Spatial Preservation of Nuclear Chromatin Architecture during Three-Dimensional Fluorescence in Situ Hybridization (3D-FISH)

2002 ◽  
Vol 276 (1) ◽  
pp. 10-23 ◽  
Author(s):  
Irina Solovei ◽  
Antonio Cavallo ◽  
Lothar Schermelleh ◽  
Françoise Jaunin ◽  
Catia Scasselati ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Three Dimensional ◽  
Nuclear Chromatin ◽  
Chromatin Architecture ◽  
3D Fish

scholarly journals Distinct contracted conformations of the Tcra/Tcrd locus during Tcra and Tcrd recombination

2010 ◽  
Vol 207 (9) ◽  
pp. 1835-1841 ◽  
Author(s):  
Han-Yu Shih ◽  
Michael S. Krangel
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Three Dimensional ◽  
Double Negative ◽  
Thymocyte Development ◽  
Double Positive ◽  
Long Distance ◽  
Large Pool ◽  
Antigen Receptor Loci

Studies have suggested that antigen receptor loci adopt contracted conformations to promote long-distance interactions between gene segments during V(D)J recombination. The Tcra/Tcrd locus is unique because it undergoes highly divergent Tcrd and Tcra recombination programs in CD4−CD8− double negative (DN) and CD4+CD8+ double positive (DP) thymocytes, respectively. Using three-dimensional fluorescence in situ hybridization, we asked whether these divergent recombination programs are supported by distinct conformational states of the Tcra/Tcrd locus. We found that the 3′ portion of the locus is contracted in DN and DP thymocytes but not in B cells. Remarkably, the 5′ portion of the locus is contracted in DN thymocytes but is decontracted in DP thymocytes. We propose that the fully contracted conformation in DN thymocytes allows Tcrd rearrangements involving Vδ gene segments distributed over 1 Mb, whereas the unique 3′-contracted, 5′-decontracted conformation in DP thymocytes biases initial Tcra rearrangements to the most 3′ of the available Vα gene segments. This would maintain a large pool of distal 5′ Vα gene segments for subsequent rounds of recombination. Thus, distinct contracted conformations of the Tcra/Tcrd locus may facilitate a transition from a Tcrd to a Tcra mode of recombination during thymocyte development.

scholarly journals Single Copy Oligonucleotide Fluorescence In Situ Hybridization Probe Design Platforms: Development, Application and Evaluation

2021 ◽  
Vol 22 (13) ◽  
pp. 7124
Author(s):  
Guanqing Liu ◽  
Tao Zhang
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Large Scale ◽  
Three Dimensional ◽  
Single Copy ◽  
Probe Design ◽  
Design Tools ◽  
Hybridization Probe ◽  
Research Areas

Oligonucleotides fluorescence in situ hybridization (Oligo-FISH) is an emerging technology and is an important tool in research areas such as detection of chromosome variation, identification of allopolyploid, and deciphering of three-dimensional (3D) genome structures. Based on the demand for highly efficient oligo probes for oligo-FISH experiments, increasing numbers of tools have been developed for probe design in recent years. Obsolete oligonucleotide design tools have been adapted for oligo-FISH probe design because of their similar considerations. With the development of DNA sequencing and large-scale synthesis, novel tools have been designed to increase the specificity of designed oligo probes and enable genome-scale oligo probe design, which has greatly improved the application of single copy oligo-FISH. Despite this, few studies have introduced the development of the oligo-FISH probe design tools and their application in FISH experiments systematically. Besides, a comprehensive comparison and evaluation is lacking for the available tools. In this review, we provide an overview of the oligo-FISH probe design process, summarize the development and application of the available tools, evaluate several state-of-art tools, and eventually provide guidance for single copy oligo-FISH probe design.

scholarly journals Three-Dimensional Fluorescence In Situ Hybridization in Mouse Embryos Using Repetitive Probe Sequences

2010 ◽  
pp. 401-408 ◽  
Author(s):  
Walid E. Maalouf ◽  
Tiphaine Aguirre-Lavin ◽  
Laetitia Herzog ◽  
Isabelle Bataillon ◽  
Pascale Debey ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Three Dimensional ◽  
Mouse Embryos

890: Multiple Fluorescence in Situ Hybridization (FISH) Probes Increase Sensitivity for Detection of Bladder Cancer

2006 ◽  
Vol 175 (4S) ◽  
pp. 287-288 ◽  
Author(s):  
Juliann M. Dziubinski ◽  
Michael F. Sarosdy ◽  
Paul R. Kahn ◽  
Mark D. Ziffer ◽  
William R. Love ◽  
...  
Keyword(s):  
Bladder Cancer ◽  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization
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