Chromatin fibers are formed by heterogeneous groups of nucleosomes in vivo

Cell
Maria Aurelia RicciMaria Pia Cosma

Abstract

Nucleosomes help structure chromosomes by compacting DNA into fibers. To gain insight into how nucleosomes are arranged in vivo, we combined quantitative super-resolution nanoscopy with computer simulations to visualize and count nucleosomes along the chromatin fiber in single nuclei. Nucleosomes assembled in heterogeneous groups of varying sizes, here termed "clutches," and these were interspersed with nucleosome-depleted regions. The median number of nucleosomes inside clutches and their compaction defined as nucleosome density were cell-type-specific. Ground-state pluripotent stem cells had, on average, less dense clutches containing fewer nucleosomes and clutch size strongly correlated with the pluripotency potential of induced pluripotent stem cells. RNA polymerase II preferentially associated with the smallest clutches while linker histone H1 and heterochromatin were enriched in the largest ones. Our results reveal how the chromatin fiber is formed at nanoscale level and link chromatin fiber architecture to stem cell state.

References

Jun 1, 1976·Proceedings of the National Academy of Sciences of the United States of America·J T Finch, A Klug
Feb 1, 1992·Proceedings of the National Academy of Sciences of the United States of America·J Widom
Aug 5, 2004·Journal of Cell Science·Katalin Fejes TóthKarsten Rippe
Feb 3, 2005·Genes & Development·Rohinton T Kamakaka, Sue Biggins
Jan 10, 2006·Developmental Cell·Eran MeshorerTom Misteli
Mar 1, 2006·Chromosome Research : an International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology·Christopher L WoodcockYuhong Fan
Aug 10, 2006·Nature Methods·Michael J RustXiaowei Zhuang
Mar 19, 2008·Genes & Development·Megan F ColeRichard A Young
May 9, 2008·Cell Stem Cell·Sol EfroniEran Meshorer
Feb 11, 2009·Nature Reviews. Genetics·Cizhong Jiang, B Franklin Pugh
Aug 5, 2009·Proceedings of the National Academy of Sciences of the United States of America·Sergei A GrigoryevTamar Schlick
Jul 28, 2010·Biochemical Society Transactions·Jason WrayAustin G Smith
Aug 10, 2010·Nature Methods·Richard WombacherMarkus Sauer
Sep 8, 2010·Biophysical Journal·Manfred BohnChristoph Cremer
Oct 12, 2010·Trends in Biochemical Sciences·Eden FussnerDavid P Bazett-Jones
Dec 15, 2010·Neuron·Adish DaniXiaowei Zhuang
Apr 5, 2011·Nature Methods·Keisuke OkitaShinya Yamanaka
Apr 7, 2011·The EMBO Journal·Eden FussnerDavid P Bazett-Jones
Jul 7, 2011·Proceedings of the National Academy of Sciences of the United States of America·Frederic LluisMaria Pia Cosma
May 1, 2012·Cell·Hendrik MarksHendrik G Stunnenberg
Jul 25, 2012·Nucleus·Yasumasa JotiKazuhiro Maeshima
Aug 31, 2012·Cellular and Molecular Life Sciences : CMLS·Frederic Lluis, Maria Pia Cosma
Sep 19, 2012·EMBO Reports·Eden FussnerDavid P Bazett-Jones
Jan 15, 2013·Current Opinion in Genetics & Development·Peter Meister, Angela Taddei
Mar 7, 2013·Nature Structural & Molecular Biology·Kevin Struhl, Eran Segal
May 16, 2013·Nature Reviews. Molecular Cell Biology·Patrick Cahan, George Q Daley
Aug 21, 2013·Cell·Andrew B StergachisJohn A Stamatoyannopoulos
Oct 8, 2013·Nature Structural & Molecular Biology·Yusuke MiyanariMaria-Elena Torres-Padilla
Feb 19, 2014·Current Opinion in Genetics & Development·Kerstin S Wendt, Frank G Grosveld
May 6, 2014·Current Opinion in Chemical Biology·Nela DurisicMelike Lakadamyali

❮ Previous
Next ❯

Citations

Aug 12, 2015·Genes·Daniël P MeltersYamini Dalal
Feb 16, 2016·Genomics, Proteomics & Bioinformatics·Vijay RamaniZhijun Duan
Jul 21, 2015·Genes·Virlana M ShchukaJennifer A Mitchell
Dec 29, 2015·Current Opinion in Structural Biology·Pablo D DansModesto Orozco
Jan 31, 2016·Current Opinion in Genetics & Development·Kazuhiro MaeshimaMasaki Sasai
Mar 18, 2016·Current Molecular Biology Reports·Jonathan Christopher DubéJosée Dostie
Apr 22, 2015·FEBS Letters·Melike Lakadamyali, Maria Pia Cosma
Oct 27, 2015·Proceedings of the National Academy of Sciences of the United States of America·Adrian L SanbornErez Lieberman Aiden
Jan 21, 2016·Proceedings of the National Academy of Sciences of the United States of America·Sergei A GrigoryevTamar Schlick
Dec 5, 2015·Biophysical Journal·Ji YiVadim Backman
Nov 8, 2015·Trends in Cell Biology·Andrew M SydorVito Mennella
Aug 2, 2015·Current Opinion in Microbiology·Ivan Marazzi, Adolfo Garcia-Sastre
Jul 28, 2015·Molecular Cell·Bing-Rui ZhouYawen Bai
Nov 14, 2015·ACS Chemical Biology·Beat Fierz
Oct 2, 2015·Nature Communications·Gražvydas LukinavičiusKai Johnsson
Jun 11, 2015·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Molly R GordonDavid M Gilbert
Jun 3, 2015·The Plant Journal : for Cell and Molecular Biology·Célia Baroux, Daphné Autran
Jul 15, 2015·Histochemistry and Cell Biology·Charlene Lemaître, Wendy A Bickmore
Jun 4, 2016·Molecular Cell·Alexey A SoshnevC David Allis
May 25, 2016·The Journal of Physical Chemistry. B·Gavin D BascomTamar Schlick
Jul 26, 2016·Frontiers in Genetics·Aleksander SzczurekChristoph Cremer
Nov 1, 2015·Biochimica Et Biophysica Acta·G P VicentM Beato
Jul 31, 2016·BMC Genomics·Guénola DrillonAlain Arneodo
Aug 11, 2016·Scientific Reports·Arun ShivanandanAleksandra Radenovic
Aug 19, 2016·Proceedings of the National Academy of Sciences of the United States of America·Biqin DongVadim Backman
Sep 7, 2016·Molecular Brain·Alejandro Medrano-Fernández, Angel Barco
Aug 30, 2016·Cell Biology International·Maria A Kuznetsova, Eugene V Sheval
Oct 16, 2016·Nature Reviews. Genetics·Boyan Bonev, Giacomo Cavalli
Nov 2, 2016·Molecular Biology of the Cell·Chen ChenLu Gan
Nov 5, 2016·Molecular Biology of the Cell·Gerhard HummerMike Heilemann
Feb 6, 2017·Biophysical Journal·Gavin Bascom, Tamar Schlick
Feb 15, 2017·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Christos KarathanasisMike Heilemann
Mar 14, 2017·Chemical Reviews·Markus Sauer, Mike Heilemann
Dec 13, 2016·Nucleic Acids Research·Ekaterina V NizovtsevaVasily M Studitsky
Jun 7, 2017·Nature Structural & Molecular Biology·Mo LiValerio Orlando
Jun 27, 2017·Nature Methods·Francesca Cella ZanacchiMelike Lakadamyali

❮ Previous
Next ❯

Related Concepts

Related Feeds

Adult Stem Cells

Adult stem cells reside in unique niches that provide vital cues for their survival, self-renewal, and differentiation. They hold great promise for use in tissue repair and regeneration as a novel therapeutic strategies. Here is the latest research.

Cell eTOC

Cell is a scientific journal publishing research across a broad range of disciplines within the life sciences field. Discover the latest research from Cell here.

Related Papers

Nihon rinsho. Japanese journal of clinical medicine
Naoki Yahata, Haruhisa Inoue
Horizons in Biochemistry and Biophysics
A Klug, P J Butler
Revista de investigación clínica; organo del Hospital de Enfermedades de la Nutrición
Rubén Lisker-Y
© 2021 Meta ULC. All rights reserved