Differential chromosome conformations as hallmarks of cellular identity revealed by mathematical polymer modeling.
Inherently dynamic, chromosomes adopt many different conformations in response to DNA metabolism. Models of chromosome organization in the yeast nucleus obtained from genome-wide chromosome conformation data or biophysical simulations provide important insights into the average behavior but fail to...
Main Authors: | , , , , |
---|---|
Format: | Article |
Language: | English |
Published: |
Public Library of Science (PLoS)
2015-06-01
|
Series: | PLoS Computational Biology |
Online Access: | https://doi.org/10.1371/journal.pcbi.1004306 |
id |
doaj-4fe6ae461b674366b8519076b2b49a49 |
---|---|
record_format |
Article |
spelling |
doaj-4fe6ae461b674366b8519076b2b49a492021-04-21T15:00:23ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582015-06-01116e100430610.1371/journal.pcbi.1004306Differential chromosome conformations as hallmarks of cellular identity revealed by mathematical polymer modeling.Imen LassadiAlain KamgouéIsabelle GoiffonNicolas Tanguy-le-GacKerstin BystrickyInherently dynamic, chromosomes adopt many different conformations in response to DNA metabolism. Models of chromosome organization in the yeast nucleus obtained from genome-wide chromosome conformation data or biophysical simulations provide important insights into the average behavior but fail to reveal features from dynamic or transient events that are only visible in a fraction of cells at any given moment. We developed a method to determine chromosome conformation from relative positions of three fluorescently tagged DNA in living cells imaged in 3D. Cell type specific chromosome folding properties could be assigned based on positional combinations between three loci on yeast chromosome 3. We determined that the shorter left arm of chromosome 3 is extended in MATα cells, but can be crumpled in MATa cells. Furthermore, we implemented a new mathematical model that provides for the first time an estimate of the relative physical constraint of three linked loci related to cellular identity. Variations in this estimate allowed us to predict functional consequences from chromatin structural alterations in asf1 and recombination enhancer deletion mutant cells. The computational method is applicable to identify and characterize dynamic chromosome conformations in any cell type.https://doi.org/10.1371/journal.pcbi.1004306 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Imen Lassadi Alain Kamgoué Isabelle Goiffon Nicolas Tanguy-le-Gac Kerstin Bystricky |
spellingShingle |
Imen Lassadi Alain Kamgoué Isabelle Goiffon Nicolas Tanguy-le-Gac Kerstin Bystricky Differential chromosome conformations as hallmarks of cellular identity revealed by mathematical polymer modeling. PLoS Computational Biology |
author_facet |
Imen Lassadi Alain Kamgoué Isabelle Goiffon Nicolas Tanguy-le-Gac Kerstin Bystricky |
author_sort |
Imen Lassadi |
title |
Differential chromosome conformations as hallmarks of cellular identity revealed by mathematical polymer modeling. |
title_short |
Differential chromosome conformations as hallmarks of cellular identity revealed by mathematical polymer modeling. |
title_full |
Differential chromosome conformations as hallmarks of cellular identity revealed by mathematical polymer modeling. |
title_fullStr |
Differential chromosome conformations as hallmarks of cellular identity revealed by mathematical polymer modeling. |
title_full_unstemmed |
Differential chromosome conformations as hallmarks of cellular identity revealed by mathematical polymer modeling. |
title_sort |
differential chromosome conformations as hallmarks of cellular identity revealed by mathematical polymer modeling. |
publisher |
Public Library of Science (PLoS) |
series |
PLoS Computational Biology |
issn |
1553-734X 1553-7358 |
publishDate |
2015-06-01 |
description |
Inherently dynamic, chromosomes adopt many different conformations in response to DNA metabolism. Models of chromosome organization in the yeast nucleus obtained from genome-wide chromosome conformation data or biophysical simulations provide important insights into the average behavior but fail to reveal features from dynamic or transient events that are only visible in a fraction of cells at any given moment. We developed a method to determine chromosome conformation from relative positions of three fluorescently tagged DNA in living cells imaged in 3D. Cell type specific chromosome folding properties could be assigned based on positional combinations between three loci on yeast chromosome 3. We determined that the shorter left arm of chromosome 3 is extended in MATα cells, but can be crumpled in MATa cells. Furthermore, we implemented a new mathematical model that provides for the first time an estimate of the relative physical constraint of three linked loci related to cellular identity. Variations in this estimate allowed us to predict functional consequences from chromatin structural alterations in asf1 and recombination enhancer deletion mutant cells. The computational method is applicable to identify and characterize dynamic chromosome conformations in any cell type. |
url |
https://doi.org/10.1371/journal.pcbi.1004306 |
work_keys_str_mv |
AT imenlassadi differentialchromosomeconformationsashallmarksofcellularidentityrevealedbymathematicalpolymermodeling AT alainkamgoue differentialchromosomeconformationsashallmarksofcellularidentityrevealedbymathematicalpolymermodeling AT isabellegoiffon differentialchromosomeconformationsashallmarksofcellularidentityrevealedbymathematicalpolymermodeling AT nicolastanguylegac differentialchromosomeconformationsashallmarksofcellularidentityrevealedbymathematicalpolymermodeling AT kerstinbystricky differentialchromosomeconformationsashallmarksofcellularidentityrevealedbymathematicalpolymermodeling |
_version_ |
1714668023671947264 |