High resolution imaging reveals heterogeneity in chromatin states between cells that is not inherited through cell division

David Dickerson, Marek Gierlinski, Vijender Singh, Etsushi Kitamura, Graeme Ball, Tomoyuki U. Tanaka, Thomas Owen-Hughes (Lead / Corresponding author)

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Abstract

Background
Genomes of eukaryotes exist as chromatin, and it is known that different chromatin states can influence gene regulation. Chromatin is not a static structure, but is known to be dynamic and vary between cells. In order to monitor the organisation of chromatin in live cells we have engineered fluorescent fusion proteins which recognize specific operator sequences to tag pairs of syntenic gene loci. The separation of these loci was then tracked in three dimensions over time using fluorescence microscopy.

Results
We established a work flow for measuring the distance between two fluorescently tagged, syntenic gene loci with a mean measurement error of 63 nm. In general, physical separation was observed to increase with increasing genomic separations. However, the extent to which chromatin is compressed varies for different genomic regions. No correlation was observed between compaction and the distribution of chromatin markers from genomic datasets or with contacts identified using capture based approaches. Variation in spatial separation was also observed within cells over time and between cells. Differences in the conformation of individual loci can persist for minutes in individual cells. Separation of reporter loci was found to be similar in related and unrelated daughter cell pairs.

Conclusions
The directly observed physical separation of reporter loci in live cells is highly dynamic both over time and from cell to cell. However, consistent differences in separation are observed over some chromosomal regions that do not correlate with factors known to influence chromatin states. We conclude that as yet unidentified parameters influence chromatin configuration. We also find that while heterogeneity in chromatin states can be maintained for minutes between cells, it is not inherited through cell division. This may contribute to cell-to-cell transcriptional heterogeneity.
Original languageEnglish
Article number33
Number of pages16
JournalBMC Cell Biology
Volume17
DOIs
Publication statusPublished - 8 Sep 2016

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Cell Division
Chromatin
Genes
Workflow
Eukaryota
Fluorescence Microscopy

Keywords

  • Chromatin structure
  • Fluorescence microscopy
  • Live cell imaging
  • Epigenetic inheritance

Cite this

@article{ce1f97b13358492fa4f6cbd58a81e5b9,
title = "High resolution imaging reveals heterogeneity in chromatin states between cells that is not inherited through cell division",
abstract = "BackgroundGenomes of eukaryotes exist as chromatin, and it is known that different chromatin states can influence gene regulation. Chromatin is not a static structure, but is known to be dynamic and vary between cells. In order to monitor the organisation of chromatin in live cells we have engineered fluorescent fusion proteins which recognize specific operator sequences to tag pairs of syntenic gene loci. The separation of these loci was then tracked in three dimensions over time using fluorescence microscopy.ResultsWe established a work flow for measuring the distance between two fluorescently tagged, syntenic gene loci with a mean measurement error of 63 nm. In general, physical separation was observed to increase with increasing genomic separations. However, the extent to which chromatin is compressed varies for different genomic regions. No correlation was observed between compaction and the distribution of chromatin markers from genomic datasets or with contacts identified using capture based approaches. Variation in spatial separation was also observed within cells over time and between cells. Differences in the conformation of individual loci can persist for minutes in individual cells. Separation of reporter loci was found to be similar in related and unrelated daughter cell pairs.ConclusionsThe directly observed physical separation of reporter loci in live cells is highly dynamic both over time and from cell to cell. However, consistent differences in separation are observed over some chromosomal regions that do not correlate with factors known to influence chromatin states. We conclude that as yet unidentified parameters influence chromatin configuration. We also find that while heterogeneity in chromatin states can be maintained for minutes between cells, it is not inherited through cell division. This may contribute to cell-to-cell transcriptional heterogeneity.",
keywords = "Chromatin structure, Fluorescence microscopy, Live cell imaging, Epigenetic inheritance",
author = "David Dickerson and Marek Gierlinski and Vijender Singh and Etsushi Kitamura and Graeme Ball and Tanaka, {Tomoyuki U.} and Thomas Owen-Hughes",
note = "This work was supported by BBSRC grant BB/K008676/1 Wellcome Senior Research Fellowship [095062], MRC Next Generation Optical Microscopy Award (Ref: MR/K015869/1), Wellcome Principal Research Fellowship [096535], and Wellcome Trust strategic award 097945/B/11/Z.",
year = "2016",
month = "9",
day = "8",
doi = "10.1186/s12860-016-0111-y",
language = "English",
volume = "17",
journal = "BMC Cell Biology",
issn = "1471-2121",
publisher = "Springer Verlag",

}

TY - JOUR

T1 - High resolution imaging reveals heterogeneity in chromatin states between cells that is not inherited through cell division

AU - Dickerson, David

AU - Gierlinski, Marek

AU - Singh, Vijender

AU - Kitamura, Etsushi

AU - Ball, Graeme

AU - Tanaka, Tomoyuki U.

AU - Owen-Hughes, Thomas

N1 - This work was supported by BBSRC grant BB/K008676/1 Wellcome Senior Research Fellowship [095062], MRC Next Generation Optical Microscopy Award (Ref: MR/K015869/1), Wellcome Principal Research Fellowship [096535], and Wellcome Trust strategic award 097945/B/11/Z.

PY - 2016/9/8

Y1 - 2016/9/8

N2 - BackgroundGenomes of eukaryotes exist as chromatin, and it is known that different chromatin states can influence gene regulation. Chromatin is not a static structure, but is known to be dynamic and vary between cells. In order to monitor the organisation of chromatin in live cells we have engineered fluorescent fusion proteins which recognize specific operator sequences to tag pairs of syntenic gene loci. The separation of these loci was then tracked in three dimensions over time using fluorescence microscopy.ResultsWe established a work flow for measuring the distance between two fluorescently tagged, syntenic gene loci with a mean measurement error of 63 nm. In general, physical separation was observed to increase with increasing genomic separations. However, the extent to which chromatin is compressed varies for different genomic regions. No correlation was observed between compaction and the distribution of chromatin markers from genomic datasets or with contacts identified using capture based approaches. Variation in spatial separation was also observed within cells over time and between cells. Differences in the conformation of individual loci can persist for minutes in individual cells. Separation of reporter loci was found to be similar in related and unrelated daughter cell pairs.ConclusionsThe directly observed physical separation of reporter loci in live cells is highly dynamic both over time and from cell to cell. However, consistent differences in separation are observed over some chromosomal regions that do not correlate with factors known to influence chromatin states. We conclude that as yet unidentified parameters influence chromatin configuration. We also find that while heterogeneity in chromatin states can be maintained for minutes between cells, it is not inherited through cell division. This may contribute to cell-to-cell transcriptional heterogeneity.

AB - BackgroundGenomes of eukaryotes exist as chromatin, and it is known that different chromatin states can influence gene regulation. Chromatin is not a static structure, but is known to be dynamic and vary between cells. In order to monitor the organisation of chromatin in live cells we have engineered fluorescent fusion proteins which recognize specific operator sequences to tag pairs of syntenic gene loci. The separation of these loci was then tracked in three dimensions over time using fluorescence microscopy.ResultsWe established a work flow for measuring the distance between two fluorescently tagged, syntenic gene loci with a mean measurement error of 63 nm. In general, physical separation was observed to increase with increasing genomic separations. However, the extent to which chromatin is compressed varies for different genomic regions. No correlation was observed between compaction and the distribution of chromatin markers from genomic datasets or with contacts identified using capture based approaches. Variation in spatial separation was also observed within cells over time and between cells. Differences in the conformation of individual loci can persist for minutes in individual cells. Separation of reporter loci was found to be similar in related and unrelated daughter cell pairs.ConclusionsThe directly observed physical separation of reporter loci in live cells is highly dynamic both over time and from cell to cell. However, consistent differences in separation are observed over some chromosomal regions that do not correlate with factors known to influence chromatin states. We conclude that as yet unidentified parameters influence chromatin configuration. We also find that while heterogeneity in chromatin states can be maintained for minutes between cells, it is not inherited through cell division. This may contribute to cell-to-cell transcriptional heterogeneity.

KW - Chromatin structure

KW - Fluorescence microscopy

KW - Live cell imaging

KW - Epigenetic inheritance

UR - http://dx.doi.org/10.17867/10000102

U2 - 10.1186/s12860-016-0111-y

DO - 10.1186/s12860-016-0111-y

M3 - Article

VL - 17

JO - BMC Cell Biology

JF - BMC Cell Biology

SN - 1471-2121

M1 - 33

ER -