The dynamic interactome and genomic targets of Polycomb complexes during stem-cell differentiation.
Although the core subunits of Polycomb group (PcG) complexes are well characterized, little is known about the dynamics of these protein complexes during cellular differentiation. We used quantitative interaction proteomics and genome-wide profiling to study PcG proteins in mouse embryonic stem cells (ESCs) and neural progenitor cells (NPCs). We found that the stoichiometry and genome-wide binding of PRC1 and PRC2 were highly dynamic during neural differentiation. Intriguingly, we observed a downregulation and loss of PRC2 from chromatin marked with trimethylated histone H3 K27 (H3K27me3) during differentiation, whereas PRC1 was retained at these sites. Additionally, we found PRC1 at enhancer and promoter regions independently of PRC2 binding and H3K27me3. Finally, overexpression of NPC-specific PRC1 interactors in ESCs led to increased Ring1b binding to, and decreased expression of, NPC-enriched Ring1b-target genes. In summary, our integrative analyses uncovered dynamic PcG subcomplexes and their widespread colocalization with active chromatin marks during differentiation.
Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, The Netherlands.
Susan L
SL
Kloet
Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, The Netherlands.
Matthew M
MM
Makowski
Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, The Netherlands.
H Irem
HI
Baymaz
Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, The Netherlands.
Lisa
L
van Voorthuijsen
Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, The Netherlands.
Ino D
ID
Karemaker
Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.|Department of Biomedical Genetics, Universitat Pompeu Fabra (UPF), Barcelona, Spain.
Alexandra
A
Santanach
Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, The Netherlands.
Pascal W T C
PWTC
Jansen
Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.|Department of Biomedical Genetics, Universitat Pompeu Fabra (UPF), Barcelona, Spain.|Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain.
Luciano
L
Di Croce
Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, The Netherlands.|Cancer GenomiCs.nl (CGC.nl) Consortium, Center for Molecular Medicine, UMC Utrecht, The Netherlands.
Michiel
M
Vermeulen
D000818:Animals; D002454:Cell Differentiation / Q000235:genetics*; D002460:Cell Line; D002843:Chromatin / Q000737:chemistry / Q000378:metabolism*; D002853:Chromatography, Liquid; D022202:Chromosomes, Artificial, Bacterial; D005786:Gene Expression Regulation; D055106:Genome-Wide Association Study; D006657:Histones / Q000235:genetics* / Q000378:metabolism; D051379:Mice; D000066450:Mouse Embryonic Stem Cells / Q000166:cytology / Q000378:metabolism*; D058953:Neural Stem Cells / Q000166:cytology / Q000378:metabolism*; D063146:Polycomb-Group Proteins / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D025941:Protein Interaction Mapping; D040901:Proteomics / Q000379:methods; D015398:Signal Transduction; D053719:Tandem Mass Spectrometry
D002843:Chromatin; D006657:Histones; D063146:Polycomb-Group Proteins