PMID- 25512564
OWN - NLM
STAT- MEDLINE
DCOM- 20150209
LR  - 20240322
IS  - 1549-5477 (Electronic)
IS  - 0890-9369 (Print)
IS  - 0890-9369 (Linking)
VI  - 28
IP  - 24
DP  - 2014 Dec 15
TI  - Spatial genome organization: contrasting views from chromosome conformation 
      capture and fluorescence in situ hybridization.
PG  - 2778-91
LID - 10.1101/gad.251694.114 [doi]
AB  - Although important for gene regulation, most studies of genome organization use 
      either fluorescence in situ hybridization (FISH) or chromosome conformation 
      capture (3C) methods. FISH directly visualizes the spatial relationship of 
      sequences but is usually applied to a few loci at a time. The frequency at which 
      sequences are ligated together by formaldehyde cross-linking can be measured 
      genome-wide by 3C methods, with higher frequencies thought to reflect shorter 
      distances. FISH and 3C should therefore give the same views of genome 
      organization, but this has not been tested extensively. We investigated the 
      murine HoxD locus with 3C carbon copy (5C) and FISH in different developmental 
      and activity states and in the presence or absence of epigenetic regulators. We 
      identified situations in which the two data sets are concordant but found other 
      conditions under which chromatin topographies extrapolated from 5C or FISH data 
      are not compatible. We suggest that products captured by 3C do not always reflect 
      spatial proximity, with ligation occurring between sequences located hundreds of 
      nanometers apart, influenced by nuclear environment and chromatin composition. We 
      conclude that results obtained at high resolution with either 3C methods or FISH 
      alone must be interpreted with caution and that views about genome organization 
      should be validated by independent methods.
CI  - (c) 2014 Williamson et al.; Published by Cold Spring Harbor Laboratory Press.
FAU - Williamson, Iain
AU  - Williamson I
AD  - MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University 
      of Edinburgh, Edinburgh EH4 2XU, United Kingdom;
FAU - Berlivet, Soizik
AU  - Berlivet S
AD  - Department of Biochemistry, Goodman Cancer Research Center, McGill University, 
      Montreal, Quebec H3G1Y6, Canada.
FAU - Eskeland, Ragnhild
AU  - Eskeland R
AD  - MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University 
      of Edinburgh, Edinburgh EH4 2XU, United Kingdom;
FAU - Boyle, Shelagh
AU  - Boyle S
AD  - MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University 
      of Edinburgh, Edinburgh EH4 2XU, United Kingdom;
FAU - Illingworth, Robert S
AU  - Illingworth RS
AD  - MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University 
      of Edinburgh, Edinburgh EH4 2XU, United Kingdom;
FAU - Paquette, Denis
AU  - Paquette D
AD  - Department of Biochemistry.
FAU - Dostie, Josee
AU  - Dostie J
AD  - Department of Biochemistry, wendy.bickmore@igmm.ed.ac.uk josee.dostie@mcgill.ca.
FAU - Bickmore, Wendy A
AU  - Bickmore WA
AD  - MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University 
      of Edinburgh, Edinburgh EH4 2XU, United Kingdom; wendy.bickmore@igmm.ed.ac.uk 
      josee.dostie@mcgill.ca.
LA  - eng
GR  - MC_PC_U127527202/MRC_/Medical Research Council/United Kingdom
GR  - MOP-86716/Canadian Institutes of Health Research/Canada
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PL  - United States
TA  - Genes Dev
JT  - Genes & development
JID - 8711660
RN  - 0 (Chromatin)
RN  - 0 (Homeodomain Proteins)
RN  - 0 (Hoxd1 protein, mouse)
RN  - 0 (Polycomb-Group Proteins)
SB  - IM
MH  - Animals
MH  - Cell Differentiation
MH  - Cells, Cultured
MH  - Chromatin/*chemistry/*metabolism
MH  - Embryonic Stem Cells/cytology
MH  - Genetic Techniques/standards
MH  - Genome/*genetics
MH  - Homeodomain Proteins/genetics/metabolism
MH  - In Situ Hybridization, Fluorescence/*standards
MH  - Mice
MH  - Mutation
MH  - Polycomb-Group Proteins/genetics
MH  - Protein Structure, Tertiary
MH  - Staining and Labeling/*standards
PMC - PMC4265680
OTO - NOTNLM
OT  - 3C
OT  - FISH
OT  - Hox genes
OT  - nuclear organization
OT  - polycomb
EDAT- 2014/12/17 06:00
MHDA- 2015/02/11 06:00
PMCR- 2014/12/15
CRDT- 2014/12/17 06:00
PHST- 2014/12/17 06:00 [entrez]
PHST- 2014/12/17 06:00 [pubmed]
PHST- 2015/02/11 06:00 [medline]
PHST- 2014/12/15 00:00 [pmc-release]
AID - 28/24/2778 [pii]
AID - 10.1101/gad.251694.114 [doi]
PST - ppublish
SO  - Genes Dev. 2014 Dec 15;28(24):2778-91. doi: 10.1101/gad.251694.114.