Home LiteratureArticle Details
PMID: 25858977 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

RNA imaging. Spatially resolved, highly multiplexed RNA profiling in single cells.

Science (New York, N.Y.) ·Vol. 348 ·No. 6233 ·2015-04-24 ·Pages aaa6090

Chen KH, Boettiger AN, Moffitt JR, Wang S, Zhuang X

Abstract

Knowledge of the expression profile and spatial landscape of the transcriptome in individual cells is essential for understanding the rich repertoire of cellular behaviors. Here, we report multiplexed error-robust fluorescence in situ hybridization (MERFISH), a single-molecule imaging approach that allows the copy numbers and spatial localizations of thousands of RNA species to be determined in single cells. Using error-robust encoding schemes to combat single-molecule labeling and detection errors, we demonstrated the imaging of 100 to 1000 distinct RNA species in hundreds of individual cells. Correlation analysis of the ~10(4) to 10(6) pairs of genes allowed us to constrain gene regulatory networks, predict novel functions for many unannotated genes, and identify distinct spatial distribution patterns of RNAs that correlate with properties of the encoded proteins.

MeSH Terms
Fibroblasts Gene Expression Profiling/methods High-Throughput Screening Assays Humans In Situ Hybridization, Fluorescence/methods Molecular Imaging/methods RNA Probes RNA, Messenger/analysis Single-Cell Analysis/methods Transcriptome
Chemicals
RNA Probes RNA, Messenger
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Chen Kok Hao
Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.
Boettiger Alistair N
Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.
Moffitt Jeffrey R
Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.
Wang Siyuan
Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.
Zhuang Xiaowei
Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA. Department of Physics, Harvard University, Cambridge, MA 02138, USA. [email protected].
References (50)
50 references, click to expand
  1. Single-cell systems biology by super-resolution imaging and combinatorial labeling.
    Nat Methods. 2012 Jul;9(7):743-8 PMID: 22660740
  2. KIAA1199, a deafness gene of unknown function, is a new hyaluronan binding protein involved in hyaluronan depolymerization.
    Proc Natl Acad Sci U S A. 2013 Apr 2;110(14):5612-7 PMID: 23509262
  3. Changing perspectives in yeast research nearly a decade after the genome sequence.
    Genome Res. 2005 Dec;15(12):1611-9 PMID: 16339358
  4. Microscopy and its focal switch.
    Nat Methods. 2009 Jan;6(1):24-32 PMID: 19116611
  5. Fast compressed sensing analysis for super-resolution imaging using L1-homotopy.
    Opt Express. 2013 Nov 18;21(23):28583-96 PMID: 24514370
  6. Localization of all seven messenger RNAs for the actin-polymerization nucleator Arp2/3 complex in the protrusions of fibroblasts.
    J Cell Sci. 2005 Jun 1;118(Pt 11):2425-33 PMID: 15923655
  7. Cluster analysis and display of genome-wide expression patterns.
    Proc Natl Acad Sci U S A. 1998 Dec 8;95(25):14863-8 PMID: 9843981
  8. In the right place at the right time: visualizing and understanding mRNA localization.
    Nat Rev Mol Cell Biol. 2015 Feb;16(2):95-109 PMID: 25549890
  9. Single-molecule approaches to stochastic gene expression.
    Annu Rev Biophys. 2009;38:255-70 PMID: 19416069
  10. Remote control of gene function by local translation.
    Cell. 2014 Mar 27;157(1):26-40 PMID: 24679524
  11. Spatially resolved transcriptomics and beyond.
    Nat Rev Genet. 2015 Jan;16(1):57-66 PMID: 25446315
  12. Design of 240,000 orthogonal 25mer DNA barcode probes.
    Proc Natl Acad Sci U S A. 2009 Feb 17;106(7):2289-94 PMID: 19171886
  13. Acidification of the oxygen scavenging system in single-molecule fluorescence studies: in situ sensing with a ratiometric dual-emission probe.
    Anal Chem. 2010 Jul 15;82(14):6132-8 PMID: 20583766
  14. Nonblinking and long-lasting single-molecule fluorescence imaging.
    Nat Methods. 2006 Nov;3(11):891-3 PMID: 17013382
  15. Protein translocation across the eukaryotic endoplasmic reticulum and bacterial plasma membranes.
    Nature. 2007 Nov 29;450(7170):663-9 PMID: 18046402
  16. Visualization of omics data for systems biology.
    Nat Methods. 2010 Mar;7(3 Suppl):S56-68 PMID: 20195258
  17. Breaking the diffraction barrier: super-resolution imaging of cells.
    Cell. 2010 Dec 23;143(7):1047-58 PMID: 21168201
  18. GeneCards Version 3: the human gene integrator.
    Database (Oxford). 2010;2010:baq020 PMID: 20689021
  19. The embryo as a laboratory: quantifying transcription in Drosophila.
    Trends Genet. 2014 Aug;30(8):364-75 PMID: 25005921
  20. A high-density 3D localization algorithm for stochastic optical reconstruction microscopy.
    Opt Nanoscopy. 2012;1(6):null PMID: 25431749
  21. Using variability in gene expression as a tool for studying gene regulation.
    Wiley Interdiscip Rev Syst Biol Med. 2013 Nov-Dec;5(6):751-9 PMID: 23996796
  22. Single-molecule methods leap ahead.
    Nat Methods. 2014 Oct;11(10):1015-8 PMID: 25264779
  23. An integrated encyclopedia of DNA elements in the human genome.
    Nature. 2012 Sep 6;489(7414):57-74 PMID: 22955616
  24. A single molecule view of gene expression.
    Trends Cell Biol. 2009 Nov;19(11):630-7 PMID: 19819144
  25. Faster STORM using compressed sensing.
    Nat Methods. 2012 Jul;9(7):721-3 PMID: 22522657
  26. Visualization of single RNA transcripts in situ.
    Science. 1998 Apr 24;280(5363):585-90 PMID: 9554849
  27. Single-cell gene expression profiling.
    Science. 2002 Aug 2;297(5582):836-40 PMID: 12161654
  28. Single-chromosome transcriptional profiling reveals chromosomal gene expression regulation.
    Nat Methods. 2013 Mar;10(3):246-8 PMID: 23416756
  29. GENCODE: the reference human genome annotation for The ENCODE Project.
    Genome Res. 2012 Sep;22(9):1760-74 PMID: 22955987
  30. Methods for the preparation of large quantities of complex single-stranded oligonucleotide libraries.
    PLoS One. 2014;9(4):e94752 PMID: 24733454
  31. BLAST+: architecture and applications.
    BMC Bioinformatics. 2009;10:421 PMID: 20003500
  32. Mechanisms and cellular roles of local protein synthesis in mammalian cells.
    Curr Opin Cell Biol. 2008 Apr;20(2):144-9 PMID: 18378131
  33. Versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes.
    Proc Natl Acad Sci U S A. 2012 Dec 26;109(52):21301-6 PMID: 23236188
  34. Cell migration: a physically integrated molecular process.
    Cell. 1996 Feb 9;84(3):359-69 PMID: 8608589
  35. Imaging individual mRNA molecules using multiple singly labeled probes.
    Nat Methods. 2008 Oct;5(10):877-9 PMID: 18806792
  36. Principles of ER cotranslational translocation revealed by proximity-specific ribosome profiling.
    Science. 2014 Nov 7;346(6210):1257521 PMID: 25378630
  37. General properties of transcriptional time series in Escherichia coli.
    Nat Genet. 2011 Jun;43(6):554-60 PMID: 21532574
  38. Single β-actin mRNA detection in neurons reveals a mechanism for regulating its translatability.
    Science. 2014 Jan 24;343(6169):419-22 PMID: 24458642
  39. Mechanisms of transcriptional precision in animal development.
    Trends Genet. 2012 Aug;28(8):409-16 PMID: 22513408
  40. Polysomes, P bodies and stress granules: states and fates of eukaryotic mRNAs.
    Curr Opin Cell Biol. 2009 Jun;21(3):403-8 PMID: 19394210
  41. Using gene expression noise to understand gene regulation.
    Science. 2012 Apr 13;336(6078):183-7 PMID: 22499939
  42. Single molecule imaging of RNA in situ.
    Methods Mol Biol. 2011;714:3-13 PMID: 21431731
  43. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks.
    Nat Protoc. 2012 Mar;7(3):562-78 PMID: 22383036
  44. Single-cell in situ RNA profiling by sequential hybridization.
    Nat Methods. 2014 Apr;11(4):360-1 PMID: 24681720
  45. OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach.
    Nucleic Acids Res. 2003 Jun 15;31(12):3057-62 PMID: 12799432
  46. Intracellular localization of messenger RNAs for cytoskeletal proteins.
    Cell. 1986 May 9;45(3):407-15 PMID: 3698103
  47. Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells.
    Science. 2010 Jul 30;329(5991):533-8 PMID: 20671182
  48. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
    Nat Genet. 2000 May;25(1):25-9 PMID: 10802651
  49. Image-based transcriptomics in thousands of single human cells at single-molecule resolution.
    Nat Methods. 2013 Nov;10(11):1127-33 PMID: 24097269
  50. Genetic determinants and cellular constraints in noisy gene expression.
    Science. 2013 Dec 6;342(6163):1188-93 PMID: 24311680
Article Info
Journal
Science (New York, N.Y.)
Abbr.
Science
ISSN
1095-9203
DOI
10.1126/science.aaa6090
Email
[email protected]
Published
2015-04-24
Epub
2015-00-09
Pages
aaa6090
Language
English
Region
United States
NLM ID
0404511
PMCID
PMC4662681
Subset
IM
Grants
NIGMS NIH HHS · R01 GM096450 · United States
NIGMS NIH HHS · R01 GM105637 · United States
Howard Hughes Medical Institute · United States
Databases
GEO
GSE67685
Corrections
CommentIn
PMID: 25948245
CommentIn
PMID: 26013647
CommentIn
PMID: 26221655
External Links
PubMed source DOI: 10.1126/science.aaa6090 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: [email protected]

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2