PMID- 31110282
OWN - NLM
STAT- MEDLINE
DCOM- 20190708
LR  - 20210331
IS  - 1548-7105 (Electronic)
IS  - 1548-7091 (Print)
IS  - 1548-7091 (Linking)
VI  - 16
IP  - 6
DP  - 2019 Jun
TI  - SABER amplifies FISH: enhanced multiplexed imaging of RNA and DNA in cells and 
      tissues.
PG  - 533-544
LID - 10.1038/s41592-019-0404-0 [doi]
AB  - Fluorescence in situ hybridization (FISH) reveals the abundance and positioning 
      of nucleic acid sequences in fixed samples. Despite recent advances in 
      multiplexed amplification of FISH signals, it remains challenging to achieve high 
      levels of simultaneous amplification and sequential detection with high sampling 
      efficiency and simple workflows. Here we introduce signal amplification by 
      exchange reaction (SABER), which endows oligonucleotide-based FISH probes with 
      long, single-stranded DNA concatemers that aggregate a multitude of short 
      complementary fluorescent imager strands. We show that SABER amplified RNA and 
      DNA FISH signals (5- to 450-fold) in fixed cells and tissues. We also applied 17 
      orthogonal amplifiers against chromosomal targets simultaneously and detected 
      mRNAs with high efficiency. We then used 10-plex SABER-FISH to identify in vivo 
      introduced enhancers with cell-type-specific activity in the mouse retina. SABER 
      represents a simple and versatile molecular toolkit for rapid and cost-effective 
      multiplexed imaging of nucleic acid targets.
FAU - Kishi, Jocelyn Y
AU  - Kishi JY
AD  - Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, 
      MA, USA.
AD  - Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
FAU - Lapan, Sylvain W
AU  - Lapan SW
AD  - Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 
      USA.
FAU - Beliveau, Brian J
AU  - Beliveau BJ
AUID- ORCID: 0000-0003-1314-3118
AD  - Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, 
      MA, USA. beliveau@uw.edu.
AD  - Department of Systems Biology, Harvard Medical School, Boston, MA, USA. 
      beliveau@uw.edu.
AD  - Department of Genome Sciences, University of Washington, Seattle, WA, USA. 
      beliveau@uw.edu.
FAU - West, Emma R
AU  - West ER
AD  - Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 
      USA.
FAU - Zhu, Allen
AU  - Zhu A
AD  - Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, 
      MA, USA.
AD  - Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
FAU - Sasaki, Hiroshi M
AU  - Sasaki HM
AD  - Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, 
      MA, USA.
AD  - Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
FAU - Saka, Sinem K
AU  - Saka SK
AD  - Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, 
      MA, USA.
AD  - Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
FAU - Wang, Yu
AU  - Wang Y
AD  - Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, 
      MA, USA.
AD  - Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
FAU - Cepko, Constance L
AU  - Cepko CL
AUID- ORCID: 0000-0002-9945-6387
AD  - Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 
      USA. cepko@genetics.med.harvard.edu.
AD  - Howard Hughes Medical Institute, Chevy Chase, MD, USA. 
      cepko@genetics.med.harvard.edu.
FAU - Yin, Peng
AU  - Yin P
AUID- ORCID: 0000-0002-2769-6357
AD  - Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, 
      MA, USA. py@hms.harvard.edu.
AD  - Department of Systems Biology, Harvard Medical School, Boston, MA, USA. 
      py@hms.harvard.edu.
LA  - eng
GR  - UG3 HL145600/HL/NHLBI NIH HHS/United States
GR  - U01 MH106011/MH/NIMH NIH HHS/United States
GR  - K99 EY028215/EY/NEI NIH HHS/United States
GR  - T32 GM096911/GM/NIGMS NIH HHS/United States
GR  - R01 GM124401/GM/NIGMS NIH HHS/United States
GR  - R01 EB018659/EB/NIBIB NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
PT  - Research Support, Non-U.S. Gov't
PT  - Research Support, U.S. Gov't, Non-P.H.S.
DEP - 20190520
PL  - United States
TA  - Nat Methods
JT  - Nature methods
JID - 101215604
RN  - 0 (DNA, Single-Stranded)
RN  - 0 (Fluorescent Dyes)
RN  - 0 (Oligonucleotides)
RN  - 63231-63-0 (RNA)
RN  - 9007-49-2 (DNA)
SB  - IM
MH  - Animals
MH  - Cells, Cultured
MH  - DNA/*analysis/genetics
MH  - DNA, Single-Stranded/chemistry
MH  - Fluorescent Dyes/*metabolism
MH  - Humans
MH  - In Situ Hybridization, Fluorescence/*methods
MH  - Mice
MH  - Oligonucleotides/*chemistry
MH  - Optical Imaging/*methods
MH  - RNA/*analysis/genetics
MH  - Retina/diagnostic imaging/*metabolism
PMC - PMC6544483
MID - NIHMS1526200
COIS- Competing Financial Interests: A provisional US patent has been filed based on 
      this work. P.Y. is co-founder of Ultivue Inc. and NuProbe Global.
EDAT- 2019/05/22 06:00
MHDA- 2019/07/10 06:00
PMCR- 2019/11/20
CRDT- 2019/05/22 06:00
PHST- 2018/10/27 00:00 [received]
PHST- 2019/04/03 00:00 [accepted]
PHST- 2019/05/22 06:00 [pubmed]
PHST- 2019/07/10 06:00 [medline]
PHST- 2019/05/22 06:00 [entrez]
PHST- 2019/11/20 00:00 [pmc-release]
AID - 10.1038/s41592-019-0404-0 [pii]
AID - 10.1038/s41592-019-0404-0 [doi]
PST - ppublish
SO  - Nat Methods. 2019 Jun;16(6):533-544. doi: 10.1038/s41592-019-0404-0. Epub 2019 
      May 20.