Spatially Resolved Quantification of Chromatin Condensation through Differential Local Rheology in Cell Nuclei Fluorescence Lifetime Imaging

PloS One
Stephen T Spagnol, Kris Noel Dahl

Abstract

The linear sequence of DNA encodes access to the complete set of proteins that carry out cellular functions. Yet, much of the functionality appropriate for each cell is nested within layers of dynamic regulation and organization, including a hierarchy of chromatin structural states and spatial arrangement within the nucleus. There remain limitations in our understanding of gene expression within the context of nuclear organization from an inability to characterize hierarchical chromatin organization in situ. Here we demonstrate the use of fluorescence lifetime imaging microscopy (FLIM) to quantify and spatially resolve chromatin condensation state using cell-permeable, DNA-binding dyes (Hoechst 33342 and PicoGreen). Through in vitro and in situ experiments we demonstrate the sensitivity of fluorescence lifetime to condensation state through the mechanical effects that accompany the structural changes and are reflected through altered viscosity. The establishment of FLIM for resolving and quantifying chromatin condensation state opens the door for single-measurement mechanical studies of the nucleus and for characterizing the role of genome structure and organization in nuclear processes that accompany physiological and patholog...Continue Reading

References

Mar 1, 1980·Analytical Biochemistry·C Labarca, K Paigen
Sep 9, 1994·Science·C BustamanteS Smith
Jan 1, 1997·Biopolymers·V A Bloomfield
Nov 2, 2001·The American Journal of Surgical Pathology·T SeidalH Battifora
Jun 18, 2002·Nature Cell Biology·Melpomeni PlataniJason R Swedlow
Sep 3, 2004·Nature Reviews. Cancer·Daniele ZinkJeffrey A Nickerson
May 5, 2005·Annual Review of Biophysics and Biomolecular Structure·Nicholas V Hud, Igor D Vilfan
Aug 2, 2005·Biophysical Journal·Kris Noel DahlDennis E Discher
Dec 27, 2006·Methods : a Companion to Methods in Enzymology·Felipe Mora-Bermúdez, Jan Ellenberg
Sep 26, 2007·Proceedings of the National Academy of Sciences of the United States of America·J David PajerowskiDennis E Discher
Aug 23, 2008·Biochimica Et Biophysica Acta·Elena Fedorova, Daniele Zink
Jan 6, 2009·Dalton Transactions : an International Journal of Inorganic Chemistry·D Roeland BoerMiquel Coll
Mar 27, 2009·Current Opinion in Genetics & Development·Elena Fedorova, Daniele Zink
Apr 23, 2009·Journal of Cell Science·Catherine MartinDean A Jackson
Oct 7, 2009·Journal of Biomechanics·Kris Noel DahlBenoît Ladoux
Nov 10, 2009·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·Robert M Martin, M Cristina Cardoso
Nov 21, 2009·The Journal of Pathology·Elliott Lever, Denise Sheer
Dec 2, 2009·The Journal of Cell Biology·David LlèresAngus I Lamond
Apr 2, 2010·Chemical Reviews·Mikhail Y Berezin, Samuel Achilefu
May 11, 2010·Cold Spring Harbor Perspectives in Biology·Christopher L Woodcock, Rajarshi P Ghosh
Jul 2, 2010·Cold Spring Harbor Perspectives in Biology·Tom Misteli
Sep 9, 2010·Proceedings of the National Academy of Sciences of the United States of America·Elizabeth HindeEnrico Gratton
Jan 8, 2011·Cell Stem Cell·Richard P KocheAlexander Meissner
Apr 1, 2011·Current Opinion in Cell Biology·Pamela K GeyerLori L Wallrath
Aug 9, 2011·Nature Biotechnology·Jérémie CapouladeMichael Knop
Sep 8, 2011·Nucleic Acids Research·Ken HiranoKenichi Yoshikawa
Sep 9, 2011·Trends in Cell Biology·Lauren Meldi, Jason H Brickner
Oct 4, 2011·Journal of Nanobiotechnology·Peter N YaronKris Noel Dahl
Mar 28, 2012·Molecular and Cellular Biology·Craig J BurdTrevor K Archer
Oct 16, 2012·Biophysical Journal·K Venkatesan IyerG V Shivashankar
Nov 13, 2012·Cell·Lacramioara BintuCarlos Bustamante
Mar 19, 2013·Cell·Vincent Dion, Susan M Gasser
Sep 11, 2013·Proceedings of the National Academy of Sciences of the United States of America·Alexandra ZidovskaTimothy J Mitchison
Mar 13, 2014·Integrative Biology : Quantitative Biosciences From Nano to Macro·Stephen T Spagnol, Kris Noel Dahl
Mar 29, 2014·Scientific Reports·Yejun WangG V Shivashankar

❮ Previous
Next ❯

Citations

Dec 6, 2016·Journal of Biomechanical Engineering·Spencer E Szczesny, Robert L Mauck
Jan 16, 2018·Biomicrofluidics·Zeina S KhanFazle Hussain
Feb 23, 2018·Nature Cell Biology·Tyler J Kirby, Jan Lammerding
Mar 31, 2018·Scientific Reports·Ying GaoLi Lan
Jun 18, 2020·Frontiers in Cell and Developmental Biology·Tony FischerClaudia Tanja Mierke
Apr 23, 2020·Scientific Reports·Diego Herráez-AguilarJavier Redondo-Muñoz
Oct 18, 2020·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Recardia SchoemanCarminita Frost
Mar 10, 2021·Chromosome Research : an International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology·S W BotchwayM Yusuf
Jun 25, 2017·Journal of Cell Science·Yekaterina A MiroshnikovaSara A Wickström
Jul 4, 2020·Food and Chemical Toxicology : an International Journal Published for the British Industrial Biological Research Association·Debasish Kumar DeySun Chul Kang
Dec 28, 2016·ACS Nano·Clément Y J HémonnotSarah Köster
Nov 4, 2021·Light, Science & Applications·Svitlana M LevchenkoJunle Qu

❮ Previous
Next ❯

Methods Mentioned

BETA
electron microscopy
light microscopy
fluorescence lifetime imaging microscopy
Fluorescence
dynamic light scattering
chemical treatments
transfection

Software Mentioned

MATLAB
FLIM

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.