PMID- 27147055
OWN - NLM
STAT- MEDLINE
DCOM- 20171207
LR  - 20180110
IS  - 1940-6029 (Electronic)
IS  - 1064-3745 (Linking)
VI  - 1411
DP  - 2016
TI  - Visualizing the Spatial Relationship of the Genome with the Nuclear Envelope 
      Using Fluorescence In Situ Hybridization.
PG  - 387-406
LID - 10.1007/978-1-4939-3530-7_24 [doi]
AB  - The genome has a special relationship with the nuclear envelope in cells. Much of 
      the genome is anchored at the nuclear periphery, tethered by chromatin binding 
      proteins such nuclear lamins and other integral membrane proteins. Even though 
      there are global assays such as DAM-ID or ChIP to assess what parts of the genome 
      are associated with the nuclear envelope, it is also essential to be able to 
      visualize regions of the genome in order to reveal their individual relationships 
      with nuclear structures in single cells. This is executed by fluorescence in situ 
      hybridization (FISH) in 2-dimensional flattened nuclei (2D-FISH) or 
      3-dimensionally preserved cells (3D-FISH) in combination with indirect 
      immunofluorescence to reveal structural proteins. This chapter explains the 
      protocols for 2D- and 3D-FISH in combination with indirect immunofluorescence and 
      discusses options for image capture and analysis. Due to the nuclear envelope 
      proteins being part of the non-extractable nucleoskeleton, we also describe how 
      to prepare DNA halos through salt extraction and how they can be used to study 
      genome behavior and association when combined with 2D-FISH.
FAU - Clements, Craig S
AU  - Clements CS
AD  - Division of Biosciences, College of Life and Health Sciences, Brunel University 
      London, Uxbridge, London, UB8 3PH, UK.
FAU - Bikkul, Ural
AU  - Bikkul U
AD  - Division of Biosciences, College of Life and Health Sciences, Brunel University 
      London, Uxbridge, London, UB8 3PH, UK.
FAU - Ahmed, Mai Hassan
AU  - Ahmed MH
AD  - Division of Biosciences, College of Life and Health Sciences, Brunel University 
      London, Uxbridge, London, UB8 3PH, UK.
FAU - Foster, Helen A
AU  - Foster HA
AD  - Division of Biosciences, College of Life and Health Sciences, Brunel University 
      London, Uxbridge, London, UB8 3PH, UK.
FAU - Godwin, Lauren S
AU  - Godwin LS
AD  - Division of Biosciences, College of Life and Health Sciences, Brunel University 
      London, Uxbridge, London, UB8 3PH, UK.
FAU - Bridger, Joanna M
AU  - Bridger JM
AD  - Division of Biosciences, College of Life and Health Sciences, Brunel University 
      London, Uxbridge, London, UB8 3PH, UK. Joanna.bridger@brunel.ac.uk.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PL  - United States
TA  - Methods Mol Biol
JT  - Methods in molecular biology (Clifton, N.J.)
JID - 9214969
RN  - 0 (Biomarkers)
RN  - 0 (Chromatin)
RN  - 0 (DNA Probes)
RN  - 0 (Ki-67 Antigen)
SB  - IM
MH  - Biomarkers
MH  - Cell Nucleus/*metabolism
MH  - Cells, Cultured
MH  - Chromatin/genetics/metabolism
MH  - DNA Probes
MH  - *Genome
MH  - *In Situ Hybridization, Fluorescence
MH  - Ki-67 Antigen/metabolism
MH  - Microscopy, Fluorescence
MH  - Nuclear Envelope/*metabolism
OTO - NOTNLM
OT  - 2D-FISH
OT  - 3D-FISH
OT  - Chromosome territories
OT  - Fluorescence in situ hybridization
OT  - Gene positioning
OT  - Genome organization
OT  - Nuclear envelope
OT  - Nuclear lamins
EDAT- 2016/05/06 06:00
MHDA- 2017/12/08 06:00
CRDT- 2016/05/06 06:00
PHST- 2016/05/06 06:00 [entrez]
PHST- 2016/05/06 06:00 [pubmed]
PHST- 2017/12/08 06:00 [medline]
AID - 10.1007/978-1-4939-3530-7_24 [doi]
PST - ppublish
SO  - Methods Mol Biol. 2016;1411:387-406. doi: 10.1007/978-1-4939-3530-7_24.