skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Divergent cytosine DNA methylation patterns in single-cell, soybean root hairs

Abstract

Not provided.

Authors:
 [1]; ORCiD logo [2];  [3];  [4];  [1];  [4];  [1];  [5];  [6];  [6];  [7];  [4];  [3];  [8];  [1]
  1. Divisions of Plant Science and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia MO 65211 USA
  2. Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road La Jolla CA 92037 USA; Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba Ibaraki 30508602 Japan
  3. Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road Athens GA 30602-6810 USA
  4. Department of Computer Science, Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri-Columbia, Columbia MO 65211 USA
  5. Department of Computer Science, Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri-Columbia, Columbia MO 65211 USA; Department of Molecular Microbiology and Immunology and Office of Research, School of Medicine, University of Missouri, Columbia MO 65211 USA
  6. HudsonAlpha Genome Sequencing Center, 601 Genome Way Huntsville AL 35806 USA
  7. Department of Genetics, The University of Georgia, 120 East Green Street Athens GA 30602 USA
  8. Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road La Jolla CA 92037 USA
Publication Date:
Research Org.:
Univ. of Missouri, Columbia, MO (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1536766
DOE Contract Number:  
SC0004898
Resource Type:
Journal Article
Journal Name:
New Phytologist
Additional Journal Information:
Journal Volume: 214; Journal Issue: 2; Journal ID: ISSN 0028-646X
Publisher:
Wiley
Country of Publication:
United States
Language:
English
Subject:
Plant Sciences

Citation Formats

Hossain, Md Shakhawat, Kawakatsu, Taiji, Kim, Kyung Do, Zhang, Ning, Nguyen, Cuong T., Khan, Saad M., Batek, Josef M., Joshi, Trupti, Schmutz, Jeremy, Grimwood, Jane, Schmitz, Robert J., Xu, Dong, Jackson, Scott A., Ecker, Joseph R., and Stacey, Gary. Divergent cytosine DNA methylation patterns in single-cell, soybean root hairs. United States: N. p., 2017. Web. doi:10.1111/nph.14421.
Hossain, Md Shakhawat, Kawakatsu, Taiji, Kim, Kyung Do, Zhang, Ning, Nguyen, Cuong T., Khan, Saad M., Batek, Josef M., Joshi, Trupti, Schmutz, Jeremy, Grimwood, Jane, Schmitz, Robert J., Xu, Dong, Jackson, Scott A., Ecker, Joseph R., & Stacey, Gary. Divergent cytosine DNA methylation patterns in single-cell, soybean root hairs. United States. doi:10.1111/nph.14421.
Hossain, Md Shakhawat, Kawakatsu, Taiji, Kim, Kyung Do, Zhang, Ning, Nguyen, Cuong T., Khan, Saad M., Batek, Josef M., Joshi, Trupti, Schmutz, Jeremy, Grimwood, Jane, Schmitz, Robert J., Xu, Dong, Jackson, Scott A., Ecker, Joseph R., and Stacey, Gary. Fri . "Divergent cytosine DNA methylation patterns in single-cell, soybean root hairs". United States. doi:10.1111/nph.14421.
@article{osti_1536766,
title = {Divergent cytosine DNA methylation patterns in single-cell, soybean root hairs},
author = {Hossain, Md Shakhawat and Kawakatsu, Taiji and Kim, Kyung Do and Zhang, Ning and Nguyen, Cuong T. and Khan, Saad M. and Batek, Josef M. and Joshi, Trupti and Schmutz, Jeremy and Grimwood, Jane and Schmitz, Robert J. and Xu, Dong and Jackson, Scott A. and Ecker, Joseph R. and Stacey, Gary},
abstractNote = {Not provided.},
doi = {10.1111/nph.14421},
journal = {New Phytologist},
issn = {0028-646X},
number = 2,
volume = 214,
place = {United States},
year = {2017},
month = {1}
}

Works referenced in this record:

HTSeq--a Python framework to work with high-throughput sequencing data
journal, September 2014


The tissue-specific methylation of the human Tyrosine Hydroxylase gene reveals new regulatory elements in the first exon
journal, July 2005


Epigenetics and Bacterial Infections
journal, December 2012


Trimmomatic: a flexible trimmer for Illumina sequence data
journal, April 2014


Control of leghaemoglobin synthesis in snake beans
journal, December 1971

  • Broughton, W. J.; Dilworth, M. J.
  • Biochemical Journal, Vol. 125, Issue 4
  • DOI: 10.1042/bj1251075

Reprogramming of DNA Methylation in Pollen Guides Epigenetic Inheritance via Small RNA
journal, September 2012


Stress and transposable elements: co-evolution or useful parasites?
journal, January 2000


How a Retrotransposon Exploits the Plant's Heat Stress Response for Its Activation
journal, January 2014


Epigenetic regulation of stress responses in plants
journal, April 2009


SoyTEdb: a comprehensive database of transposable elements in the soybean genome
journal, January 2010


DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation
journal, May 2015


Epigenetics and the environment: emerging patterns and implications
journal, January 2012

  • Feil, Robert; Fraga, Mario F.
  • Nature Reviews Genetics, Vol. 13, Issue 2
  • DOI: 10.1038/nrg3142

Transposon integration enhances expression of stress response genes
journal, November 2012

  • Feng, Gang; Leem, Young-Eun; Levin, Henry L.
  • Nucleic Acids Research, Vol. 41, Issue 2
  • DOI: 10.1093/nar/gks1185

Root Hairs
journal, January 2014

  • Grierson, Claire; Nielsen, Erik; Ketelaarc, Tijs
  • The Arabidopsis Book, Vol. 12
  • DOI: 10.1199/tab.0172

System approaches to study root hairs as a single cell plant model: current status and future perspectives
journal, May 2015

  • Hossain, Md Shakhawat; Joshi, Trupti; Stacey, Gary
  • Frontiers in Plant Science, Vol. 6
  • DOI: 10.3389/fpls.2015.00363

DNA methylation in cell differentiation and reprogramming: an emerging systematic view
journal, July 2010

  • Huang, Kevin; Fan, Guoping
  • Regenerative Medicine, Vol. 5, Issue 4
  • DOI: 10.2217/rme.10.35

Active DNA Demethylation in Plant Companion Cells Reinforces Transposon Methylation in Gametes
journal, September 2012


An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress
journal, March 2011

  • Ito, Hidetaka; Gaubert, Hervé; Bucher, Etienne
  • Nature, Vol. 472, Issue 7341
  • DOI: 10.1038/nature09861

Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions
journal, July 2016


Unique cell-type-specific patterns of DNA methylation in the root meristem
journal, April 2016


DNA methylation and epigenetic control of cellular differentiation
journal, October 2010

  • Khavari, David A.; Sen, George L.; Rinn, John L.
  • Cell Cycle, Vol. 9, Issue 19
  • DOI: 10.4161/cc.9.19.13385

A Comparative Epigenomic Analysis of Polyploidy-Derived Genes in Soybean and Common Bean
journal, July 2015

  • Kim, Kyung Do; El Baidouri, Moaine; Abernathy, Brian
  • Plant Physiology, Vol. 168, Issue 4
  • DOI: 10.1104/pp.15.00408

Establishing, maintaining and modifying DNA methylation patterns in plants and animals
journal, February 2010

  • Law, Julie A.; Jacobsen, Steven E.
  • Nature Reviews Genetics, Vol. 11, Issue 3
  • DOI: 10.1038/nrg2719

Root hair systems biology
journal, November 2010


Complete Transcriptome of the Soybean Root Hair Cell, a Single-Cell Model, and Its Alteration in Response to Bradyrhizobium japonicum Infection
journal, November 2009

  • Libault, Marc; Farmer, Andrew; Brechenmacher, Laurent
  • Plant Physiology, Vol. 152, Issue 2
  • DOI: 10.1104/pp.109.148379

Role of transposable elements in heterochromatin and epigenetic control
journal, July 2004

  • Lippman, Zachary; Gendrel, Anne-Valérie; Black, Michael
  • Nature, Vol. 430, Issue 6998
  • DOI: 10.1038/nature02651

Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells
journal, February 2011

  • Lister, Ryan; Pelizzola, Mattia; Kida, Yasuyuki S.
  • Nature, Vol. 471, Issue 7336
  • DOI: 10.1038/nature09798

Transposable Elements Contribute to Activation of Maize Genes in Response to Abiotic Stress
journal, January 2015


Genome-wide DNA methylation analysis in precursor B-cells
journal, December 2014


Integrated methylome and transcriptome analysis reveals novel regulatory elements in pediatric acute lymphoblastic leukemia
journal, June 2015


<span class="fa fa-external-link" aria-hidden="true"></span></a> <small class="text-muted" style="text-transform:uppercase; font-size:0.75rem;"><br/> <span class="type">journal</span>, <span class="date" data-date="2002-06-01">June 2002</span></small> </h2> <ul class="small references-list" style="list-style-type:none; margin-top: 0.5em; padding-left: 0; line-height:1.8em;"> <li> <span style="color:#7cb342;"> Minorsky, Peter V.</span> </li> <li> Plant Physiology, Vol. 129, Issue 2</li> <li> <span class="text-muted related-url">DOI: <a href="https://doi.org/10.1104/pp.900038" class="text-muted" target="_blank" rel="noopener noreferrer">10.1104/pp.900038<span class="fa fa-external-link" aria-hidden="true"></span></a></span> </li> </ul> <hr/> </div> <div> <h2 class="title" style="margin-bottom:0;" data-apporder=""> <a href="https://doi.org/10.1016/j.pbi.2011.03.004" target="_blank" rel="noopener noreferrer" class="name">Epigenetic contribution to stress adaptation in plants<span class="fa fa-external-link" aria-hidden="true"></span></a> <small class="text-muted" style="text-transform:uppercase; font-size:0.75rem;"><br/> <span class="type">journal</span>, <span class="date" data-date="2011-06-01">June 2011</span></small> </h2> <ul class="small references-list" style="list-style-type:none; margin-top: 0.5em; padding-left: 0; line-height:1.8em;"> <li> <span style="color:#7cb342;"> Mirouze, Marie; Paszkowski, Jerzy</span> </li> <li> Current Opinion in Plant Biology, Vol. 14, Issue 3</li> <li> <span class="text-muted related-url">DOI: <a href="https://doi.org/10.1016/j.pbi.2011.03.004" class="text-muted" target="_blank" rel="noopener noreferrer">10.1016/j.pbi.2011.03.004<span class="fa fa-external-link" aria-hidden="true"></span></a></span> </li> </ul> <hr/> </div> <div> <h2 class="title" style="margin-bottom:0;" data-apporder=""> <a href="https://doi.org/10.1093/mp/sst165" target="_blank" rel="noopener noreferrer" class="name">Covering Your Bases: Inheritance of DNA Methylation in Plant Genomes<span class="fa fa-external-link" aria-hidden="true"></span></a> <small class="text-muted" style="text-transform:uppercase; font-size:0.75rem;"><br/> <span class="type">journal</span>, <span class="date" data-date="2014-03-01">March 2014</span></small> </h2> <ul class="small references-list" style="list-style-type:none; margin-top: 0.5em; padding-left: 0; line-height:1.8em;"> <li> <span style="color:#7cb342;"> Niederhuth, Chad E.; Schmitz, Robert J.</span> </li> <li> Molecular Plant, Vol. 7, Issue 3</li> <li> <span class="text-muted related-url">DOI: <a href="https://doi.org/10.1093/mp/sst165" class="text-muted" target="_blank" rel="noopener noreferrer">10.1093/mp/sst165<span class="fa fa-external-link" aria-hidden="true"></span></a></span> </li> </ul> <hr/> </div> <div> <h2 class="title" style="margin-bottom:0;" data-apporder=""> <a href="https://doi.org/10.1006/anbo.2001.1410" target="_blank" rel="noopener noreferrer" class="name">Dissecting Symbiosis: Developments in Nod Factor Signal Transduction<span class="fa fa-external-link" aria-hidden="true"></span></a> <small class="text-muted" style="text-transform:uppercase; font-size:0.75rem;"><br/> <span class="type">journal</span>, <span class="date" data-date="2001-06-01">June 2001</span></small> </h2> <ul class="small references-list" style="list-style-type:none; margin-top: 0.5em; padding-left: 0; line-height:1.8em;"> <li> <span style="color:#7cb342;"> Oldroyd, G.</span> </li> <li> Annals of Botany, Vol. 87, Issue 6</li> <li> <span class="text-muted related-url">DOI: <a href="https://doi.org/10.1006/anbo.2001.1410" class="text-muted" target="_blank" rel="noopener noreferrer">10.1006/anbo.2001.1410<span class="fa fa-external-link" aria-hidden="true"></span></a></span> </li> </ul> <hr/> </div> <div> <h2 class="title" style="margin-bottom:0;" data-apporder=""> <a href="https://doi.org/10.1105/tpc.110.078493" target="_blank" rel="noopener noreferrer" class="name">Epigenetic Regulation of Repetitive Elements Is Attenuated by Prolonged Heat Stress in <em>Arabidopsis</em><span class="fa fa-external-link" aria-hidden="true"></span></a> <small class="text-muted" style="text-transform:uppercase; font-size:0.75rem;"><br/> <span class="type">journal</span>, <span class="date" data-date="2010-09-01">September 2010</span></small> </h2> <ul class="small references-list" style="list-style-type:none; margin-top: 0.5em; padding-left: 0; line-height:1.8em;"> <li> <span style="color:#7cb342;"> Pecinka, Ales; Dinh, Huy Q.; Baubec, Tuncay</span> </li> <li> The Plant Cell, Vol. 22, Issue 9</li> <li> <span class="text-muted related-url">DOI: <a href="https://doi.org/10.1105/tpc.110.078493" class="text-muted" target="_blank" rel="noopener noreferrer">10.1105/tpc.110.078493<span class="fa fa-external-link" aria-hidden="true"></span></a></span> </li> </ul> <hr/> </div> <div> <h2 class="title" style="margin-bottom:0;" data-apporder=""> <a href="https://doi.org/10.1016/j.amc.2011.03.124" target="_blank" rel="noopener noreferrer" class="name">Computing the confidence levels for a root-mean-square test of goodness-of-fit<span class="fa fa-external-link" aria-hidden="true"></span></a> <small class="text-muted" style="text-transform:uppercase; font-size:0.75rem;"><br/> <span class="type">journal</span>, <span class="date" data-date="2011-07-01">July 2011</span></small> </h2> <ul class="small references-list" style="list-style-type:none; margin-top: 0.5em; padding-left: 0; line-height:1.8em;"> <li> <span style="color:#7cb342;"> Perkins, William; Tygert, Mark; Ward, Rachel</span> </li> <li> Applied Mathematics and Computation, Vol. 217, Issue 22</li> <li> <span class="text-muted related-url">DOI: <a href="https://doi.org/10.1016/j.amc.2011.03.124" class="text-muted" target="_blank" rel="noopener noreferrer">10.1016/j.amc.2011.03.124<span class="fa fa-external-link" aria-hidden="true"></span></a></span> </li> </ul> <hr/> </div> <div> <h2 class="title" style="margin-bottom:0;" data-apporder=""> <a href="https://doi.org/10.1104/pp.109.148668" target="_blank" rel="noopener noreferrer" class="name">Systems Biology Update: Cell Type-Specific Transcriptional Regulatory Networks<span class="fa fa-external-link" aria-hidden="true"></span></a> <small class="text-muted" style="text-transform:uppercase; font-size:0.75rem;"><br/> <span class="type">journal</span>, <span class="date" data-date="2009-12-04">December 2009</span></small> </h2> <ul class="small references-list" style="list-style-type:none; margin-top: 0.5em; padding-left: 0; line-height:1.8em;"> <li> <span style="color:#7cb342;"> Pu, Li; Brady, Siobhan</span> </li> <li> Plant Physiology, Vol. 152, Issue 2</li> <li> <span class="text-muted related-url">DOI: <a href="https://doi.org/10.1104/pp.109.148668" class="text-muted" target="_blank" rel="noopener noreferrer">10.1104/pp.109.148668<span class="fa fa-external-link" aria-hidden="true"></span></a></span> </li> </ul> <hr/> </div> <div> <h2 class="title" style="margin-bottom:0;" data-apporder=""> <a href="https://doi.org/10.1104/pp.15.00826" target="_blank" rel="noopener noreferrer" class="name">The Methylome of Soybean Roots during the Compatible Interaction with the Soybean Cyst Nematode<span class="fa fa-external-link" aria-hidden="true"></span></a> <small class="text-muted" style="text-transform:uppercase; font-size:0.75rem;"><br/> <span class="type">journal</span>, <span class="date" data-date="2015-06-22">June 2015</span></small> </h2> <ul class="small references-list" style="list-style-type:none; margin-top: 0.5em; padding-left: 0; line-height:1.8em;"> <li> <span style="color:#7cb342;"> Rambani, Aditi; Rice, J. Hollis; Liu, Jinyi</span> </li> <li> Plant Physiology, Vol. 168, Issue 4</li> <li> <span class="text-muted related-url">DOI: <a href="https://doi.org/10.1104/pp.15.00826" class="text-muted" target="_blank" rel="noopener noreferrer">10.1104/pp.15.00826<span class="fa fa-external-link" aria-hidden="true"></span></a></span> </li> </ul> <hr/> </div> <div> <h2 class="title" style="margin-bottom:0;" data-apporder=""> <a href="https://doi.org/10.1093/bioinformatics/btp616" target="_blank" rel="noopener noreferrer" class="name">edgeR: a Bioconductor package for differential expression analysis of digital gene expression data<span class="fa fa-external-link" aria-hidden="true"></span></a> <small class="text-muted" style="text-transform:uppercase; font-size:0.75rem;"><br/> <span class="type">journal</span>, <span class="date" data-date="2009-11-11">November 2009</span></small> </h2> <ul class="small references-list" style="list-style-type:none; margin-top: 0.5em; padding-left: 0; line-height:1.8em;"> <li> <span style="color:#7cb342;"> Robinson, M. D.; McCarthy, D. J.; Smyth, G. K.</span> </li> <li> Bioinformatics, Vol. 26, Issue 1</li> <li> <span class="text-muted related-url">DOI: <a href="https://doi.org/10.1093/bioinformatics/btp616" class="text-muted" target="_blank" rel="noopener noreferrer">10.1093/bioinformatics/btp616<span class="fa fa-external-link" aria-hidden="true"></span></a></span> </li> </ul> <hr/> </div> <div> <h2 class="title" style="margin-bottom:0;" data-apporder=""> <a href="https://doi.org/10.1101/gr.152538.112" target="_blank" rel="noopener noreferrer" class="name">Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population<span class="fa fa-external-link" aria-hidden="true"></span></a> <small class="text-muted" style="text-transform:uppercase; font-size:0.75rem;"><br/> <span class="type">journal</span>, <span class="date" data-date="2013-06-05">June 2013</span></small> </h2> <ul class="small references-list" style="list-style-type:none; margin-top: 0.5em; padding-left: 0; line-height:1.8em;"> <li> <span style="color:#7cb342;"> Schmitz, R. J.; He, Y.; Valdes-Lopez, O.</span> </li> <li> Genome Research, Vol. 23, Issue 10</li> <li> <span class="text-muted related-url">DOI: <a href="https://doi.org/10.1101/gr.152538.112" class="text-muted" target="_blank" rel="noopener noreferrer">10.1101/gr.152538.112<span class="fa fa-external-link" aria-hidden="true"></span></a></span> </li> </ul> <hr/> </div> <div> <h2 class="title" style="margin-bottom:0;" data-apporder=""> <a href="https://doi.org/10.1038/nature08670" target="_blank" rel="noopener noreferrer" class="name">Genome sequence of the palaeopolyploid soybean<span class="fa fa-external-link" aria-hidden="true"></span></a> <small class="text-muted" style="text-transform:uppercase; font-size:0.75rem;"><br/> <span class="type">journal</span>, <span class="date" data-date="2010-01-01">January 2010</span></small> </h2> <ul class="small references-list" style="list-style-type:none; margin-top: 0.5em; padding-left: 0; line-height:1.8em;"> <li> <span style="color:#7cb342;"> Schmutz, Jeremy; Cannon, Steven B.; Schlueter, Jessica</span> </li> <li> Nature, Vol. 463, Issue 7278</li> <li> <span class="text-muted related-url">DOI: <a href="https://doi.org/10.1038/nature08670" class="text-muted" target="_blank" rel="noopener noreferrer">10.1038/nature08670<span class="fa fa-external-link" aria-hidden="true"></span></a></span> </li> </ul> <hr/> </div> <div> <h2 class="title" style="margin-bottom:0;" data-apporder=""> <a href="https://doi.org/10.1038/nature14465" target="_blank" rel="noopener noreferrer" class="name">Human body epigenome maps reveal noncanonical DNA methylation variation<span class="fa fa-external-link" aria-hidden="true"></span></a> <small class="text-muted" style="text-transform:uppercase; font-size:0.75rem;"><br/> <span class="type">journal</span>, <span class="date" data-date="2015-06-01">June 2015</span></small> </h2> <ul class="small references-list" style="list-style-type:none; margin-top: 0.5em; padding-left: 0; line-height:1.8em;"> <li> <span style="color:#7cb342;"> Schultz, Matthew D.; He, Yupeng; Whitaker, John W.</span> </li> <li> Nature, Vol. 523, Issue 7559</li> <li> <span class="text-muted related-url">DOI: <a href="https://doi.org/10.1038/nature14465" class="text-muted" target="_blank" rel="noopener noreferrer">10.1038/nature14465<span class="fa fa-external-link" aria-hidden="true"></span></a></span> </li> </ul> <hr/> </div> <div> <h2 class="title" style="margin-bottom:0;" data-apporder=""> <a href="https://doi.org/10.1038/nrg2072" target="_blank" rel="noopener noreferrer" class="name">Transposable elements and the epigenetic regulation of the genome<span class="fa fa-external-link" aria-hidden="true"></span></a> <small class="text-muted" style="text-transform:uppercase; font-size:0.75rem;"><br/> <span class="type">journal</span>, <span class="date" data-date="2007-04-01">April 2007</span></small> </h2> <ul class="small references-list" style="list-style-type:none; margin-top: 0.5em; padding-left: 0; line-height:1.8em;"> <li> <span style="color:#7cb342;"> Slotkin, R. Keith; Martienssen, Robert</span> </li> <li> Nature Reviews Genetics, Vol. 8, Issue 4</li> <li> <span class="text-muted related-url">DOI: <a href="https://doi.org/10.1038/nrg2072" class="text-muted" target="_blank" rel="noopener noreferrer">10.1038/nrg2072<span class="fa fa-external-link" aria-hidden="true"></span></a></span> </li> </ul> <hr/> </div> <div> <h2 class="title" style="margin-bottom:0;" data-apporder=""> <a href="https://doi.org/10.1038/nmeth.3035" target="_blank" rel="noopener noreferrer" class="name">Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity<span class="fa fa-external-link" aria-hidden="true"></span></a> <small class="text-muted" style="text-transform:uppercase; font-size:0.75rem;"><br/> <span class="type">journal</span>, <span class="date" data-date="2014-07-20">July 2014</span></small> </h2> <ul class="small references-list" style="list-style-type:none; margin-top: 0.5em; padding-left: 0; line-height:1.8em;"> <li> <span style="color:#7cb342;"> Smallwood, Sébastien A.; Lee, Heather J.; Angermueller, Christof</span> </li> <li> Nature Methods, Vol. 11, Issue 8</li> <li> <span class="text-muted related-url">DOI: <a href="https://doi.org/10.1038/nmeth.3035" class="text-muted" target="_blank" rel="noopener noreferrer">10.1038/nmeth.3035<span class="fa fa-external-link" aria-hidden="true"></span></a></span> </li> </ul> <hr/> </div> <div> <h2 class="title" style="margin-bottom:0;" data-apporder=""> <a href="https://doi.org/10.1093/mp/sst123" target="_blank" rel="noopener noreferrer" class="name">Genome-Wide Analysis of DNA Methylation in Soybean<span class="fa fa-external-link" aria-hidden="true"></span></a> <small class="text-muted" style="text-transform:uppercase; font-size:0.75rem;"><br/> <span class="type">journal</span>, <span class="date" data-date="2013-11-01">November 2013</span></small> </h2> <ul class="small references-list" style="list-style-type:none; margin-top: 0.5em; padding-left: 0; line-height:1.8em;"> <li> <span style="color:#7cb342;"> Song, Qing-Xin; Lu, Xiang; Li, Qing-Tian</span> </li> <li> Molecular Plant, Vol. 6, Issue 6</li> <li> <span class="text-muted related-url">DOI: <a href="https://doi.org/10.1093/mp/sst123" class="text-muted" target="_blank" rel="noopener noreferrer">10.1093/mp/sst123<span class="fa fa-external-link" aria-hidden="true"></span></a></span> </li> </ul> <hr/> </div> <div> <h2 class="title" style="margin-bottom:0;" data-apporder=""> <a href="https://doi.org/10.1016/j.cell.2012.10.054" target="_blank" rel="noopener noreferrer" class="name">Comprehensive Analysis of Silencing Mutants Reveals Complex Regulation of the Arabidopsis Methylome<span class="fa fa-external-link" aria-hidden="true"></span></a> <small class="text-muted" style="text-transform:uppercase; font-size:0.75rem;"><br/> <span class="type">journal</span>, <span class="date" data-date="2013-01-01">January 2013</span></small> </h2> <ul class="small references-list" style="list-style-type:none; margin-top: 0.5em; padding-left: 0; line-height:1.8em;"> <li> <span style="color:#7cb342;"> Stroud, Hume; Greenberg, Maxim V. C.; Feng, Suhua</span> </li> <li> Cell, Vol. 152, Issue 1-2</li> <li> <span class="text-muted related-url">DOI: <a href="https://doi.org/10.1016/j.cell.2012.10.054" class="text-muted" target="_blank" rel="noopener noreferrer">10.1016/j.cell.2012.10.054<span class="fa fa-external-link" aria-hidden="true"></span></a></span> </li> </ul> <hr/> </div> <div> <h2 class="title" style="margin-bottom:0;" data-apporder=""> <a href="https://doi.org/10.1093/bioinformatics/btp120" target="_blank" rel="noopener noreferrer" class="name">TopHat: discovering splice junctions with RNA-Seq<span class="fa fa-external-link" aria-hidden="true"></span></a> <small class="text-muted" style="text-transform:uppercase; font-size:0.75rem;"><br/> <span class="type">journal</span>, <span class="date" data-date="2009-03-16">March 2009</span></small> </h2> <ul class="small references-list" style="list-style-type:none; margin-top: 0.5em; padding-left: 0; line-height:1.8em;"> <li> <span style="color:#7cb342;"> Trapnell, Cole; Pachter, Lior; Salzberg, Steven L.</span> </li> <li> Bioinformatics, Vol. 25, Issue 9</li> <li> <span class="text-muted related-url">DOI: <a href="https://doi.org/10.1093/bioinformatics/btp120" class="text-muted" target="_blank" rel="noopener noreferrer">10.1093/bioinformatics/btp120<span class="fa fa-external-link" aria-hidden="true"></span></a></span> </li> </ul> <hr/> </div> <div> <h2 class="title" style="margin-bottom:0;" data-apporder=""> <a href="https://doi.org/10.1038/nbt.1621" target="_blank" rel="noopener noreferrer" class="name">Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation<span class="fa fa-external-link" aria-hidden="true"></span></a> <small class="text-muted" style="text-transform:uppercase; font-size:0.75rem;"><br/> <span class="type">journal</span>, <span class="date" data-date="2010-05-01">May 2010</span></small> </h2> <ul class="small references-list" style="list-style-type:none; margin-top: 0.5em; padding-left: 0; line-height:1.8em;"> <li> <span style="color:#7cb342;"> Trapnell, Cole; Williams, Brian A.; Pertea, Geo</span> </li> <li> Nature Biotechnology, Vol. 28, Issue 5</li> <li> <span class="text-muted related-url">DOI: <a href="https://doi.org/10.1038/nbt.1621" class="text-muted" target="_blank" rel="noopener noreferrer">10.1038/nbt.1621<span class="fa fa-external-link" aria-hidden="true"></span></a></span> </li> </ul> <hr/> </div> <div> <h2 class="title" style="margin-bottom:0;" data-apporder=""> <a href="https://doi.org/10.1093/mp/ssr039" target="_blank" rel="noopener noreferrer" class="name">Divergent DNA Methylation Patterns Associated with Abiotic Stress in Hevea brasiliensis<span class="fa fa-external-link" aria-hidden="true"></span></a> <small class="text-muted" style="text-transform:uppercase; font-size:0.75rem;"><br/> <span class="type">journal</span>, <span class="date" data-date="2011-11-01">November 2011</span></small> </h2> <ul class="small references-list" style="list-style-type:none; margin-top: 0.5em; padding-left: 0; line-height:1.8em;"> <li> <span style="color:#7cb342;"> Uthup, Thomas K.; Ravindran, Minimol; Bini, K.</span> </li> <li> Molecular Plant, Vol. 4, Issue 6</li> <li> <span class="text-muted related-url">DOI: <a href="https://doi.org/10.1093/mp/ssr039" class="text-muted" target="_blank" rel="noopener noreferrer">10.1093/mp/ssr039<span class="fa fa-external-link" aria-hidden="true"></span></a></span> </li> </ul> <hr/> </div> <div> <h2 class="title" style="margin-bottom:0;" data-apporder=""> <a href="https://doi.org/10.3389/fpls.2016.00517" target="_blank" rel="noopener noreferrer" class="name">Soybean Roots Grown under Heat Stress Show Global Changes in Their Transcriptional and Proteomic Profiles<span class="fa fa-external-link" aria-hidden="true"></span></a> <small class="text-muted" style="text-transform:uppercase; font-size:0.75rem;"><br/> <span class="type">journal</span>, <span class="date" data-date="2016-04-25">April 2016</span></small> </h2> <ul class="small references-list" style="list-style-type:none; margin-top: 0.5em; padding-left: 0; line-height:1.8em;"> <li> <span style="color:#7cb342;"> Valdés-López, Oswaldo; Batek, Josef; Gomez-Hernandez, Nicolas</span> </li> <li> Frontiers in Plant Science, Vol. 7</li> <li> <span class="text-muted related-url">DOI: <a href="https://doi.org/10.3389/fpls.2016.00517" class="text-muted" target="_blank" rel="noopener noreferrer">10.3389/fpls.2016.00517<span class="fa fa-external-link" aria-hidden="true"></span></a></span> </li> </ul> <hr/> </div> <div> <h2 class="title" style="margin-bottom:0;" data-apporder=""> <a href="https://doi.org/10.1007/s00438-004-1018-4" target="_blank" rel="noopener noreferrer" class="name">Association between up-regulation of stress-responsive genes and hypomethylation of genomic DNA in tobacco plants<span class="fa fa-external-link" aria-hidden="true"></span></a> <small class="text-muted" style="text-transform:uppercase; font-size:0.75rem;"><br/> <span class="type">journal</span>, <span class="date" data-date="2004-05-18">May 2004</span></small> </h2> <ul class="small references-list" style="list-style-type:none; margin-top: 0.5em; padding-left: 0; line-height:1.8em;"> <li> <span style="color:#7cb342;"> Wada, Y.; Miyamoto, K.; Kusano, T.</span> </li> <li> Molecular Genetics and Genomics, Vol. 271, Issue 6</li> <li> <span class="text-muted related-url">DOI: <a href="https://doi.org/10.1007/s00438-004-1018-4" class="text-muted" target="_blank" rel="noopener noreferrer">10.1007/s00438-004-1018-4<span class="fa fa-external-link" aria-hidden="true"></span></a></span> </li> </ul> <hr/> </div> <div> <h2 class="title" style="margin-bottom:0;" data-apporder=""> <a href="https://doi.org/10.1094/MPMI-18-0458" target="_blank" rel="noopener noreferrer" class="name">Proteomic Analysis of Soybean Root Hairs After Infection by <em>Bradyrhizobium japonicum</em><span class="fa fa-external-link" aria-hidden="true"></span></a> <small class="text-muted" style="text-transform:uppercase; font-size:0.75rem;"><br/> <span class="type">journal</span>, <span class="date" data-date="2005-05-01">May 2005</span></small> </h2> <ul class="small references-list" style="list-style-type:none; margin-top: 0.5em; padding-left: 0; line-height:1.8em;"> <li> <span style="color:#7cb342;"> Wan, Jinrong; Torres, Michael; Ganapathy, Ashwin</span> </li> <li> Molecular Plant-Microbe Interactions, Vol. 18, Issue 5</li> <li> <span class="text-muted related-url">DOI: <a href="https://doi.org/10.1094/MPMI-18-0458" class="text-muted" target="_blank" rel="noopener noreferrer">10.1094/MPMI-18-0458<span class="fa fa-external-link" aria-hidden="true"></span></a></span> </li> </ul> <hr/> </div> <div> <h2 class="title" style="margin-bottom:0;" data-apporder=""> <a href="https://doi.org/10.1105/tpc.111.092668" target="_blank" rel="noopener noreferrer" class="name">Parent-of-Origin Effects on Gene Expression and DNA Methylation in the Maize Endosperm<span class="fa fa-external-link" aria-hidden="true"></span></a> <small class="text-muted" style="text-transform:uppercase; font-size:0.75rem;"><br/> <span class="type">journal</span>, <span class="date" data-date="2011-12-01">December 2011</span></small> </h2> <ul class="small references-list" style="list-style-type:none; margin-top: 0.5em; padding-left: 0; line-height:1.8em;"> <li> <span style="color:#7cb342;"> Waters, Amanda J.; Makarevitch, Irina; Eichten, Steve R.</span> </li> <li> The Plant Cell, Vol. 23, Issue 12</li> <li> <span class="text-muted related-url">DOI: <a href="https://doi.org/10.1105/tpc.111.092668" class="text-muted" target="_blank" rel="noopener noreferrer">10.1105/tpc.111.092668<span class="fa fa-external-link" aria-hidden="true"></span></a></span> </li> </ul> <hr/> </div> <div> <h2 class="title" style="margin-bottom:0;" data-apporder=""> <a href="https://doi.org/10.4161/epi.26869" target="_blank" rel="noopener noreferrer" class="name">Epigenetic differences between shoots and roots in <em>Arabidopsis</em> reveals tissue-specific regulation<span class="fa fa-external-link" aria-hidden="true"></span></a> <small class="text-muted" style="text-transform:uppercase; font-size:0.75rem;"><br/> <span class="type">journal</span>, <span class="date" data-date="2013-10-29">October 2013</span></small> </h2> <ul class="small references-list" style="list-style-type:none; margin-top: 0.5em; padding-left: 0; line-height:1.8em;"> <li> <span style="color:#7cb342;"> Widman, Nicolas; Feng, Suhua; Jacobsen, Steven E.</span> </li> <li> Epigenetics, Vol. 9, Issue 2</li> <li> <span class="text-muted related-url">DOI: <a href="https://doi.org/10.4161/epi.26869" class="text-muted" target="_blank" rel="noopener noreferrer">10.4161/epi.26869<span class="fa fa-external-link" aria-hidden="true"></span></a></span> </li> </ul> <hr/> </div> <div> <h2 class="title" style="margin-bottom:0;" data-apporder=""> <a href="https://doi.org/10.1073/pnas.1009695107" target="_blank" rel="noopener noreferrer" class="name">Local DNA hypomethylation activates genes in rice endosperm<span class="fa fa-external-link" aria-hidden="true"></span></a> <small class="text-muted" style="text-transform:uppercase; font-size:0.75rem;"><br/> <span class="type">journal</span>, <span class="date" data-date="2010-10-11">October 2010</span></small> </h2> <ul class="small references-list" style="list-style-type:none; margin-top: 0.5em; padding-left: 0; line-height:1.8em;"> <li> <span style="color:#7cb342;"> Zemach, A.; Kim, M. Y.; Silva, P.</span> </li> <li> Proceedings of the National Academy of Sciences, Vol. 107, Issue 43</li> <li> <span class="text-muted related-url">DOI: <a href="https://doi.org/10.1073/pnas.1009695107" class="text-muted" target="_blank" rel="noopener noreferrer">10.1073/pnas.1009695107<span class="fa fa-external-link" aria-hidden="true"></span></a></span> </li> </ul> <hr/> </div> <div> <h2 class="title" style="margin-bottom:0;" data-apporder=""> <a href="https://doi.org/10.1038/nbt.2462" target="_blank" rel="noopener noreferrer" class="name">Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening<span class="fa fa-external-link" aria-hidden="true"></span></a> <small class="text-muted" style="text-transform:uppercase; font-size:0.75rem;"><br/> <span class="type">journal</span>, <span class="date" data-date="2013-01-27">January 2013</span></small> </h2> <ul class="small references-list" style="list-style-type:none; margin-top: 0.5em; padding-left: 0; line-height:1.8em;"> <li> <span style="color:#7cb342;"> Zhong, Silin; Fei, Zhangjun; Chen, Yun-Ru</span> </li> <li> Nature Biotechnology, Vol. 31, Issue 2</li> <li> <span class="text-muted related-url">DOI: <a href="https://doi.org/10.1038/nbt.2462" class="text-muted" target="_blank" rel="noopener noreferrer">10.1038/nbt.2462<span class="fa fa-external-link" aria-hidden="true"></span></a></span> </li> </ul> <hr/> </div> </div> <div class="pagination-container small"> <a class="pure-button prev page" href="#" rel="prev"><span class="fa fa-angle-left"></span></a><ul class="pagination d-inline-block" style="padding-left:.2em;"></ul><a class="pure-button next page" href="#" rel="next"><span class="fa fa-angle-right"></span></a> </div> </div> </div> <div class="col-sm-3 order-sm-3"> <ul class="nav nav-stacked"> <li class="active"><a href="" class="reference-type-filter tab-nav" data-tab="biblio-references" data-filter="type" data-pattern="*"><span class="fa fa-angle-right"></span> All References</a></li> <li class="small" style="margin-left:.75em; text-transform:capitalize;"><a href="" class="reference-type-filter tab-nav" data-tab="biblio-references" data-filter="type" data-pattern="journal"><span class="fa fa-angle-right"></span> journal<small class="text-muted"> (56)</small></a></li> </ul> <div style="margin-top:2em;"> <form class="pure-form small text-muted reference-search"> <label for="reference-search-text" class="sr-only">Search</label> <input class="search form-control pure-input-1" id="reference-search-text" placeholder="Search" style="margin-bottom:10px;" /> <fieldset> <div style="margin-left:1em; font-weight:normal; line-height: 1.6em;"><input type="radio" class="sort" name="references-sort" data-sort="name" style="position:relative;top:2px;" id="reference-search-sort-name"><label for="reference-search-sort-name" style="margin-left: .3em;">Sort by title</label></div> <div style="margin-left:1em; font-weight:normal; line-height: 1.6em;"><input type="radio" class="sort" name="references-sort" data-sort="date" data-order="desc" style="position:relative;top:2px;" id="reference-search-sort-date"><label for="reference-search-sort-date" style="margin-left: .3em;">Sort by date</label></div> </fieldset> <div class="text-left" style="margin-left:1em;"> <a href="" class="filter-clear clearfix" title="Clear filter / sort" style="font-weight:normal; float:none;">[ × clear filter / sort ]</a> </div> </form> </div> </div> </div> </section> <section id="biblio-related" class="tab-content tab-content-sec " data-tab="biblio"> <div class="row"> <div class="col-sm-9 order-sm-9"> <section id="biblio-similar" class="tab-content tab-content-sec active" data-tab="related"> <div class="padding"> <p class="lead text-muted" style="font-size: 18px; margin-top:0px;">Similar records in OSTI.GOV collections:</p> <aside> <ul class="item-list" itemscope itemtype="http://schema.org/ItemList" style="padding-left:0; list-style-type: none;"> <li> <div class="article item document" itemprop="itemListElement" itemscope itemtype="http://schema.org/WebPage"><meta itemprop="position" content="0" /><div class="item-info"> <h2 class="title" itemprop="name headline"><a href="/biblio/1357046-soybean-roots-grown-under-heat-stress-show-global-changes-transcriptional-proteomic-profiles" itemprop="url">Soybean Roots Grown under Heat Stress Show Global Changes in Their Transcriptional and Proteomic Profiles</a></h2> <div class="metadata"> <small class="text-muted" style="text-transform:uppercase;display:block;line-height:2.5em;">Journal Article</small><span class="authors"> <span class="author">Valdés-López, Oswaldo</span> ; <span class="author">Batek, Josef</span> ; <span class="author">Gomez-Hernandez, Nicolas</span> ; <span class="author">...</span> <span class="text-muted pubdata"> - Frontiers in Plant Science</span> </span> </div> <div class="abstract">Heat stress is likely to be a key factor in the negative impact of climate change on crop production. Heat stress significantly influences the functions of roots, which provide support, water, and nutrients to other plant organs. Likewise, roots play an important role in the establishment of symbiotic associations with different microorganisms. Despite the physiological relevance of roots, few studies have examined their response to heat stress. Here in this study, we performed genome-wide transcriptomic and proteomic analyses on isolated root hairs, which are a single, epidermal cell type, and compared their response to stripped roots. On average, we identified<a href='#' onclick='$(this).hide().next().show().next().show();return false;' style='margin-left:10px;'>more »</a><span style='display:none;'> 1849 and 3091 genes differentially regulated in root hairs and stripped roots, respectively, in response to heat stress. Our gene regulatory module analysis identified 10 key modules that might control the majority of the transcriptional response to heat stress. We also conducted proteomic analysis on membrane fractions isolated from root hairs and compared these responses to stripped roots. These experiments identified a variety of proteins whose expression changed within 3 h of application of heat stress. Most of these proteins were predicted to play a significant role in thermo-tolerance, as well as in chromatin remodeling and post-transcriptional regulation. In conclusion, the data presented represent an in-depth analysis of the heat stress response of a single cell type in soybean.</span><a href='#' onclick='$(this).hide().prev().hide().prev().show();return false;' style='margin-left:10px;display:none;'>« less</a></div><div class="metadata-links small clearfix text-muted" style="margin-top:15px;"> <span class="fa fa-book text-muted" aria-hidden="true"></span> Cited by 6<div class="pure-menu pure-menu-horizontal pull-right" style="width:unset;"> <ul class="pure-menu-list"> <li class="pure-menu-item"><span class="item-info-ftlink">DOI: <a class="misc doi-link " href="https://doi.org/10.3389/fpls.2016.00517" target="_blank" rel="noopener" title="Link to document DOI" data-ostiid="1357046" data-product-type="Journal Article" data-product-subtype="AM" >10.3389/fpls.2016.00517</a></span></li> <li class="pure-menu-item"><span class="item-info-ftlink"><a class="misc fulltext-link " href="/servlets/purl/1357046" title="Link to document media" target="_blank" rel="noopener" data-ostiid="1357046" data-product-type="Journal Article" data-product-subtype="AM" >Full Text Available</a></span></li> </ul> </div> </div> </div> <div class="clearfix"></div> </div> </li> <li> <div class="article item document" itemprop="itemListElement" itemscope itemtype="http://schema.org/WebPage"><meta itemprop="position" content="1" /><div class="item-info"> <h2 class="title" itemprop="name headline"><a href="/biblio/1064583-quantitative-phosphoproteomic-analysis-soybean-root-hairs-inoculated-bradyrhizobium-japonicum" itemprop="url">Quantitative Phosphoproteomic Analysis of Soybean Root Hairs Inoculated with Bradyrhizobium japonicum</a></h2> <div class="metadata"> <small class="text-muted" style="text-transform:uppercase;display:block;line-height:2.5em;">Journal Article</small><span class="authors"> <span class="author">Nguyen, Tran H.</span> ; <span class="author">Brechenmacher, Laurent</span> ; <span class="author">Aldrich, Joshua T.</span> ; <span class="author">...</span> <span class="text-muted pubdata"> - Molecular & Cellular Proteomics. MCP, 11(11):1140-1155</span> </span> </div> <div class="abstract">Root hairs are single hair-forming cells on roots that function to increase root surface area, enhancing water and nutrient uptake. In leguminous plants, root hairs also play a critical role as the site of infection by symbiotic nitrogen fixing rhizobia, leading to the formation of a novel organ, the nodule. The initial steps in the rhizobia-root hair infection process are known to involve specific receptor kinases and subsequent kinase cascades. Here, we characterize the phosphoproteome of the root hairs and the corresponding stripped roots (i.e., roots from which root hairs were removed) during rhizobial colonization and infection to gain insight<a href='#' onclick='$(this).hide().next().show().next().show();return false;' style='margin-left:10px;'>more »</a><span style='display:none;'> into the molecular mechanism of root hair cell biology. We chose soybean (Glycine max L.), one of the most important crop plants in the legume family, for this study because of its larger root size, which permits isolation of sufficient root hair material for phosphoproteomic analysis. Phosphopeptides derived from root hairs and stripped roots, mock inoculated or inoculated with the soybean-specific rhizobium Bradyrhizobium japonicum, were labeled with the isobaric tag 8-plex ITRAQ, enriched using Ni-NTA magnetic beads and subjected to nRPLC-MS/MS analysis using HCD and decision tree guided CID/ETD strategy. A total of 1,625 unique phosphopeptides, spanning 1,659 non-redundant phosphorylation sites, were detected from 1,126 soybean phosphoproteins. Among them, 273 phosphopeptides corresponding to 240 phosphoproteins were found to be significantly regulated (>1.5 fold abundance change) in response to inoculation with B. japonicum. The data reveal unique features of the soybean root hair phosphoproteome, including root hair and stripped root-specific phosphorylation suggesting a complex network of kinase-substrate and phosphatase-substrate interactions in response to rhizobial inoculation.</span><a href='#' onclick='$(this).hide().prev().hide().prev().show();return false;' style='margin-left:10px;display:none;'>« less</a></div><div class="metadata-links small clearfix text-muted" style="margin-top:15px;"> <div class="pure-menu pure-menu-horizontal pull-right" style="width:unset;"> <ul class="pure-menu-list"> <li class="pure-menu-item"><span class="item-info-ftlink">DOI: <a class="misc doi-link " href="https://doi.org/10.1074/mcp.M112.018028" target="_blank" rel="noopener" title="Link to document DOI" data-ostiid="1064583" data-product-type="Journal Article" data-product-subtype="AC" >10.1074/mcp.M112.018028</a></span></li> </ul> </div> </div> </div> <div class="clearfix"></div> </div> </li> <li> <div class="article item document" itemprop="itemListElement" itemscope itemtype="http://schema.org/WebPage"><meta itemprop="position" content="2" /><div class="item-info"> <h2 class="title" itemprop="name headline"><a href="/biblio/22462270-dynamic-heterogeneity-dna-methylation-hydroxymethylation-embryonic-stem-cell-populations-captured-single-cell-high-content-analysis" itemprop="url">Dynamic heterogeneity of DNA methylation and hydroxymethylation in embryonic stem cell populations captured by single-cell 3D high-content analysis</a></h2> <div class="metadata"> <small class="text-muted" style="text-transform:uppercase;display:block;line-height:2.5em;">Journal Article</small><span class="authors"> <span class="author">Tajbakhsh, Jian, E-mail: tajbakhshj@cshs.org</span> ; <span class="author">Translational Cytomics Group, Cedars-Sinai Medical Center, Los Angeles, CA 90048</span> ; <span class="author">Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048</span> ; <span class="author">...</span> <span class="text-muted pubdata"> - Experimental Cell Research</span> </span> </div> <div class="abstract">Cell-surface markers and transcription factors are being used in the assessment of stem cell fate and therapeutic safety, but display significant variability in stem cell cultures. We assessed nuclear patterns of 5-hydroxymethylcytosine (5hmC, associated with pluripotency), a second important epigenetic mark, and its combination with 5-methylcytosine (5mC, associated with differentiation), also in comparison to more established markers of pluripotency (Oct-4) and endodermal differentiation (FoxA2, Sox17) in mouse embryonic stem cells (mESC) over a 10-day differentiation course in vitro: by means of confocal and super-resolution imaging together with 3D high-content analysis, an essential tool in single-cell screening. In summary: 1) We<a href='#' onclick='$(this).hide().next().show().next().show();return false;' style='margin-left:10px;'>more »</a><span style='display:none;'> did not measure any significant correlation of putative markers with global 5mC or 5hmC. 2) While average Oct-4 levels stagnated on a cell-population base (0.015 lnIU/day), Sox17 and FoxA2 increased 22-fold and 3-fold faster, respectively (Sox17: 0.343 lnIU/day; FoxA2: 0.046 lnIU/day). In comparison, global DNA methylation levels increased 4-fold faster (0.068 lnIU/day), and global hydroxymethylation declined at 0.046 lnIU/day, both with a better explanation of the temporal profile. 3) This progression was concomitant with the occurrence of distinct nuclear codistribution patterns that represented a heterogeneous spectrum of states in differentiation; converging to three major coexisting 5mC/5hmC phenotypes by day 10: 5hmC{sup +}/5mC{sup −}, 5hmC{sup +}/5mC{sup +}, and 5hmC{sup −}/5mC{sup +} cells. 4) Using optical nanoscopy we could delineate the respective topologies of 5mC/5hmC colocalization in subregions of nuclear DNA: in the majority of 5hmC{sup +}/5mC{sup +} cells 5hmC and 5mC predominantly occupied mutually exclusive territories resembling euchromatic and heterochromatic regions, respectively. Simultaneously, in a smaller subset of cells we observed a tighter colocalization of the two cytosine variants, presumably delineating chromatin domains in remodeling. We conclude that 1) 5mC emerges as the most differential marker in our model system. 2) However, the combined enrollment of the two DNA modifications provided higher-definition screening and lead to the identification of cell subpopulations based on differential 5hmC/5mC phenotypes corresponding to different 5hmC/5mC ratios. The results encourage: a) assessing the regenerative potential of early-endodermal cells enriched for the three DNA methylation/hydroxymethylation categories, and b) exploring the universality of this type of epigenetic phenotyping across other lineage-specific differentiations. - Highlights: • First reported single-molecule super-resolution 3D-visualization of 5mC/5hmC sites in cells. • Identification of cells with differential 5mC/5hmC nuclear codistribution phenotypes. • Application of principle component and robust regression analyses for evaluation of 3D high-content-screening data. • Global 5mC constitutes a highly differential spatiotemporal in situ marker in early endodermal cell differentiation.</span><a href='#' onclick='$(this).hide().prev().hide().prev().show();return false;' style='margin-left:10px;display:none;'>« less</a></div><div class="metadata-links small clearfix text-muted" style="margin-top:15px;"> <div class="pure-menu pure-menu-horizontal pull-right" style="width:unset;"> <ul class="pure-menu-list"> <li class="pure-menu-item"><span class="item-info-ftlink">DOI: <a class="misc doi-link " href="https://doi.org/10.1016/J.YEXCR.2015.02.004" target="_blank" rel="noopener" title="Link to document DOI" data-ostiid="22462270" data-product-type="Journal Article" data-product-subtype="AC" >10.1016/J.YEXCR.2015.02.004</a></span></li> </ul> </div> </div> </div> <div class="clearfix"></div> </div> </li> <li> <div class="article item document" itemprop="itemListElement" itemscope itemtype="http://schema.org/WebPage"><meta itemprop="position" content="3" /><div class="item-info"> <h2 class="title" itemprop="name headline"><a href="/biblio/1092015-identification-soybean-proteins-from-single-cell-type-root-hair" itemprop="url">Identification of soybean proteins from a single cell type: The root hair</a></h2> <div class="metadata"> <small class="text-muted" style="text-transform:uppercase;display:block;line-height:2.5em;">Journal Article</small><span class="authors"> <span class="author">Brechenmacher, Laurent</span> ; <span class="author">Nguyen, Tran H.</span> ; <span class="author">Hixson, Kim K.</span> ; <span class="author">...</span> <span class="text-muted pubdata"> - Proteomics, 12(22):3365-3373</span> </span> </div> <div class="abstract">Root hairs are a terminally differentiated single cell type, mainly involved in water and nutrient uptake from the soil. The soybean root hair cell represents an excellent model for the study of single cell systems biology. In this study, we identified 5702 proteins, with at least two peptides, from soybean root hairs using an accurate mass and time tag approach, establishing the most comprehensive proteome reference map of this single cell type. We also showed that trypsin is the most appropriate enzyme for soybean proteomic studies by performing an in silico digestion of the soybean proteome database using different proteases.<a href='#' onclick='$(this).hide().next().show().next().show();return false;' style='margin-left:10px;'>more »</a><span style='display:none;'> Although the majority of proteins identified in this study are involved in basal metabolism, the function of others are more related to root hair formation/function and include proteins involved in nutrient uptake (transporters) or vesicular trafficking (cytoskeleton and RAB proteins). Interestingly, some of these proteins appear to be specifically expressed in root hairs and constitute very good candidates for further studies to elucidate unique features of this single cell model.</span><a href='#' onclick='$(this).hide().prev().hide().prev().show();return false;' style='margin-left:10px;display:none;'>« less</a></div><div class="metadata-links small clearfix text-muted" style="margin-top:15px;"> <div class="pure-menu pure-menu-horizontal pull-right" style="width:unset;"> <ul class="pure-menu-list"> <li class="pure-menu-item"><span class="item-info-ftlink">DOI: <a class="misc doi-link " href="https://doi.org/10.1002/pmic.201200160" target="_blank" rel="noopener" title="Link to document DOI" data-ostiid="1092015" data-product-type="Journal Article" data-product-subtype="AC" >10.1002/pmic.201200160</a></span></li> </ul> </div> </div> </div> <div class="clearfix"></div> </div> </li> <li> <div class="article item document" itemprop="itemListElement" itemscope itemtype="http://schema.org/WebPage"><meta itemprop="position" content="4" /><div class="item-info"> <h2 class="title" itemprop="name headline"><a href="/biblio/1327138-soybean-roots-grown-under-heat-stress-show-global-changes-transcriptional-proteomic-profiles" itemprop="url">Soybean Roots Grown under Heat Stress Show Global Changes in Their Transcriptional and Proteomic Profiles</a></h2> <div class="metadata"> <small class="text-muted" style="text-transform:uppercase;display:block;line-height:2.5em;">Journal Article</small><span class="authors"> <span class="author">Valdés-López, Oswaldo</span> ; <span class="author">Batek, Josef</span> ; <span class="author">Gomez-Hernandez, Nicolas</span> ; <span class="author">...</span> <span class="text-muted pubdata"> - Frontiers in Plant Science</span> </span> </div> <div class="abstract">Heat stress is likely to be a key factor in the negative impact of climate change on crop production. Roots provide support, water and nutrients to other plant organs. Likewise, roots play an important role in the establishment of symbiotic associations with different microorganisms. Despite the physiological relevance of roots, few studies have examined the response of these plant organs to heat stress. In this study, we performed genome-wide transcriptomic and proteomic analyses on isolated root hairs, which are a single, epidermal cell type, and compared their response to whole roots. We identified 2,013 genes differentially regulated in root hairs<a href='#' onclick='$(this).hide().next().show().next().show();return false;' style='margin-left:10px;'>more »</a><span style='display:none;'> in response to heat stress. Our gene regulatory module analysis identified ten, key modules that controlled the majority of the transcriptional response to heat stress. We also conducted proteomic analysis on membrane fractions isolated from roots and root hairs. These experiments identified a variety of proteins whose expression changed within 3 hours of application of heat stress. Most of these proteins were predicted to play a role in thermotolerance, as well as in chromatin remodeling and post-transcriptional regulation. The data presented represent an in-depth analysis of the heat stress response of a single cell type in soybean.</span><a href='#' onclick='$(this).hide().prev().hide().prev().show();return false;' style='margin-left:10px;display:none;'>« less</a></div><div class="metadata-links small clearfix text-muted" style="margin-top:15px;"> <div class="pure-menu pure-menu-horizontal pull-right" style="width:unset;"> <ul class="pure-menu-list"> <li class="pure-menu-item"><span class="item-info-ftlink">DOI: <a class="misc doi-link " href="https://doi.org/10.3389/fpls.2016.00517" target="_blank" rel="noopener" title="Link to document DOI" data-ostiid="1327138" data-product-type="Journal Article" data-product-subtype="AC" >10.3389/fpls.2016.00517</a></span></li> </ul> </div> </div> </div> <div class="clearfix"></div> </div> </li> </ul> </aside> </div> </section> </div> <div class="col-sm-3 order-sm-3"> <ul class="nav nav-stacked"> <li class="active"><a class="tab-nav disabled" data-tab="related" style="color: #636c72 !important; opacity: 1;"><span class="fa fa-angle-right"></span> Similar Records</a></li> </ul> </div> </div> </section> </div></div> </div> </div> </section> <footer class="" style="background-color:#f9f9f9; /* padding-top: 0.5rem; */"> <div class="footer-minor"> <div class="container"> <hr class="footer-separator" /> <div class="text-center" style="margin-top:1.25rem;"> <div class="pure-menu pure-menu-horizontal"> <ul class="pure-menu-list" id="footer-org-menu"> <li class="pure-menu-item d-block d-inline-small"> <a href="https://energy.gov" target="_blank" rel="noopener noreferrer"> <img src="data:image/gif;base64,R0lGODlhAQABAIAAAP///wAAACH5BAEAAAAALAAAAAABAAEAAAICRAEAOw==" class="sprite sprite-footer-us-doe-min" alt="U.S. Department of Energy" /> </a> </li> <li class="pure-menu-item d-block d-inline-small"> <a href="https://www.energy.gov/science/office-science" target="_blank" rel="noopener noreferrer"> <img src="data:image/gif;base64,R0lGODlhAQABAIAAAP///wAAACH5BAEAAAAALAAAAAABAAEAAAICRAEAOw==" class="sprite sprite-footer-office-of-science-min" alt="Office of Science" /> </a> </li> <li class="pure-menu-item d-block d-inline-small"> <a href="/"> <img src="data:image/gif;base64,R0lGODlhAQABAIAAAP///wAAACH5BAEAAAAALAAAAAABAAEAAAICRAEAOw==" class="sprite sprite-footer-osti-min" alt="Office of Scientific and Technical Information" /> </a> </li> </ul> </div> </div> <div class="text-center small" style="margin-top:0.5em;margin-bottom:2.0rem;"> <div class="pure-menu pure-menu-horizontal"> <ul class="pure-menu-list"> <li class="pure-menu-item"><a href="/disclaim" class="pure-menu-link"><span class="fa fa-institution"></span> Website Policies <span class="d-none d-sm-inline" style="color:#737373;">/ Important Links</span></a></li> <li class="pure-menu-item"><a href="/contact" class="pure-menu-link"><span class="fa fa-comments-o"></span> Contact Us</a></li> <li class="d-block d-md-none mb-1"></li> <li class="pure-menu-item"><a href="https://www.facebook.com/ostigov" target="_blank" rel="noopener noreferrer" class="pure-menu-link social"><span class="fa fa-facebook" style=""></span></a></li> <li class="pure-menu-item"><a href="https://twitter.com/OSTIgov" target="_blank" rel="noopener noreferrer" class="pure-menu-link social"><span class="fa fa-twitter" style=""></span></a></li> <li class="pure-menu-item"><a href="https://www.youtube.com/user/ostigov" target="_blank" rel="noopener noreferrer" class="pure-menu-link social"><span class="fa fa-youtube-play" style=""></span></a></li> </ul> </div> </div> </div> </div> </footer> <link href="/css/ostigov.fonts.191107.1502.css" rel="stylesheet"> <script src="/js/ostigov.191107.1502.js"></script><noscript></noscript> <script defer src="/js/ostigov.biblio.191107.1502.js"></script><noscript></noscript> <script defer src="/js/lity.js"></script><noscript></noscript> <script async type="text/javascript" src="/js/Universal-Federated-Analytics-Min.js?agency=DOE" id="_fed_an_ua_tag"></script><noscript></noscript> </body> <!-- OSTI.GOV v.191107.1502 --> </html>