PMID- 38502488
OWN - NLM
STAT- MEDLINE
DCOM- 20240321
LR  - 20240321
IS  - 1940-6029 (Electronic)
IS  - 1064-3745 (Linking)
VI  - 2784
DP  - 2024
TI  - Combined 3D DNA FISH, Single-Molecule RNA FISH, and Immunofluorescence.
PG  - 203-214
LID - 10.1007/978-1-0716-3766-1_14 [doi]
AB  - Nuclear architecture is a potential regulator of gene expression in eukaryotic 
      cells. Studies connecting nuclear architecture to gene expression are often 
      population-averaged and do not report on the cell-level heterogeneity in genome 
      organization and associated gene expression. In this report we present a simple 
      way to combine fluorescence in situ hybridization (FISH)-based detection of DNA, 
      with single-molecule RNA FISH (smFISH) and immunofluorescence (IF), while also 
      preserving the three-dimensional (3D) nuclear architecture of a cell. Recently 
      developed smFISH techniques enable the detection of individual RNA molecules; 
      while using 3D DNA FISH, copy numbers and positions of genes inside the nucleus 
      can be interrogated without interfering with 3D nuclear architecture. Our method 
      to combine 3D DNA FISH with smFISH and IF enables a unique quantitative handle on 
      the central dogma of molecular biology.
CI  - (c) 2024. The Author(s), under exclusive license to Springer Science+Business 
      Media, LLC, part of Springer Nature.
FAU - Sen, Souvik
AU  - Sen S
AD  - Tata Institute of Fundamental Research Hyderabad, Hyderabad, Telangana, India.
FAU - Dhuppar, Shivnarayan
AU  - Dhuppar S
AD  - Tata Institute of Fundamental Research Hyderabad, Hyderabad, Telangana, India.
AD  - Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and 
      Women's Hospital and Harvard Medical School, Boston, MA, USA.
FAU - Mazumder, Aprotim
AU  - Mazumder A
AD  - Tata Institute of Fundamental Research Hyderabad, Hyderabad, Telangana, India. 
      aprotim@tifrh.res.in.
LA  - eng
PT  - Journal Article
PL  - United States
TA  - Methods Mol Biol
JT  - Methods in molecular biology (Clifton, N.J.)
JID - 9214969
RN  - 63231-63-0 (RNA)
RN  - 9007-49-2 (DNA)
SB  - IM
MH  - *RNA/genetics
MH  - In Situ Hybridization, Fluorescence/methods
MH  - *DNA/genetics
MH  - Fluorescent Antibody Technique
MH  - Genome
OTO - NOTNLM
OT  - 3D DNA FISH
OT  - Fluorescence in situ hybridization (FISH)
OT  - Immunofluorescence (IF)
OT  - Single-molecule RNA FISH (smFISH)
EDAT- 2024/03/19 18:42
MHDA- 2024/03/21 12:47
CRDT- 2024/03/19 12:21
PHST- 2024/03/21 12:47 [medline]
PHST- 2024/03/19 18:42 [pubmed]
PHST- 2024/03/19 12:21 [entrez]
AID - 10.1007/978-1-0716-3766-1_14 [doi]
PST - ppublish
SO  - Methods Mol Biol. 2024;2784:203-214. doi: 10.1007/978-1-0716-3766-1_14.