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Mapping a multiplexed zoo of mRNA expression

Choi, Harry M. T. and Calvert, Colby R. and Husain, Naeem and Barsi, Julius C. and Deverman, Benjamin E. and Hunter, Ryan C. and Kato, Mihoko and Lee, S. Melanie and Abelin, Anna C. T. and Rosenthal, Adam Z. and Akbari, Omar S. and Li, Yuwei and Hay, Bruce A. and Sternberg, Paul W. and Patterson, Paul H. and Davidson, Eric H. and Mazmanian, Sarkis K. and Prober, David A. and Leadbetter, Jared R. and Newman, Dianne K. and Readhead, Carol and Bronner, Marianne E. and Wold, Barbara and Fraser, Scott E. and Pierce, Niles A. (2016) Mapping a multiplexed zoo of mRNA expression. Development, 143 (19). pp. 3632-3637. ISSN 0950-1991. PMCID PMC5087610. doi:10.1242/dev.140137.

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In situ hybridization methods are used across the biological sciences to map mRNA expression within intact specimens. Multiplexed experiments, in which multiple target mRNAs are mapped in a single sample, are essential for studying regulatory interactions, but remain cumbersome in most model organisms. Programmable in situ amplifiers based on the mechanism of hybridization chain reaction (HCR) overcome this longstanding challenge by operating independently within a sample, enabling multiplexed experiments to be performed with an experimental timeline independent of the number of target mRNAs. To assist biologists working across a broad spectrum of organisms, we demonstrate multiplexed in situ HCR in diverse imaging settings: bacteria, whole-mount nematode larvae, whole-mount fruit fly embryos, whole-mount sea urchin embryos, whole-mount zebrafish larvae, whole-mount chicken embryos, whole-mount mouse embryos and formalin-fixed paraffin-embedded human tissue sections. In addition to straightforward multiplexing, in situ HCR enables deep sample penetration, high contrast and subcellular resolution, providing an incisive tool for the study of interlaced and overlapping expression patterns, with implications for research communities across the biological sciences.

Item Type:Article
Related URLs:
URLURL TypeDescription Information CentralArticle
Choi, Harry M. T.0000-0002-1530-0773
Husain, Naeem0000-0003-4962-7237
Barsi, Julius C.0000-0002-5161-6708
Deverman, Benjamin E.0000-0002-6223-9303
Hunter, Ryan C.0000-0003-3841-1676
Kato, Mihoko0000-0003-3827-8879
Rosenthal, Adam Z.0000-0002-6936-3665
Akbari, Omar S.0000-0002-6853-9884
Li, Yuwei0000-0001-7753-4869
Hay, Bruce A.0000-0002-5486-0482
Sternberg, Paul W.0000-0002-7699-0173
Mazmanian, Sarkis K.0000-0003-2713-1513
Prober, David A.0000-0002-7371-4675
Leadbetter, Jared R.0000-0002-7033-0844
Newman, Dianne K.0000-0003-1647-1918
Bronner, Marianne E.0000-0003-4274-1862
Wold, Barbara0000-0003-3235-8130
Fraser, Scott E.0000-0002-5377-0223
Pierce, Niles A.0000-0003-2367-4406
Additional Information:© 2016. Published by The Company of Biologists Ltd. Received May 20, 2016. Accepted August 1, 2016. This work was funded by the National Institutes of Health (NIH) [5R01EB006192]; the National Science Foundation Molecular Programming Project [NSF-CCF-1317694]; the Gordon and Betty Moore Foundation [GBMF2809]; the Beckman Institute at Caltech (PMTC); the Translational Biomedical Imaging Laboratory at CHLA; the Translational Imaging Center at USC; a Christensen Fellowship at St Catherine's College, University of Oxford; and by the John Simon Guggenheim Memorial Foundation. Deposited in PMC for release after 12 months. Competing interests: The authors declare competing financial interests in the form of patents and pending patent applications. Author contributions: Study conceived by N.A.P. in consultation with M.E.B., E.H.D., S.E.F., B.A.H., J.R.L., D.K.N., P.H.P., M.v.d.R., B.W. Experiments designed by H.M.T.C. and N.A.P. Preliminary studies and protocol adaptation performed by S.M.L., R.C.H., A.Z.R., H.M.T.C. (bacteria), C.R.C. (nematode), N.H. (fly), J.C.B., C.R.C. (urchin), H.M.T.C. (zebrafish), T.S.-S., C.R.C. (chicken), A.C.T.A., B.E.D., D.H., H.M.T.C. (mouse), and H.M.T.C., N.H. (human), in consultation with D.K.N., J.R.L. (bacteria), M.K. (nematode), R.L., S.E.F. (chicken), R.L., C.R.C., S.E.F., B.W. (mouse), M.v.d.R. (human), and H.M.T.C., N.A.P. (all organisms). Final protocols optimized and final data collected by H.M.T.C. (bacteria, zebrafish, mouse), C.R.C. (nematode, urchin, chicken) and N.H. (fly, human). Final data analyzed by: S.M.L., S.K.M., R.C.H., D.K.N., A.Z.R., J.R.L. (bacteria), M.K., P.S., C.R.C. (nematode), O.S.A., B.A.H., N.H. (fly), J.C.B., C.R.C. (urchin), D.A.P., S.E.F. (fish), T.S.-S., M.E.B., C.R.C. (chicken), A.C.T.A., B.W., B.E.D., D.H., Y.L., C.R., R.L., S.E.F. (mouse), A.C.M., M.v.d.R., N.H. (human) and H.M.T.C and N.A.P. (all organisms). Paper and supplementary information written by H.M.T.C. and N.A.P. Paper was edited and approved by all coauthors.
Group:UNSPECIFIED, Division of Geological and Planetary Sciences
Funding AgencyGrant Number
Gordon and Betty Moore FoundationGBMF2809
Caltech Beckman InstituteUNSPECIFIED
CHLA Translational Biomedical Imaging LaboratoryUNSPECIFIED
USC Translational Imaging CenterUNSPECIFIED
St. Catharine’s CollegeUNSPECIFIED
University of OxfordUNSPECIFIED
John Simon Guggenheim Memorial FoundationUNSPECIFIED
Subject Keywords:In situ hybridization, In situ amplification, Hybridization chain reaction (HCR), Multiplexing, Deep sample penetration, High contrast, Subcellular resolution, Bacteria, Whole-mount embryos and larvae, Tissue sections
Issue or Number:19
PubMed Central ID:PMC5087610
Record Number:CaltechAUTHORS:20161011-070233463
Persistent URL:
Official Citation:Mapping a multiplexed zoo of mRNA expression Harry M. T. Choi, Colby R. Calvert, Naeem Husain, David Huss, Julius C. Barsi, Benjamin E. Deverman, Ryan C. Hunter, Mihoko Kato, S. Melanie Lee, Anna C. T. Abelin, Adam Z. Rosenthal, Omar S. Akbari, Yuwei Li, Bruce A. Hay, Paul W. Sternberg, Paul H. Patterson, Eric H. Davidson, Sarkis K. Mazmanian, David A. Prober, Matt van de Rijn, Jared R. Leadbetter, Dianne K. Newman, Carol Readhead, Marianne E. Bronner, Barbara Wold, Rusty Lansford, Tatjana Sauka-Spengler, Scott E. Fraser, Niles A. Pierce Development 2016 143: 3632-3637; doi: 10.1242/dev.140137
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:70986
Deposited By: Ruth Sustaita
Deposited On:11 Oct 2016 20:47
Last Modified:14 Apr 2022 17:29

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