRNA primer binding site (MuERV-L; also known as MERVL) and the transcription factor 2CLC display increased three-dimensional Dux in this developmental progression structural plasticity genome-wide (Hendrickson et al. 2017; De Iaco et al. 2017), To determine the chromatin conformation land- highlighting the effectiveness of 2CLC to uncover scape during the reprogramming of pluripotent novel molecular mechanisms related to the estab- mESC towards the totipotent-like 2CLC state, we lishment of totipotency in vivo. In parallel to epi- performed in situ Hi-C in 2CLC. To do so, we genetic remodelling of chromatin marks (Wu et first generated 2CLC by depleting the histone al. 2016; Liu et al. 2016; Dahl et al. 2016; Zhang chaperone CAF-1 in mESC in vitro, as previously et al. 2016), the three-dimensional organisation of described (Ishiuchi et al. 2015) (Fig. 1a). Briefly, chromatin is rapidly reprogrammed during early we used an eGFP reporter construct under the mammalian development following zygotic ge- control of a MERVL long terminal repeat (LTR), nome activation at the 2-cell embryo stage (Du et which faithfully identified 2CLC (Macfarlan et al. al. 2017; Ke et al. 2017). While the molecular 2012; Ishiuchi et al. 2015; Rodriguez-Terrones et mechanisms involved in the establishment of this al. 2018). This allowed us to separate GFP-posi- critical layer of genome regulation in mammals tive (2CLC) from GFP-negative cells (mESC) us- are unknown, work in Drosophila has revealed the ing FACS sorting (Fig. 1a and Extended Data Fig. establishment of early insulation mediated by the 1a). Immunostaining using an OCT4 antibody pioneer transcription factor Zelda (Hug et al. and chromocentre inspection confirmed success- 2017), suggesting a role for pioneer factors in the ful separation and purification of 2CLC and establishment of 3D chromatin during early em- mESC (Fig. 1b) (Ishiuchi et al. 2015). bryonic development (Hug and Vaquerizas 2018). To examine chromatin conformation changes In this study, we demonstrate that the chroma- accompanying the mESC to 2CLC transition, we tin conformation changes that occur during early performed in situ Hi-C modified for low cell num- embryonic development in mouse are driven by bers on both types of cells (Fig. 1c-h) with close the MERVL family of TEs. We first used a new to a billion sequenced read pairs per sample (Sup- low input Hi-C method to produce high-quality plementary Table 1) (Díaz et al. 2018). In addi- genome-wide chromatin contact maps of mESC tion, we compared the obtained mESC and 2CLC and 2CLC. Our data indicate that the chromatin Hi-C maps to those from lymphoblastoid cells conformation of 2CLC recapitulates features of (Rao et al. 2014), providing a reference for fully pre-implantation developmental stages, in agree- differentiated cells. On a whole-chromosome ment with their reported higher level of cellular level, chromatin appeared to gain three-dimen- potency. Unexpectedly, we show that hundreds of sional structure progressively, particularly at long MERVL-containing genomic regions in 2CLC contact ranges, as potency levels decrease (Fig. undergo 3D chromatin remodelling, specifically 1c). Indeed, an analysis of A/B compartment gaining domain-insulating properties. We further strength (Lieberman-Aiden et al. 2009) showed demonstrate that such structural changes are di- an increase of contacts within the active (A) and rectly caused by the integration of MERVL ele- inactive (B) compartments, as well as gain of sep- ments in the genome, and that structural remodel- aration between A and B compartments as cellu- ling occurs in conjunction with the binding of the lar differentiation progresses (Fig. 1d, I). Further developmental pioneer transcription factor Dux. comparisons at the megabase-level showed a sim- Finally, analysis of chromatin contact maps in ilar increase of structure throughout development vivo during mouse preimplantation development (Fig. 1e), in agreement with recent observations revealed that the early 2-cell embryo undergoes during mouse

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