Enhancer-associated H3K4 methylation safeguards in vitro germline competence

Tore Bleckwehl*, Giuliano Crispatzu, Kaitlin Schaaf, Patricia Respuela, Michaela Bartusel, Laura Benson, Stephen J. Clark, Kristel M. Dorighi, Antonio Barral, Magdalena Laugsch, Wilfred F.J. van IJcken, Miguel Manzanares, Joanna Wysocka, Wolf Reik, Álvaro Rada-Iglesias

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

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Abstract

Germline specification in mammals occurs through an inductive process whereby competent cells in the post-implantation epiblast differentiate into primordial germ cells (PGC). The intrinsic factors that endow epiblast cells with the competence to respond to germline inductive signals remain unknown. Single-cell RNA sequencing across multiple stages of an in vitro PGC-like cells (PGCLC) differentiation system shows that PGCLC genes initially expressed in the naïve pluripotent stage become homogeneously dismantled in germline competent epiblast like-cells (EpiLC). In contrast, the decommissioning of enhancers associated with these germline genes is incomplete. Namely, a subset of these enhancers partly retain H3K4me1, accumulate less heterochromatic marks and remain accessible and responsive to transcriptional activators. Subsequently, as in vitro germline competence is lost, these enhancers get further decommissioned and lose their responsiveness to transcriptional activators. Importantly, using H3K4me1-deficient cells, we show that the loss of this histone modification reduces the germline competence of EpiLC and decreases PGCLC differentiation efficiency. Our work suggests that, although H3K4me1 might not be essential for enhancer function, it can facilitate the (re)activation of enhancers and the establishment of gene expression programs during specific developmental transitions.

Original languageEnglish
Article number5771
JournalNature Communications
Volume12
Issue number1
DOIs
Publication statusPublished - 1 Oct 2021

Bibliographical note

Funding Information:
We thank the Rada-Iglesias lab members for insightful comments and critical reading of the manuscript, Antonio Simeone, and Christa Bücker for generously providing the Otx2-/- cell line. Library preparations and next-generation sequencing experiments were performed in the NGS Core Facility of the Cologne Center for Genomics (CCG). Computational analyses were performed on the Cologne High Efficient Operating Platform for Science (CHEOPS). Cell sorting and Flow cytometry experiments were performed in the FACS Facility of the Center for Molecular Medicine (CMMC) and the FACS & Imaging Core Facility at the Max Planck Institute for Biology of Ageing. Tore Bleckwehl was supported by a doctoral fellowship from the Studienstiftung des deutschen Volkes (Germany). Giuliano Crispatzu is supported by funding within the CRU329 (DFG 386793560). Kaitlin Schaaf was supported by a Research Internships in Science and Engineering (RISE) Scholarship of the Deutscher Akademischer Austauschdienst (DAAD). Work in the Rada-Iglesias laboratory was supported by CMMC intramural funding (Germany), the German Research Foundation (DFG) (Research Grant RA 2547/ 2-1), “Programa STAR-Santander Universidades, Campus Cantabria Internacional de la convocatoria CEI 2015 de Campus de Excelencia Internacional” (Spain), the Spanish Ministry of Science, Innovation, and Universities (Research Grant PGC2018-095301-BI00) and the European Research Council (ERC CoG “PoisedLogic”; 862022). AB and MM were supported by the Spanish Ministry of Science, Innovation, and Universities (BFU2017-84914-P), and the CNIC is supported by the Instituto de Salud Carlos III (ISCIII), the Spanish Ministry of Science, Innovation, and Universities, and the Pro CNIC Foundation, and is a Severo Ochoa Center of Excellence (SEV-2015-0505).

Publisher Copyright:
© 2021, The Author(s).

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