PMID- 37573342
OWN - NLM
STAT- MEDLINE
DCOM- 20230814
LR  - 20240212
IS  - 2041-1723 (Electronic)
IS  - 2041-1723 (Linking)
VI  - 14
IP  - 1
DP  - 2023 Aug 12
TI  - SnapFISH: a computational pipeline to identify chromatin loops from multiplexed 
      DNA FISH data.
PG  - 4873
LID - 10.1038/s41467-023-40658-3 [doi]
LID - 4873
AB  - Multiplexed DNA fluorescence in situ hybridization (FISH) imaging technologies 
      have been developed to map the folding of chromatin fibers at tens of nanometers 
      and up to several kilobases in resolution in single cells. However, computational 
      methods to reliably identify chromatin loops from such imaging datasets are still 
      lacking. Here we present a Single-Nucleus Analysis Pipeline for multiplexed DNA 
      FISH (SnapFISH), to process the multiplexed DNA FISH data and identify chromatin 
      loops. SnapFISH can identify known chromatin loops from mouse embryonic stem 
      cells with high sensitivity and accuracy. In addition, SnapFISH obtains 
      comparable results of chromatin loops across datasets generated from diverse 
      imaging technologies. SnapFISH is freely available at 
      https://github.com/HuMingLab/SnapFISH .
CI  - (c) 2023. Springer Nature Limited.
FAU - Lee, Lindsay
AU  - Lee L
AD  - Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland 
      Clinic Foundation, Cleveland, OH, USA.
FAU - Yu, Hongyu
AU  - Yu H
AD  - Department of Statistics, University of Wisconsin Madison, Madison, WI, USA.
AD  - Department of Biochemistry, University of Wisconsin Madison, Madison, WI, USA.
FAU - Jia, Bojing Blair
AU  - Jia BB
AD  - Bioinformatics and Systems Biology Graduate Program, University of California San 
      Diego, La Jolla, CA, USA.
AD  - Medical Scientist Training Program, University of California San Diego, La Jolla, 
      CA, USA.
FAU - Jussila, Adam
AU  - Jussila A
AD  - Bioinformatics and Systems Biology Graduate Program, University of California San 
      Diego, La Jolla, CA, USA.
FAU - Zhu, Chenxu
AU  - Zhu C
AUID- ORCID: 0000-0003-4216-6562
AD  - Ludwig Institute for Cancer Research, La Jolla, CA, USA.
AD  - New York Genome Center, New York, NY, USA.
AD  - Department of Physiology and Biophysics, Institute for Computational Biomedicine, 
      Weill Cornell Medicine, New York, NY, USA.
FAU - Chen, Jiawen
AU  - Chen J
AD  - Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA.
FAU - Xie, Liangqi
AU  - Xie L
AD  - Department of Infection Biology, Lerner Research Institute, Cleveland Clinic 
      Foundation, Cleveland, OH, USA.
AD  - Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic 
      Foundation, Cleveland, OH, USA.
FAU - Hafner, Antonina
AU  - Hafner A
AD  - Department of Developmental Biology, Stanford University, Stanford, CA, USA.
FAU - Mishra, Shreya
AU  - Mishra S
AD  - Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland 
      Clinic Foundation, Cleveland, OH, USA.
FAU - Wang, Duan Dennis
AU  - Wang DD
AD  - Chapel Hill High School, Chapel Hill, NC, USA.
FAU - Strambio-De-Castillia, Caterina
AU  - Strambio-De-Castillia C
AUID- ORCID: 0000-0002-1069-1816
AD  - Program in Molecular Medicine, University of Massachusetts Chan Medical School, 
      Worcester, MA, USA.
FAU - Boettiger, Alistair
AU  - Boettiger A
AD  - Department of Developmental Biology, Stanford University, Stanford, CA, USA.
FAU - Ren, Bing
AU  - Ren B
AD  - Ludwig Institute for Cancer Research, La Jolla, CA, USA.
AD  - Center for Epigenomics & Department of Cellular and Molecular Medicine, 
      University of California San Diego, La Jolla, CA, USA.
FAU - Li, Yun
AU  - Li Y
AUID- ORCID: 0000-0002-9275-4189
AD  - Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA. 
      yunli@med.unc.edu.
AD  - Department of Genetics, University of North Carolina, Chapel Hill, NC, USA. 
      yunli@med.unc.edu.
AD  - Department of Computer Science, University of North Carolina, Chapel Hill, NC, 
      USA. yunli@med.unc.edu.
FAU - Hu, Ming
AU  - Hu M
AUID- ORCID: 0000-0003-0987-2916
AD  - Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland 
      Clinic Foundation, Cleveland, OH, USA. hum@ccf.org.
LA  - eng
GR  - R01 MH125236/MH/NIMH NIH HHS/United States
GR  - R01 HL163972/HL/NHLBI NIH HHS/United States
GR  - U01 DA052713/DA/NIDA NIH HHS/United States
GR  - UM1 HG011585/HG/NHGRI NIH HHS/United States
GR  - R35 HG011922/HG/NHGRI NIH HHS/United States
GR  - U01 HG011720/HG/NHGRI NIH HHS/United States
GR  - U24 AR076730/AR/NIAMS NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
DEP - 20230812
PL  - England
TA  - Nat Commun
JT  - Nature communications
JID - 101528555
RN  - 0 (Chromatin)
RN  - 9007-49-2 (DNA)
SB  - IM
MH  - Animals
MH  - Mice
MH  - *Chromatin/genetics
MH  - In Situ Hybridization, Fluorescence/methods
MH  - *DNA/genetics
PMC - PMC10423204
COIS- B.R. is a cofounder and shareholder of Arima Genomics, Inc. and Epigenome 
      Technologies, Inc. The remaining authors declare no competing interest.
EDAT- 2023/08/13 00:44
MHDA- 2023/08/14 06:42
PMCR- 2023/08/12
CRDT- 2023/08/12 23:17
PHST- 2023/05/11 00:00 [received]
PHST- 2023/08/01 00:00 [accepted]
PHST- 2023/08/14 06:42 [medline]
PHST- 2023/08/13 00:44 [pubmed]
PHST- 2023/08/12 23:17 [entrez]
PHST- 2023/08/12 00:00 [pmc-release]
AID - 10.1038/s41467-023-40658-3 [pii]
AID - 40658 [pii]
AID - 10.1038/s41467-023-40658-3 [doi]
PST - epublish
SO  - Nat Commun. 2023 Aug 12;14(1):4873. doi: 10.1038/s41467-023-40658-3.