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The histone chaperone CAF-1 safeguards somatic cell identity

Cheloufi, Sihem and Ninova, Maria and Aravin, Alexei (2015) The histone chaperone CAF-1 safeguards somatic cell identity. Nature, 528 (7581). pp. 218-224. ISSN 0028-0836. PMCID PMC4866648.

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[img] Image (JPEG) (Extended Data Figure 1: Validation of hits from chromatin-focused shRNA screens) - Supplemental Material
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[img] Image (JPEG) (Extended Data Figure 2: Germline transmission of iPS cells, genetic interaction of shRNA hits and effect of CAF-1 or Ube2i suppression on reprogramming dynamics) - Supplemental Material
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[img] Image (JPEG) (Extended Data Figure 3: Effect of CAF-1 suppression on OKSM levels and cellular growth, and shRNA rescue experiment) - Supplemental Material
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[img] Image (JPEG) (Extended Data Figure 4: Confirmation of CAF-1 reprogramming phenotype with alternative transgenic and non-transgenic vector systems) - Supplemental Material
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[img] Image (JPEG) (Extended Data Figure 5: Effects of CAF-1 dose on NIH3T3 growth and reprogramming potential) - Supplemental Material
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[img] Image (JPEG) (Extended Data Figure 6: Effect of CAF-1 suppression on HSP cell reprogramming and transdifferentiation) - Supplemental Material
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[img] Image (JPEG) (Extended Data Figure 7: CAF-1 suppression promotes chromatin accessibility at enhancer elements) - Supplemental Material
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[img] Image (JPEG) (Extended Data Figure 8: CAF-1 suppression facilitates Sox2 binding to chromatin) - Supplemental Material
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[img] Image (JPEG) (Extended Data Figure 9: CAF-1 suppression induces specific depletion of H3K9me3 at somatic heterochromatin domains) - Supplemental Material
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Cellular differentiation involves profound remodelling of chromatic landscapes, yet the mechanisms by which somatic cell identity is subsequently maintained remain incompletely understood. To further elucidate regulatory pathways that safeguard the somatic state, we performed two comprehensive RNA interference (RNAi) screens targeting chromatin factors during transcription-factor-mediated reprogramming of mouse fibroblasts to induced pluripotent stem cells (iPS cells). Subunits of the chromatin assembly factor-1 (CAF-1) complex, including Chaf1a and Chaf1b, emerged as the most prominent hits from both screens, followed by modulators of lysine sumoylation and heterochromatin maintenance. Optimal modulation of both CAF-1 and transcription factor levels increased reprogramming efficiency by several orders of magnitude and facilitated iPS cell formation in as little as 4 days. Mechanistically, CAF-1 suppression led to a more accessible chromatin structure at enhancer elements early during reprogramming. These changes were accompanied by a decrease in somatic heterochromatin domains, increased binding of Sox2 to pluripotency-specific targets and activation of associated genes. Notably, suppression of CAF-1 also enhanced the direct conversion of B cells into macrophages and fibroblasts into neurons. Together, our findings reveal the histone chaperone CAF-1 to be a novel regulator of somatic cell identity during transcription-factor-induced cell-fate transitions and provide a potential strategy to modulate cellular plasticity in a regenerative setting.

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Ninova, Maria0000-0001-5051-5502
Additional Information:© 2015 Macmillan Publishers Limited. Received 23 February 2015; Accepted 28 September 2015. Published online 09 December 2015. We thank B. Kingston, C. Vakoc, M. Tolstorukov and G. Hannon for guidance and discussions, B. Bernstein, K. Plath, K. Chronis, Y. Shen and O. Tam for advice on the ATAC-seq analysis, P. Brown for providing the Dot1l inhibitor, B. Stillman for sharing the Chaf1b antibody and T. Graf for sharing the C10 cell line. We thank C. Nakada and Y. Kiyota (Nikon) for providing software to quantify iPS cell formation and A. Huebner for help with transdifferentiation experiments. We are grateful to H. Hock and the HSCI-CRM flow cytometry core for help with flow data analysis and to W. Mallard for initial RNA-sequencing analysis. We further thank B. Ma, S. Muller, M. Weissenboeck and the IMP/IMBA Biooptics and Transgenic core facility as well the CSF NGS laboratory for technical assistance and all members of the Hochedlinger, Zuber, Penninger, Elling, Shi and Kingston laboratories for their feedback on various aspects of this project. We thank A. Stark, A. Deaton and L. Barrett for critical reading of the manuscript. S.C. was supported by the PRCRP at the Department of Defense (CA 120212). H.Y.C. by was supported by NIH P50-HG007735. U.E. was funded by grants from IMBA and the Austrian National Foundation. S.W.L. was supported by a cancer center support grant and program project grant from the NCI and is an HHMI investigator. J.M.P. was supported by IMBA, ERC GA (number 341036) and the Innovator Award/Era of Hope Award Number W81XWH-12-1-0093. J.Z. was funded by an ERC starting grant (number 336860) and generous institutional funding from Boehringer Ingelheim. K.H. was supported by funds from the MGH, HHMI, NIH (R01 HD058013-06) and the Gerald and Darlene Jordan Chair in Regenerative Medicine. Author Contributions: Y. L. Jung and B. Hopfgartner contributed equally to this work. S.C., K.H., U.E. and J.Z. designed primary screens, analysed and interpreted data. S.C., J.M. and N.A. performed the arrayed screen and S.C. conducted follow-up cell biology and chromatin studies. U.E. and B.H. performed the multiplexed screen. U.E. performed validation experiments, genetic interaction assays and cell biology experiments with support from B.H., M.H. and D.W. Human reprogramming experiments were performed by S.C. and J.B.; N.T. and S.W.L. assisted in the generation of inducible Col1a1::tetOP-Chaf1a shRNA cell lines. S.C., A.I.B., A.B. and Y.S. performed B-cell to macrophage conversion experiments. C.E.A. and M.W. conducted MEF to induced neuron transdifferentiation experiments. Y.L.J., M.N., A.A., F.F. and P.J.P. performed bioinformatics analyses. M.H. and U.E. conducted the CiA assay with support from O.B. D.J.W. assisted with the SONO-seq experiments and H.Y.C. helped with the ATAC-seq assay. J.M., M.H. and M.Z. assisted with western blot and chromatin studies. D.T. and J.R. conducted ChIP experiments and library construction. M.S. and S.E.V. provided secondary Oct4–tdTomato MEFs. J.Z. and S.W.L. provided the arrayed library. J.Z. and P.R. designed the extended chromatin library. M.F., J.J. and B.H. generated lentiviral vectors and RNAi reagents. J.M.P. and G.A. provided intellectual support and mentoring. K.H., S.C., J.Z. and U.E. wrote the paper with input from all co-authors. The authors declare no competing financial interests. All SONO-seq, ATAC-seq, ChIP-seq, RNA-seq and microarray data have been deposited in the Gene Expression Omnibus database under accession number GSE66534.
Funding AgencyGrant Number
Department of DefenseCA 120212
FWF Der WissenschaftsfondsUNSPECIFIED
National Cancer InstituteUNSPECIFIED
Howard Hughes Medical Institute (HHMI)UNSPECIFIED
European Research Council (ERC)341036
Innovator Award/Era of Hope AwardW81XWH-12-1-0093
European Research Council (ERC)336860
Boehringer IngelheimUNSPECIFIED
NIHR01 HD058013-06
Gerald and Darlene Jordan Chair in Regenerative MedicineUNSPECIFIED
Subject Keywords:Pluripotent stem cells; Reprogramming; Induced pluripotent stem cells
Issue or Number:7581
PubMed Central ID:PMC4866648
Record Number:CaltechAUTHORS:20160105-101557021
Persistent URL:
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:63373
Deposited By: Tony Diaz
Deposited On:05 Jan 2016 20:31
Last Modified:03 Oct 2019 09:27

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