DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Control over single-cell distribution of G1 lengths by WNT governs pluripotency

Abstract

The link between single-cell variation and population-level fate choices lacks a mechanistic explanation despite extensive observations of gene expression and epigenetic variation among individual cells. Here, we found that single human embryonic stem cells (hESCs) have different and biased differentiation potentials toward either neuroectoderm or mesendoderm depending on their G1 lengths before the onset of differentiation. Single-cell variation in G1 length operates in a dynamic equilibrium that establishes a G1 length probability distribution for a population of hESCs and predicts differentiation outcome toward neuroectoderm or mesendoderm lineages. Although sister stem cells generally share G1 lengths, a variable proportion of cells have asymmetric G1 lengths, which maintains the population dispersion. Environmental Wingless-INT (WNT) levels can control the G1 length distribution, apparently as a means of priming the fate of hESC populations once they undergo differentiation. As a downstream mechanism, global 5-hydroxymethylcytosine levels are regulated by G1 length and thereby link G1 length to differentiation outcomes of hESCs. Overall, our findings suggest that intrapopulation heterogeneity in G1 length underlies the pluripotent differentiation potential of stem cell populations.

Authors:
ORCiD logo [1]; ORCiD logo [1];  [1]; ORCiD logo [1];  [1];  [1];  [1]; ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [1];  [1];  [1]
  1. Univ. of California, Santa Barbara, CA (United States)
Publication Date:
Research Org.:
Univ. of California, Santa Barbara, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1611177
Grant/Contract Number:  
SC0008975
Resource Type:
Accepted Manuscript
Journal Name:
PLoS Biology (Online)
Additional Journal Information:
Journal Name: PLoS Biology (Online); Journal Volume: 17; Journal Issue: 9; Journal ID: ISSN 1545-7885
Publisher:
Public Library of Science
Country of Publication:
United States
Language:
English
Subject:
60 APPLIED LIFE SCIENCES; Biochemistry & Molecular Biology; Life Sciences & Biomedicine - Other Topics

Citation Formats

Jang, Jiwon, Han, Dasol, Golkaram, Mahdi, Audouard, Morgane, Liu, Guojing, Bridges, Daniel, Hellander, Stefan, Chialastri, Alex, Dey, Siddharth S., Petzold, Linda R., Kosik, Kenneth S., and Brickman, Joshua Mark. Control over single-cell distribution of G1 lengths by WNT governs pluripotency. United States: N. p., 2019. Web. doi:10.1371/journal.pbio.3000453.
Jang, Jiwon, Han, Dasol, Golkaram, Mahdi, Audouard, Morgane, Liu, Guojing, Bridges, Daniel, Hellander, Stefan, Chialastri, Alex, Dey, Siddharth S., Petzold, Linda R., Kosik, Kenneth S., & Brickman, Joshua Mark. Control over single-cell distribution of G1 lengths by WNT governs pluripotency. United States. https://doi.org/10.1371/journal.pbio.3000453
Jang, Jiwon, Han, Dasol, Golkaram, Mahdi, Audouard, Morgane, Liu, Guojing, Bridges, Daniel, Hellander, Stefan, Chialastri, Alex, Dey, Siddharth S., Petzold, Linda R., Kosik, Kenneth S., and Brickman, Joshua Mark. Thu . "Control over single-cell distribution of G1 lengths by WNT governs pluripotency". United States. https://doi.org/10.1371/journal.pbio.3000453. https://www.osti.gov/servlets/purl/1611177.
@article{osti_1611177,
title = {Control over single-cell distribution of G1 lengths by WNT governs pluripotency},
author = {Jang, Jiwon and Han, Dasol and Golkaram, Mahdi and Audouard, Morgane and Liu, Guojing and Bridges, Daniel and Hellander, Stefan and Chialastri, Alex and Dey, Siddharth S. and Petzold, Linda R. and Kosik, Kenneth S. and Brickman, Joshua Mark},
abstractNote = {The link between single-cell variation and population-level fate choices lacks a mechanistic explanation despite extensive observations of gene expression and epigenetic variation among individual cells. Here, we found that single human embryonic stem cells (hESCs) have different and biased differentiation potentials toward either neuroectoderm or mesendoderm depending on their G1 lengths before the onset of differentiation. Single-cell variation in G1 length operates in a dynamic equilibrium that establishes a G1 length probability distribution for a population of hESCs and predicts differentiation outcome toward neuroectoderm or mesendoderm lineages. Although sister stem cells generally share G1 lengths, a variable proportion of cells have asymmetric G1 lengths, which maintains the population dispersion. Environmental Wingless-INT (WNT) levels can control the G1 length distribution, apparently as a means of priming the fate of hESC populations once they undergo differentiation. As a downstream mechanism, global 5-hydroxymethylcytosine levels are regulated by G1 length and thereby link G1 length to differentiation outcomes of hESCs. Overall, our findings suggest that intrapopulation heterogeneity in G1 length underlies the pluripotent differentiation potential of stem cell populations.},
doi = {10.1371/journal.pbio.3000453},
journal = {PLoS Biology (Online)},
number = 9,
volume = 17,
place = {United States},
year = {Thu Sep 26 00:00:00 EDT 2019},
month = {Thu Sep 26 00:00:00 EDT 2019}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Citation Metrics:
Cited by: 7 works
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

Cell-Cycle Control of Developmentally Regulated Transcription Factors Accounts for Heterogeneity in Human Pluripotent Cells
journal, December 2013


Concise Review: Control of Cell Fate Through Cell Cycle and Pluripotency Networks: Cell Cycle and Pluripotency
journal, March 2016

  • Boward, Ben; Wu, Tianming; Dalton, Stephen
  • STEM CELLS, Vol. 34, Issue 6
  • DOI: 10.1002/stem.2345

Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein
journal, November 2004

  • Shaner, Nathan C.; Campbell, Robert E.; Steinbach, Paul A.
  • Nature Biotechnology, Vol. 22, Issue 12
  • DOI: 10.1038/nbt1037

TGF-β-Superfamily Signaling Regulates Embryonic Stem Cell Heterogeneity: Self-Renewal as a Dynamic and Regulated Equilibrium
journal, December 2012

  • Galvin-Burgess, Katherine E.; Travis, Emily D.; Pierson, Kelsey E.
  • STEM CELLS, Vol. 31, Issue 1
  • DOI: 10.1002/stem.1252

The cyclic gene Hes1 contributes to diverse differentiation responses of embryonic stem cells
journal, August 2009

  • Kobayashi, T.; Mizuno, H.; Imayoshi, I.
  • Genes & Development, Vol. 23, Issue 16
  • DOI: 10.1101/gad.1823109

Gene expression heterogeneities in embryonic stem cell populations: origin and function
journal, December 2011

  • Martinez Arias, Alfonso; Brickman, Joshua M.
  • Current Opinion in Cell Biology, Vol. 23, Issue 6
  • DOI: 10.1016/j.ceb.2011.09.007

A short G1 phase is an intrinsic determinant of naïve embryonic stem cell pluripotency
journal, January 2013

  • Coronado, Diana; Godet, Murielle; Bourillot, Pierre-Yves
  • Stem Cell Research, Vol. 10, Issue 1
  • DOI: 10.1016/j.scr.2012.10.004

The cyclin D1 gene is a target of the  -catenin/LEF-1 pathway
journal, May 1999

  • Shtutman, M.; Zhurinsky, J.; Simcha, I.
  • Proceedings of the National Academy of Sciences, Vol. 96, Issue 10
  • DOI: 10.1073/pnas.96.10.5522

Dynamic Equilibrium and Heterogeneity of Mouse Pluripotent Stem Cells with Distinct Functional and Epigenetic States
journal, October 2008

  • Hayashi, Katsuhiko; Lopes, Susana M. Chuva de Sousa; Tang, Fuchou
  • Cell Stem Cell, Vol. 3, Issue 4
  • DOI: 10.1016/j.stem.2008.07.027

Regulated subset of G1 growth-control genes in response to derepression by the Wnt pathway
journal, March 2003

  • Baek, S. H.; Kioussi, C.; Briata, P.
  • Proceedings of the National Academy of Sciences, Vol. 100, Issue 6
  • DOI: 10.1073/pnas.0330217100

The Nuclear DNA Base 5-Hydroxymethylcytosine Is Present in Purkinje Neurons and the Brain
journal, April 2009


SMADs and YAP Compete to Control Elongation of β-Catenin:LEF-1-Recruited RNAPII during hESC Differentiation
journal, June 2015


Base-Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome
journal, June 2012


Initiation of stem cell differentiation involves cell cycle-dependent regulation of developmental genes by Cyclin D
journal, February 2016

  • Pauklin, Siim; Madrigal, Pedro; Bertero, Alessandro
  • Genes & Development, Vol. 30, Issue 4
  • DOI: 10.1101/gad.271452.115

Nanog-dependent feedback loops regulate murine embryonic stem cell heterogeneity
journal, October 2012

  • MacArthur, Ben D.; Sevilla, Ana; Lenz, Michel
  • Nature Cell Biology, Vol. 14, Issue 11
  • DOI: 10.1038/ncb2603

Integrating 5-Hydroxymethylcytosine into the Epigenomic Landscape of Human Embryonic Stem Cells
journal, June 2011


Nanog safeguards pluripotency and mediates germline development
journal, December 2007

  • Chambers, Ian; Silva, Jose; Colby, Douglas
  • Nature, Vol. 450, Issue 7173
  • DOI: 10.1038/nature06403

Dissecting ensemble networks in ES cell populations reveals micro-heterogeneity underlying pluripotency
journal, January 2012

  • Trott, Jamie; Hayashi, Katsuhiko; Surani, Azim
  • Molecular BioSystems, Vol. 8, Issue 3
  • DOI: 10.1039/c1mb05398a

Donor cell type can influence the epigenome and differentiation potential of human induced pluripotent stem cells
journal, November 2011

  • Kim, Kitai; Zhao, Rui; Doi, Akiko
  • Nature Biotechnology, Vol. 29, Issue 12
  • DOI: 10.1038/nbt.2052

Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells
journal, May 2011

  • Pastor, William A.; Pape, Utz J.; Huang, Yun
  • Nature, Vol. 473, Issue 7347
  • DOI: 10.1038/nature10102

Stochasticity in gene expression: from theories to phenotypes
journal, May 2005

  • Kærn, Mads; Elston, Timothy C.; Blake, William J.
  • Nature Reviews Genetics, Vol. 6, Issue 6
  • DOI: 10.1038/nrg1615

Identification of c-MYC as a Target of the APC Pathway
journal, September 1998


A Heterogeneous Expression Pattern for Nanog in Embryonic Stem Cells
journal, October 2007


A simple tool to improve pluripotent stem cell differentiation
journal, April 2013

  • Chetty, Sundari; Pagliuca, Felicia Walton; Honore, Christian
  • Nature Methods, Vol. 10, Issue 6
  • DOI: 10.1038/nmeth.2442

Cdk4/CyclinD1 Overexpression in Neural Stem Cells Shortens G1, Delays Neurogenesis, and Promotes the Generation and Expansion of Basal Progenitors
journal, September 2009


A panel of induced pluripotent stem cells from chimpanzees: a resource for comparative functional genomics
journal, June 2015

  • Gallego Romero, Irene; Pavlovic, Bryan J.; Hernando-Herraez, Irene
  • eLife, Vol. 4
  • DOI: 10.7554/eLife.07103

Wnt/β-Catenin Signaling and Disease
journal, June 2012


A parallel circuit of LIF signalling pathways maintains pluripotency of mouse ES cells
journal, July 2009

  • Niwa, Hitoshi; Ogawa, Kazuya; Shimosato, Daisuke
  • Nature, Vol. 460, Issue 7251
  • DOI: 10.1038/nature08113

Heterogeneity of Embryonic and Adult Stem Cells
journal, November 2008


Conversion of 5-Methylcytosine to 5-Hydroxymethylcytosine in Mammalian DNA by MLL Partner TET1
journal, April 2009


Visualizing Spatiotemporal Dynamics of Multicellular Cell-Cycle Progression
journal, February 2008


Embryonic stem cells require Wnt proteins to prevent differentiation to epiblast stem cells
journal, August 2011

  • ten Berge, Derk; Kurek, Dorota; Blauwkamp, Tim
  • Nature Cell Biology, Vol. 13, Issue 9
  • DOI: 10.1038/ncb2314

Self-renewal of human embryonic stem cells is supported by a shortened G1 cell cycle phase
journal, January 2006

  • Becker, Klaus A.; Ghule, Prachi N.; Therrien, Jaclyn A.
  • Journal of Cellular Physiology, Vol. 209, Issue 3
  • DOI: 10.1002/jcp.20776

A Localized Wnt Signal Orients Asymmetric Stem Cell Division in Vitro
journal, March 2013


Regulated Fluctuations in Nanog Expression Mediate Cell Fate Decisions in Embryonic Stem Cells
journal, July 2009


Identification and characterization of subpopulations in undifferentiated ES cell culture
journal, February 2008

  • Toyooka, Y.; Shimosato, D.; Murakami, K.
  • Development, Vol. 135, Issue 5
  • DOI: 10.1242/dev.017400

The Cell-Cycle State of Stem Cells Determines Cell Fate Propensity
journal, September 2013


Single-cell 5hmC sequencing reveals chromosome-wide cell-to-cell variability and enables lineage reconstruction
journal, June 2016

  • Mooijman, Dylan; Dey, Siddharth S.; Boisset, Jean-Charles
  • Nature Biotechnology, Vol. 34, Issue 8
  • DOI: 10.1038/nbt.3598

Differentiation-defective phenotypes revealed by large-scale analyses of human pluripotent stem cells
journal, November 2013

  • Koyanagi-Aoi, M.; Ohnuki, M.; Takahashi, K.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 51
  • DOI: 10.1073/pnas.1319061110

β-Catenin regulates expression of cyclin D1 in colon carcinoma cells
journal, April 1999

  • Tetsu, Osamu; McCormick, Frank
  • Nature, Vol. 398, Issue 6726
  • DOI: 10.1038/18884

5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells
journal, January 2011


Stochastic modelling of individual cell growth using flow chamber microscopy images
journal, November 2005


Highly efficient neural conversion of human ES and iPS cells by dual inhibition of SMAD signaling
journal, March 2009

  • Chambers, Stuart M.; Fasano, Christopher A.; Papapetrou, Eirini P.
  • Nature Biotechnology, Vol. 27, Issue 3
  • DOI: 10.1038/nbt.1529

Primary Cilium-Autophagy-Nrf2 (PAN) Axis Activation Commits Human Embryonic Stem Cells to a Neuroectoderm Fate
journal, April 2016


Zscan4 regulates telomere elongation and genomic stability in ES cells
journal, March 2010

  • Zalzman, Michal; Falco, Geppino; Sharova, Lioudmila V.
  • Nature, Vol. 464, Issue 7290
  • DOI: 10.1038/nature08882

Maintenance of pluripotency in human and mouse embryonic stem cells through activation of Wnt signaling by a pharmacological GSK-3-specific inhibitor
journal, December 2003

  • Sato, Noboru; Meijer, Laurent; Skaltsounis, Leandros
  • Nature Medicine, Vol. 10, Issue 1
  • DOI: 10.1038/nm979

Coupling of growth arrest and differentiation at a distinct state in the G1 phase of the cell cycle: GD.
journal, February 1982

  • Scott, R. E.; Florine, D. L.; Wille, J. J.
  • Proceedings of the National Academy of Sciences, Vol. 79, Issue 3
  • DOI: 10.1073/pnas.79.3.845

Lengthened G1 Phase Indicates Differentiation Status in Human Embryonic Stem Cells
journal, January 2013

  • Calder, Ashley; Roth-Albin, Ivana; Bhatia, Sonam
  • Stem Cells and Development, Vol. 22, Issue 2
  • DOI: 10.1089/scd.2012.0168

CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq
journal, April 2016


AN ASYMPTOTIC TEST FOR THE EQUALITY OF COEFFICIENTS OF VARIATION FROMk POPULATIONS
journal, March 1996


Donor-dependent variations in hepatic differentiation from human-induced pluripotent stem cells
journal, July 2012

  • Kajiwara, M.; Aoi, T.; Okita, K.
  • Proceedings of the National Academy of Sciences, Vol. 109, Issue 31
  • DOI: 10.1073/pnas.1209979109

Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation
journal, April 2011

  • Ficz, Gabriella; Branco, Miguel R.; Seisenberger, Stefanie
  • Nature, Vol. 473, Issue 7347
  • DOI: 10.1038/nature10008

Canonical Wnt Signaling Induces a Primitive Endoderm Metastable State in Mouse Embryonic Stem Cells
journal, March 2013

  • Price, Feodor D.; Yin, Hang; Jones, Andrew
  • STEM CELLS, Vol. 31, Issue 4
  • DOI: 10.1002/stem.1321

Cell cycle analysis during retinoic acid induced differentiation of a human embryonal carcinoma-derived cell line
journal, March 1987

  • Mummery, Christine L.; van Rooijen, Marga A.; van den Brink, Stieneke E.
  • Cell Differentiation, Vol. 20, Issue 2-3
  • DOI: 10.1016/0045-6039(87)90429-5

Functional Heterogeneity of Embryonic Stem Cells Revealed through Translational Amplification of an Early Endodermal Transcript
journal, May 2010


Chromatin in pluripotent embryonic stem cells and differentiation
journal, May 2006

  • Meshorer, Eran; Misteli, Tom
  • Nature Reviews Molecular Cell Biology, Vol. 7, Issue 7
  • DOI: 10.1038/nrm1938

Noncytotoxic orange and red/green derivatives of DsRed-Express2 for whole-cell labeling
journal, January 2009

  • Strack, Rita L.; Bhattacharyya, Dibyendu; Glick, Benjamin S.
  • BMC Biotechnology, Vol. 9, Issue 1
  • DOI: 10.1186/1472-6750-9-32

Cell-Cycle Control of Bivalent Epigenetic Domains Regulates the Exit from Pluripotency
journal, September 2015


Age-dependent stochastic models for understanding population fluctuations in continuously cultured cells
journal, August 2013

  • Stukalin, Evgeny B.; Aifuwa, Ivie; Kim, Jin Seob
  • Journal of The Royal Society Interface, Vol. 10, Issue 85
  • DOI: 10.1098/rsif.2013.0325

FGF2 Sustains NANOG and Switches the Outcome of BMP4-Induced Human Embryonic Stem Cell Differentiation
journal, March 2011


Connection between stochastic and deterministic modelling of microbial growth
journal, January 2005

  • Kutalik, Zoltán; Razaz, Moe; Baranyi, József
  • Journal of Theoretical Biology, Vol. 232, Issue 2
  • DOI: 10.1016/j.jtbi.2004.08.013

Wnt and FGF signals interact to coordinate growth with cell fate specification during limb development
journal, August 2008

  • ten Berge, D.; Brugmann, S. A.; Helms, J. A.
  • Development, Vol. 135, Issue 19
  • DOI: 10.1242/dev.023176

The Cell-Cycle State of Stem Cells Determines Cell Fate Propensity
journal, March 2014


Cell-Cycle Control of Developmentally Regulated Transcription Factors Accounts for Heterogeneity in Human Pluripotent Cells
journal, March 2014


Self-renewal of human embryonic stem cells is supported by a shortened G1 cell cycle phase
journal, January 2006

  • Becker, Klaus A.; Ghule, Prachi N.; Therrien, Jaclyn A.
  • Journal of Cellular Physiology, Vol. 209, Issue 3
  • DOI: 10.1002/jcp.20776

Canonical Wnt Signaling Induces a Primitive Endoderm Metastable State in Mouse Embryonic Stem Cells
journal, March 2013

  • Price, Feodor D.; Yin, Hang; Jones, Andrew
  • STEM CELLS, Vol. 31, Issue 4
  • DOI: 10.1002/stem.1321

Concise Review: Control of Cell Fate Through Cell Cycle and Pluripotency Networks: Cell Cycle and Pluripotency
journal, March 2016

  • Boward, Ben; Wu, Tianming; Dalton, Stephen
  • STEM CELLS, Vol. 34, Issue 6
  • DOI: 10.1002/stem.2345

Cell cycle analysis during retinoic acid induced differentiation of a human embryonal carcinoma-derived cell line
journal, March 1987

  • Mummery, Christine L.; van Rooijen, Marga A.; van den Brink, Stieneke E.
  • Cell Differentiation, Vol. 20, Issue 2-3
  • DOI: 10.1016/0045-6039(87)90429-5

Aggregation and cell cycle dependent retinoic acid receptor mRNA expression in P19 embryonal carcinoma cells
journal, February 1992

  • Jonk, Luigi J. C.; de Jonge, Marjolijn E. J.; Kruyt, Frank A. E.
  • Mechanisms of Development, Vol. 36, Issue 3
  • DOI: 10.1016/0925-4773(92)90067-t

Gene expression heterogeneities in embryonic stem cell populations: origin and function
journal, December 2011

  • Martinez Arias, Alfonso; Brickman, Joshua M.
  • Current Opinion in Cell Biology, Vol. 23, Issue 6
  • DOI: 10.1016/j.ceb.2011.09.007

Visualizing Spatiotemporal Dynamics of Multicellular Cell-Cycle Progression
journal, February 2008


Capturing Pluripotency
journal, February 2008


Wnt/β-Catenin Signaling and Disease
journal, June 2012


Statistical Mechanics of Pluripotency
journal, August 2013


The Cell-Cycle State of Stem Cells Determines Cell Fate Propensity
journal, March 2014


Stochastic modelling of individual cell growth using flow chamber microscopy images
journal, November 2005


Connection between stochastic and deterministic modelling of microbial growth
journal, January 2005

  • Kutalik, Zoltán; Razaz, Moe; Baranyi, József
  • Journal of Theoretical Biology, Vol. 232, Issue 2
  • DOI: 10.1016/j.jtbi.2004.08.013

SMADs and YAP Compete to Control Elongation of β-Catenin:LEF-1-Recruited RNAPII during hESC Differentiation
journal, June 2015


Dynamic Equilibrium and Heterogeneity of Mouse Pluripotent Stem Cells with Distinct Functional and Epigenetic States
journal, October 2008

  • Hayashi, Katsuhiko; Lopes, Susana M. Chuva de Sousa; Tang, Fuchou
  • Cell Stem Cell, Vol. 3, Issue 4
  • DOI: 10.1016/j.stem.2008.07.027

Heterogeneity of Embryonic and Adult Stem Cells
journal, November 2008


Stem Cell States, Fates, and the Rules of Attraction
journal, May 2009


Cdk4/CyclinD1 Overexpression in Neural Stem Cells Shortens G1, Delays Neurogenesis, and Promotes the Generation and Expansion of Basal Progenitors
journal, September 2009


The Cell Cycle and Myc Intersect with Mechanisms that Regulate Pluripotency and Reprogramming
journal, August 2009


Cell-Cycle Control of Bivalent Epigenetic Domains Regulates the Exit from Pluripotency
journal, September 2015


Nanog safeguards pluripotency and mediates germline development
journal, December 2007

  • Chambers, Ian; Silva, Jose; Colby, Douglas
  • Nature, Vol. 450, Issue 7173
  • DOI: 10.1038/nature06403

Zscan4 regulates telomere elongation and genomic stability in ES cells
journal, March 2010

  • Zalzman, Michal; Falco, Geppino; Sharova, Lioudmila V.
  • Nature, Vol. 464, Issue 7290
  • DOI: 10.1038/nature08882

Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation
journal, April 2011

  • Ficz, Gabriella; Branco, Miguel R.; Seisenberger, Stefanie
  • Nature, Vol. 473, Issue 7347
  • DOI: 10.1038/nature10008

Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells
journal, May 2011

  • Pastor, William A.; Pape, Utz J.; Huang, Yun
  • Nature, Vol. 473, Issue 7347
  • DOI: 10.1038/nature10102

Embryonic stem cell potency fluctuates with endogenous retrovirus activity
journal, June 2012

  • Macfarlan, Todd S.; Gifford, Wesley D.; Driscoll, Shawn
  • Nature, Vol. 487, Issue 7405
  • DOI: 10.1038/nature11244

Donor cell type can influence the epigenome and differentiation potential of human induced pluripotent stem cells
journal, November 2011

  • Kim, Kitai; Zhao, Rui; Doi, Akiko
  • Nature Biotechnology, Vol. 29, Issue 12
  • DOI: 10.1038/nbt.2052

Single-cell 5hmC sequencing reveals chromosome-wide cell-to-cell variability and enables lineage reconstruction
journal, June 2016

  • Mooijman, Dylan; Dey, Siddharth S.; Boisset, Jean-Charles
  • Nature Biotechnology, Vol. 34, Issue 8
  • DOI: 10.1038/nbt.3598

Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein
journal, November 2004

  • Shaner, Nathan C.; Campbell, Robert E.; Steinbach, Paul A.
  • Nature Biotechnology, Vol. 22, Issue 12
  • DOI: 10.1038/nbt1037

Embryonic stem cells require Wnt proteins to prevent differentiation to epiblast stem cells
journal, August 2011

  • ten Berge, Derk; Kurek, Dorota; Blauwkamp, Tim
  • Nature Cell Biology, Vol. 13, Issue 9
  • DOI: 10.1038/ncb2314

Nanog-dependent feedback loops regulate murine embryonic stem cell heterogeneity
journal, October 2012

  • MacArthur, Ben D.; Sevilla, Ana; Lenz, Michel
  • Nature Cell Biology, Vol. 14, Issue 11
  • DOI: 10.1038/ncb2603

A simple tool to improve pluripotent stem cell differentiation
journal, April 2013

  • Chetty, Sundari; Pagliuca, Felicia Walton; Honore, Christian
  • Nature Methods, Vol. 10, Issue 6
  • DOI: 10.1038/nmeth.2442

Stochasticity in gene expression: from theories to phenotypes
journal, May 2005

  • Kærn, Mads; Elston, Timothy C.; Blake, William J.
  • Nature Reviews Genetics, Vol. 6, Issue 6
  • DOI: 10.1038/nrg1615

Dissecting ensemble networks in ES cell populations reveals micro-heterogeneity underlying pluripotency
journal, January 2012

  • Trott, Jamie; Hayashi, Katsuhiko; Surani, Azim
  • Molecular BioSystems, Vol. 8, Issue 3
  • DOI: 10.1039/c1mb05398a

Regulated subset of G1 growth-control genes in response to derepression by the Wnt pathway
journal, March 2003

  • Baek, S. H.; Kioussi, C.; Briata, P.
  • Proceedings of the National Academy of Sciences, Vol. 100, Issue 6
  • DOI: 10.1073/pnas.0330217100

Donor-dependent variations in hepatic differentiation from human-induced pluripotent stem cells
journal, July 2012

  • Kajiwara, M.; Aoi, T.; Okita, K.
  • Proceedings of the National Academy of Sciences, Vol. 109, Issue 31
  • DOI: 10.1073/pnas.1209979109

Coupling of growth arrest and differentiation at a distinct state in the G1 phase of the cell cycle: GD.
journal, February 1982

  • Scott, R. E.; Florine, D. L.; Wille, J. J.
  • Proceedings of the National Academy of Sciences, Vol. 79, Issue 3
  • DOI: 10.1073/pnas.79.3.845

Age-dependent stochastic models for understanding population fluctuations in continuously cultured cells
journal, August 2013

  • Stukalin, Evgeny B.; Aifuwa, Ivie; Kim, Jin Seob
  • Journal of The Royal Society Interface, Vol. 10, Issue 85
  • DOI: 10.1098/rsif.2013.0325

Initiation of stem cell differentiation involves cell cycle-dependent regulation of developmental genes by Cyclin D
journal, February 2016

  • Pauklin, Siim; Madrigal, Pedro; Bertero, Alessandro
  • Genes & Development, Vol. 30, Issue 4
  • DOI: 10.1101/gad.271452.115

The Nuclear DNA Base 5-Hydroxymethylcytosine Is Present in Purkinje Neurons and the Brain
journal, April 2009


Conversion of 5-Methylcytosine to 5-Hydroxymethylcytosine in Mammalian DNA by MLL Partner TET1
journal, April 2009


A Localized Wnt Signal Orients Asymmetric Stem Cell Division in Vitro
journal, March 2013


Identification of c-MYC as a Target of the APC Pathway
journal, September 1998


Genome-Wide Studies Reveal that H3K4me3 Modification in Bivalent Genes Is Dynamically Regulated during the Pluripotent Cell Cycle and Stabilized upon Differentiation
journal, December 2015

  • Grandy, Rodrigo A.; Whitfield, Troy W.; Wu, Hai
  • Molecular and Cellular Biology, Vol. 36, Issue 4
  • DOI: 10.1128/mcb.00877-15

Noncytotoxic orange and red/green derivatives of DsRed-Express2 for whole-cell labeling
journal, January 2009

  • Strack, Rita L.; Bhattacharyya, Dibyendu; Glick, Benjamin S.
  • BMC Biotechnology, Vol. 9, Issue 1
  • DOI: 10.1186/1472-6750-9-32

5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells
journal, January 2011


Identification and characterization of subpopulations in undifferentiated ES cell culture
journal, February 2008

  • Toyooka, Y.; Shimosato, D.; Murakami, K.
  • Development, Vol. 135, Issue 5
  • DOI: 10.1242/dev.017400

Wnt and FGF signals interact to coordinate growth with cell fate specification during limb development
journal, August 2008

  • ten Berge, D.; Brugmann, S. A.; Helms, J. A.
  • Development, Vol. 135, Issue 19
  • DOI: 10.1242/dev.023176

Functional Heterogeneity of Embryonic Stem Cells Revealed through Translational Amplification of an Early Endodermal Transcript
journal, May 2010


Integrating 5-Hydroxymethylcytosine into the Epigenomic Landscape of Human Embryonic Stem Cells
journal, June 2011


How the cell cycle impacts chromatin architecture and influences cell fate
journal, February 2015