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PreprintCited by 97Genomics and Chromatin DynamicsPluripotent Stem Cells ResearchEpigenetics and DNA Methylation

The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.

The transcriptionally permissive chromatin state of ES cells is acutely tuned to translational output

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Bulut-Karslioglu, Aydan, Macrae, Trisha A., Oses-Prieto, Juan A., Covarrubias, Sergio, Percharde, Michelle, Ku, Gregory, Diaz, Aaron, McManus, Michael T., Burlingame, Alma L., Ramalho-Santos, Miguel·2017·Cell stem cell
DOI 10.1101/167239PMC PMC5836508

Preprint — published as 10.1016/j.stem.2018.02.004 · Paper page

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Abstract

SUMMARY: A permissive chromatin environment coupled to hypertranscription is critical to drive the rapid proliferation of Embryonic Stem (ES) cells and peri-implantation embryos. We carried out a genome-wide screen to systematically dissect the regulation of the euchromatic state of ES cells. The results reveal that activity of cellular growth pathways, prominently protein synthesis, perpetuates the euchromatic state and hypertranscription of ES cells. Acute, mild inhibition of translation results in rapid depletion of euchromatic marks in ES cells and blastocysts, concurrent with delocalization of RNA polymerase II and reduction in nascent transcription. Remarkably, reduced translational output leads to rewiring of open chromatin within 3 hours, including decreased accessibility at a subset of active developmental enhancers and increased accessibility at histone genes and transposable elements. Using a proteome-scale analysis, we show that several euchromatin regulators are unstable proteins and thus continuously depend on a high translational output. We propose that this mechanistic interdependence of euchromatin, transcription and translation sets the pace of proliferation at peri-implantation and may be employed generally by stem/progenitor cells.

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Cites

  • Global quantification of mammalian gene expression control

    Schwanhäusser, B., Busse, D., Li, N., Dittmar, G., Schuchhardt, J., Wolf, J., Chen, W., & Selbach, M. (2011) · Nature · doi:10.1038/nature10098 · Cited by 6,566 · cited 4×

    “cerevisiae and mouse fibroblasts, where cell cycle and transcription factors were found to be preferentially unstable (Belle et al., 2006; Schwanhäusser et al., 2011).”
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Research works printed but not linked: 81

  1. 10.1093/nar/gkw343 · DOI
  2. 10.1371/journal.pone.0010531 · DOI
  3. 10.1016/j.cell.2011.03.003 · DOI
  4. 10.1016/j.cell.2013.08.061 · DOI
  5. 10.1016/j.cell.2013.01.030 · DOI · Paper page
  6. 10.1038/nmeth.1330 · DOI
  7. 10.1073/pnas.0605420103 · DOI · Paper page
  8. 10.1038/nature18282 · DOI
  9. 10.1016/j.stem.2011.12.017 · DOI
  10. 10.1016/j.stem.2012.09.011 · DOI
  11. 10.1002/0471142727.mb2129s109 · DOI · Paper page
  12. 10.1038/nature20578 · DOI · Paper page
  13. 10.1016/j.molcel.2014.05.029 · DOI · Paper page
  14. 10.1016/j.molcel.2013.01.038 · DOI · Paper page
  15. 10.1186/gb-2006-7-10-r100 · DOI
  16. 10.1158/0008-5472.CAN-05-2059 · DOI
  17. 10.1073/pnas.1100099108 · DOI
  18. 10.1242/dev.102681 · DOI
  19. 10.1093/nar/gku1197 · DOI
  20. 10.1016/j.stem.2008.03.021 · DOI
  21. 10.1038/nature11247 · DOI · Paper page
  22. 10.1016/j.cell.2008.05.031 · DOI
  23. Fedoroff, N.V. , 2012. Presidential address. Transposable elements, epigenetics, and genome evolution. Science. · DOI · Paper page
  24. 10.1038/nature04290 · DOI
  25. 10.1073/pnas.95.24.14511 · DOI
  26. 10.1038/nrm3036 · DOI
  27. 10.1038/nature08212 · DOI
  28. 10.1016/j.cell.2010.01.003 · DOI
  29. 10.1242/dev.114843 · DOI
  30. 10.1016/j.molcel.2010.05.004 · DOI · Paper page
  31. 10.1038/nmeth.3252 · DOI
  32. 10.1038/ng.409 · DOI
  33. 10.1091/mbc.E08-06-0596 · DOI
  34. 10.1186/1471-2164-13-424 · DOI
  35. 10.1093/nar/gkh103 · DOI
  36. 10.1073/pnas.1424850112 · DOI
  37. 10.1002/jcp.21714 · DOI
  38. 10.1186/gb-2012-13-10-r85 · DOI
  39. 10.1038/nmeth.1923 · DOI · Paper page
  40. 10.1016/j.cell.2012.03.017 · DOI · Paper page
  41. 10.1002/gene.10250 · DOI
  42. 10.1074/jbc.M808220200 · DOI
  43. 10.1093/bioinformatics/btp352 · DOI · Paper page
  44. 10.1016/j.stem.2012.04.023 · DOI
  45. 10.1093/nar/gkt214 · DOI · Paper page
  46. 10.1016/j.molcel.2015.07.014 · DOI
  47. 10.1038/nbt.1630 · DOI · Paper page
  48. 10.1038/ncomms1915 · DOI
  49. 10.1016/j.devcel.2005.10.017 · DOI
  50. 10.1128/MCB.20.22.8602-8612.2000 · DOI
  51. 10.1182/blood-2011-01-331892 · DOI
  52. 10.1016/j.cmet.2015.02.002 · DOI · Paper page
  53. 10.1016/j.cell.2017.05.004 · DOI · Paper page
  54. 10.1007/BF00609814 · DOI
  55. 10.1016/j.celrep.2014.10.018 · DOI · Paper page
  56. 10.1016/S0925-4773(01)00551-2 · DOI
  57. 10.1016/j.devcel.2016.11.010 · DOI
  58. 10.1016/j.celrep.2017.05.036 · DOI
  59. 10.1021/pr0703674 · DOI
  60. 10.1016/j.cell.2014.05.040 · DOI
  61. 10.1093/nar/gkw257 · DOI · Paper page
  62. 10.1186/s13072-015-0039-z · DOI
  63. 10.1146/annurev.cellbio.20.010403.095114 · DOI
  64. 10.1016/j.stem.2008.03.013 · DOI · Paper page
  65. 10.1016/j.stem.2015.11.004 · DOI
  66. 10.1016/j.cell.2015.12.033 · DOI · Paper page
  67. 10.1038/onc.2015.335 · DOI
  68. 10.1038/200675a0 · DOI
  69. 10.1038/nature13035 · DOI · Paper page
  70. 10.1242/dev.142679 · DOI
  71. 1977, Gastrulation in the mouse: Growth and regionalization of the epiblast, Development, 42, 293, 10.1242/dev.42.1.293 · DOI
  72. 10.1126/science.2898810 · DOI
  73. 10.1073/pnas.1004110107 · DOI
  74. 10.1093/emboj/cdg578 · DOI
  75. 10.1038/nsmb.1780 · DOI
  76. 10.1038/nature10002 · DOI
  77. 10.1038/nature11468 · DOI · Paper page
  78. 10.1074/jbc.M112.424515 · DOI
  79. 10.1016/j.stem.2014.02.013 · DOI
  80. 10.1038/nature06968 · DOI · Paper page
  81. 10.1126/science.1246384 · DOI · Paper page

Metadata

Authors
Bulut-Karslioglu, A., Macrae, T. A., Oses-Prieto, J. A., Covarrubias, S., Percharde, M., Ku, G., Diaz, A., McManus, M. T., Burlingame, A. L., & Ramalho-Santos, M.
Affiliations
University of California, San Francisco (US)
ORCID
Venue
Cell stem cell
Publisher
openRxiv
Published
2017-07-22
Volume
22
Issue
3
Pages
369-383.e8
ISSN
1875-9777 (ISSN-L)
DOI
10.1101/167239
PMC
PMC5836508
OpenAlex
W2792650071
Cited by
97
References
1
Citations by year
2026: 8 · 2025: 6 · 2024: 9 · 2023: 20 · 2022: 9 · 2021: 18 · 2020: 13 · 2019: 6 · 2018: 8
FWCI
3.98
Type
journal article
Language
en
Open access
Licence
www.biorxiv.org/about/FAQ#license (vor)
Locations
  • Cell stem cell (publishedVersion)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • PubMed (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
  • eScholarship (California Digital Library) (submittedVersion)
  • MPG.PuRe (Max Planck Society) (submittedVersion, other-oa)
Funders
  • Dr. Miriam and Sheldon G. Adelson Medical Research Foundation (U01MH105028)
  • Shurl and Kay Curci Foundation (R 01GM123556, 1F30HD093116, R01GM113014)
  • National Institutes of Health (R01OD012204, 1s10od016229-01, DK063720)
  • University of California, San Francisco
  • Diabetes Research Center (P30 DK063720)
  • National Institute of Mental Health (U01MH105028)
  • National Cancer Institute (P30CA082103)
  • National Institute of General Medical Sciences (T32GM007618, R01GM123556, R01GM113014, NIH NIGMS 8P41GM103481, P41GM103481, NIH 1S10OD016229)
  • National Institute of Diabetes and Digestive and Kidney Diseases (P30DK063720)
  • Eunice Kennedy Shriver National Institute of Child Health and Human Development (F30HD093116)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Pluripotent Stem Cells Research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
Keywords
embryonic stem cells, euchromatin, chromatin accessibility, translation (biology), RNA polymerase II, nascent transcription, developmental enhancers, histone genes, transposable elements, protein stability, stem cell proliferation, peri-implantation embryo, blastocyst, genome-wide screen
MeSH terms
Animals, Blastocyst, Cell Differentiation, Chromatin, DNA Transposable Elements, Enhancer Elements, Genetic, Female, Male, Models, Biological, Nuclear Proteins, Transcription, Genetic, Protein Biosynthesis, Proto-Oncogene Proteins c-myc, Genome, Euchromatin, RNA Interference, Histone Code, Mice, Embryonic Stem Cells, Protein Stability, TOR Serine-Threonine Kinases

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