PMID- 33749670
OWN - NLM
STAT- MEDLINE
DCOM- 20210416
LR  - 20240226
IS  - 1940-087X (Electronic)
IS  - 1940-087X (Linking)
IP  - 169
DP  - 2021 Mar 4
TI  - Fluorescence In Situ Hybridization on DNA Halo Preparations to Reveal Whole 
      Chromosomes, Telomeres and Gene Loci.
LID - 10.3791/62017 [doi]
AB  - The genome is associated with several structures inside cell nuclei, in order to 
      regulate its activity and anchor it in specific locations. These structures are 
      collectively known as the nucleoskeleton and include the nuclear lamina, the 
      nucleoli, and nuclear bodies. Although many variants of fluorescence in situ 
      hybridization (FISH) exist to study the genome and its organization, these are 
      often limited by resolution and provide insufficient information on the genome's 
      association with nuclear structures. The DNA halo method uses high salt 
      concentrations and nonionic detergents to generate DNA loops that remain anchored 
      to structures within nuclei through attachment regions within the genome. Here, 
      soluble nuclear proteins, such as histones, lipids, and DNA not tightly bound to 
      the nuclear matrix, are extracted. This leads to the formation of a halo of 
      unattached DNA surrounding a residual nucleus which itself contains DNA closely 
      associated with internal nuclear structures and extraction-resistant proteins. 
      These extended DNA strands enable increased resolution and can facilitate 
      physical mapping. In combination with FISH, this method has the added advantage 
      of studying genomic interactions with all the structures that the genome is 
      anchored by. This technique, termed HALO-FISH, is highly versatile whereby DNA 
      halos can be coupled with nucleic acid probes to reveal gene loci, whole 
      chromosomes, alpha satellite, telomeres and even RNA. This technique provides an 
      insight into nuclear organization and function in normal cells and in disease 
      progression such as with cancer.
FAU - Godwin, Lauren S
AU  - Godwin LS
AD  - Laboratory of Nuclear and Genomic Health, Centre for Genome Engineering and 
      Maintenance, Division of Biosciences, Department of Life Sciences, College of 
      Health, Medicine and Life Sciences, Brunel University London.
FAU - Bridger, Joanna M
AU  - Bridger JM
AD  - Laboratory of Nuclear and Genomic Health, Centre for Genome Engineering and 
      Maintenance, Division of Biosciences, Department of Life Sciences, College of 
      Health, Medicine and Life Sciences, Brunel University London; 
      joanna.bridger@brunel.ac.uk.
FAU - Foster, Helen A
AU  - Foster HA
AD  - Biosciences, Department of Clinical, Pharmaceutical and Biological Science, 
      School of Life and Medical Sciences, University of Hertfordshire.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PT  - Video-Audio Media
DEP - 20210304
PL  - United States
TA  - J Vis Exp
JT  - Journal of visualized experiments : JoVE
JID - 101313252
RN  - 9007-49-2 (DNA)
SB  - IM
EIN - J Vis Exp. 2023 Jun 5;(196):. PMID: 37405953
MH  - Cell Nucleus/metabolism
MH  - Cells, Cultured
MH  - Chromosomes/*metabolism
MH  - Chromosomes, Artificial, Bacterial/metabolism
MH  - DNA/*metabolism
MH  - Dermis/cytology
MH  - Fibroblasts/metabolism
MH  - *Genetic Loci
MH  - Humans
MH  - Image Processing, Computer-Assisted
MH  - *In Situ Hybridization, Fluorescence
MH  - Telomere/*metabolism
EDAT- 2021/03/23 06:00
MHDA- 2021/04/17 06:00
CRDT- 2021/03/22 12:45
PHST- 2021/03/22 12:45 [entrez]
PHST- 2021/03/23 06:00 [pubmed]
PHST- 2021/04/17 06:00 [medline]
AID - 10.3791/62017 [doi]
PST - epublish
SO  - J Vis Exp. 2021 Mar 4;(169). doi: 10.3791/62017.