PMID- 36825808
OWN - NLM
STAT- MEDLINE
DCOM- 20231023
LR  - 20240210
IS  - 2666-1667 (Electronic)
IS  - 2666-1667 (Linking)
VI  - 4
IP  - 1
DP  - 2023 Mar 17
TI  - Detecting RNA-protein proximity at DNA double-strand breaks using combined 
      fluorescence in situ hybridization with proximity ligation assay.
PG  - 102096
LID - S2666-1667(23)00054-0 [pii]
LID - 10.1016/j.xpro.2023.102096 [doi]
LID - 102096
AB  - RNA transcribed at DNA double-strand breaks (DSBs) contributes to accurate DNA 
      repair. Here, using the repair factors 53BP1 and TIRR as examples, we combine the 
      fluorescence in situ hybridization (FISH) and proximity ligation assay (PLA) 
      techniques to determine protein proximity to DSB-transcribed RNA. In this 
      FISH-PLA protocol, we detail steps for designing DNA probes and image analysis 
      using CellProfiler software. This approach has many potential applications for 
      the study of the RNA-binding proteins and nascent RNA interactions. For complete 
      details on the use and execution of this protocol, please refer to Ketley et al. 
      (2022).(1).
CI  - Copyright (c) 2023 The Author(s). Published by Elsevier Inc. All rights reserved.
FAU - Alagia, Adele
AU  - Alagia A
AD  - Sir William Dunn School of Pathology, University of Oxford, South Parks Road, 
      Oxford OX1 3RE, UK. Electronic address: adele.alagia@path.ox.ac.uk.
FAU - Ketley, Ruth F
AU  - Ketley RF
AD  - Sir William Dunn School of Pathology, University of Oxford, South Parks Road, 
      Oxford OX1 3RE, UK.
FAU - Gullerova, Monika
AU  - Gullerova M
AD  - Sir William Dunn School of Pathology, University of Oxford, South Parks Road, 
      Oxford OX1 3RE, UK. Electronic address: monika.gullerova@path.ox.ac.uk.
LA  - eng
GR  - 24866/CRUK_/Cancer Research UK/United Kingdom
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PT  - Research Support, U.S. Gov't, Non-P.H.S.
DEP - 20230203
PL  - United States
TA  - STAR Protoc
JT  - STAR protocols
JID - 101769501
RN  - 63231-63-0 (RNA)
RN  - 0 (RNA-Binding Proteins)
RN  - 9007-49-2 (DNA)
SB  - IM
MH  - *DNA Breaks, Double-Stranded
MH  - *RNA/genetics
MH  - In Situ Hybridization, Fluorescence
MH  - RNA-Binding Proteins/genetics
MH  - DNA/metabolism
PMC - PMC9932567
OTO - NOTNLM
OT  - Cell Biology
OT  - In Situ Hybridization
OT  - Microscopy
OT  - Molecular Biology
OT  - Molecular/Chemical Probes
COIS- Declaration of interests The authors declare no competing interests.
EDAT- 2023/02/25 06:00
MHDA- 2023/10/23 00:42
PMCR- 2023/02/03
CRDT- 2023/02/24 08:20
PHST- 2022/11/11 00:00 [received]
PHST- 2022/12/15 00:00 [revised]
PHST- 2023/01/19 00:00 [accepted]
PHST- 2023/10/23 00:42 [medline]
PHST- 2023/02/25 06:00 [pubmed]
PHST- 2023/02/24 08:20 [entrez]
PHST- 2023/02/03 00:00 [pmc-release]
AID - S2666-1667(23)00054-0 [pii]
AID - 102096 [pii]
AID - 10.1016/j.xpro.2023.102096 [doi]
PST - ppublish
SO  - STAR Protoc. 2023 Mar 17;4(1):102096. doi: 10.1016/j.xpro.2023.102096. Epub 2023 
      Feb 3.