Mouse TU tagging: A chemical/genetic intersectional method for purifying cell type-specific nascent RNA

Genes and Development

Volumn 27, Issue 1, 2013, Pages 98-115

  Gay, Leslie ^a   Miller, Michael R ^a   Ventura, P Britten ^a   Devasthali, Vidusha ^a   Vue, Zer ^b   Thompson, Heather L ^b   Temple, Sally ^c   Zong, Hui ^a   Cleary, Michael D ^b   Stankunas, Kryn ^a   Doe, Chris Q ^a  

^a UNIVERSITY OF OREGON   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c Neural Stem Cell Institute   (United States)

Author keywords

Brain; Endothelial cells; Heart; Microglia; Nascent RNA; Transcriptional profiling

Indexed keywords

4 THIOURACIL; LIPOPOLYSACCHARIDE; RNA; URACIL PHOSPHORIBOSYLTRANSFERASE;

ANALYTIC METHOD; ANIMAL EXPERIMENT; ANIMAL TISSUE; ARTICLE; BONE MARROW TRANSPLANTATION; BRAIN BLOOD VESSEL; CHIMERA; CONTROLLED STUDY; FEMALE; GENE EXPRESSION; GENETIC TRANSCRIPTION; LABELING INDEX; MALE; MICROGLIA; MOUSE; NONHUMAN; PERINATAL PERIOD; PRIORITY JOURNAL; PROTEIN EXPRESSION; RNA SEQUENCE; SPLEEN; THIOURACIL TAGGING;

ANIMALS; BONE MARROW CELLS; BONE MARROW TRANSPLANTATION; BRAIN; CHIMERA; GENE EXPRESSION PROFILING; MICE; MOLECULAR BIOLOGY; RNA; STAINING AND LABELING; THIOURACIL; TRANSGENES;

MUS;

EID: 84872299649     PISSN: 08909369     EISSN: 15495477     Source Type: Journal    
DOI: 10.1101/gad.205278.112     Document Type: Article

References (36)

1. Anders S, Huber W. 2010. Differential expression analysis for sequence count data. Genome Biol 11: R106.
2. Balda MS, Matter K. 2009. Tight junctions and the regulation of gene expression. Biochim Biophys Acta 1788: 761-767.
3. Bartfai T, Buckley PT, Eberwine J. 2012. Drug targets: Single-cell transcriptomics hastens unbiased discovery. Trends Pharmacol Sci 33: 9-16.
4. Benicky J, Sanchez-Lemus E, Pavel J, Saavedra JM. 2009. Antiinflammatory effects of angiotensin receptor blockers in the brain and the periphery. Cell Mol Neurobiol 29: 781-792
5. Brar GA, Yassour M, Friedman N, Regev A, Ingolia NT, Weissman JS. 2012. High-resolution view of the yeast meiotic program revealed by ribosome profiling. Science 335: 552-557.
6. Buttini M, Boddeke H. 1995. Peripheral lipopolysaccharide stimulation induces interleukin-1b messenger RNA in rat brain microglial cells. Neuroscience 65: 523-530.
7. Chen SK, Tvrdik P, Peden E, Cho S, Wu S, Spangrude G, Capecchi MR. 2010. Hematopoietic origin of pathological grooming in Hoxb8 mutant mice. Cell 141: 775-785.
8. Cleary MD, Meiering CD, Jan E, Guymon R, Boothroyd JC. 2005. Biosynthetic labeling of RNA with uracil phosphoribosyltransferase allows cell-specific microarray analysis of mRNA synthesis and decay. Nat Biotechnol 23: 232-237.
9. Daneman R, Zhou L, Agalliu D, Cahoy JD, Kaushal A, Barres BA. 2010. The mouse blood-brain barrier transcriptome: A new resource for understanding the development and function of brain endothelial cells. PLoS ONE 5: e13741.
10. Deal RB, Henikoff S. 2011. The INTACT method for cell type-specific gene expression and chromatin profiling in Arabidopsis thaliana. Nat Protoc 6: 56-68.
11. Diez-Roux G, Banfi S, Sultan M, Geffers L, Anand S, Rozado D, Magen A, Canidio E, Pagani M, Peluso I, et al. 2011. A high resolution anatomical atlas of the transcriptome in the mouse embryo. PLoS Biol 9: e1000582.
12. Doyle JP, Dougherty JD, Heiman M, Schmidt EF, Stevens TR, Ma G, Bupp S, Shrestha P, Shah RD, Doughty ML, et al. 2008. Application of a translational profiling approach for the comparative analysis of CNS cell types. Cell 135: 749-762
13. Ekman N, Lymboussaki A, Vastrik I, Sarvas K, Kaipainen A, Alitalo K. 1997. Bmx tyrosine kinase is specifically expressed in the endocardium and the endothelium of large arteries. Circulation 96: 1729-1732.
14. Friedel CC, Dolken L. 2009. Metabolic tagging and purification of nascent RNA: Implications for transcriptomics. Mol Biosyst 5: 1271-1278.
15. Guez-Barber D, Fanous S, Harvey BK, Zhang Y, Lehrmann E, Becker KG, Picciotto MR, Hope BT. 2012. FACS purification of immunolabeled cell types from adult rat brain. J Neurosci Methods 203: 10-18.
16. Hammer M, Mages J, Dietrich H, Servatius A, Howells N, Cato ACB, Lang R. 2006. Dual specificity phosphatase 1 (DUSP1) regulates a subset of LPS-induced genes and protects mice from lethal endotoxin shock. J Exp Med 203: 15-20.
17. He M, Liu Y, Wang X, Zhang MQ, Hannon GJ, Huang ZJ. 2012. Cell-type-based analysis of microRNA profiles in the mouse brain. Neuron 73: 35-48.
18. Heiman M, Schaefer A, Gong S, Peterson JD, Day M, Ramsey KE, Suarez-Farinas M, chwarz C, Stephan DA, Surmeier DJ, et al. 2008. A translational profiling approach for the molecular characterization of CNS cell types. Cell 135: 738-748
19. Ingolia NT, Lareau LF, Weissman JS. 2011. Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell 147: 789-802.
20. Kisanuki YY, Hammer RE, Miyazaki J, Williams SC, Richardson JA, Yanagisawa M. 2001. Tie2-Cre transgenic mice: A new model for endothelial cell-lineage analysis in vivo. Dev Biol 230: 230-242.
21. Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nat Methods 9: 357-359.
22. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. 2009. The sequence alignment/map format and SAMtools. Bioinformatics 25: 2078-2079.
23. Lobo MK, Karsten SL, Gray M, Geschwind DH, Yang XW. 2006. FACS-array profiling of striatal projection neuron subtypes in juvenile and adult mouse brains. Nat Neurosci 9: 443-452
24. Matei V, Pauley S, Kaing S, Rowitch D, Beisel KW, Morris K, Feng F, Jones K, Lee J, Fritzsch B. 2005. Smaller inner ear sensory epithelia in Neurog 1 null mice are related to earlier hair cell cycle exit. Dev Dyn 234: 633-650.
25. Melet F, Motro B, Rossi DJ, Zhang L, Bernstein A. 1996. Generation of a novel Fli-1 protein by gene targeting leads to a defect in thymus development and a delay in Friend virus induced erythroleukemia. Mol Cell Biol 16: 2708-2718.
26. Miller MR, Robinson KJ, Cleary MD, Doe CQ. 2009. TU-tagging: Cell type-specific RNA isolation from intact complex tissues. Nat Methods 6: 439-441.
27. Patel S, Leal AD, Gorski DH. 2005. The homeobox gene Gax inhibits angiogenesis through inhibition of nuclear factor-kB dependent endothelial cell gene expression. Cancer Res 65: 1414-1424.
28. Qin L, Wu X, Block ML, Liu Y, Breese GR, Hong JS, Knapp DJ, Crews FT. 2007. Systemic LPS causes chronic neuroinflammation and progressive neurodegeneration. Glia 55: 453-462
29. Sanna PP, Repunte-Canonigo V, Guidotti A. 2012. Gene profiling of laser-microdissected brain regions and individual cells in drug abuse and schizophrenia research. Methods Mol Biol 829: 541-550.
30. Sanz E, Yang L, Su T, Morris DR, McKnight GS, Amieux PS. 2009. Cell-type-specific isolation of ribosome-associated mRNA from complex tissues. Proc Natl Acad Sci 106: 13939-13944.
31. Smith-Berdan S, Nguyen A, Hassanein D, Zimmer M, Ugarte F, Ciriza J, Li D, García-Ojeda ME, Hinck L, Forsberg EC. 2011. Robo4 cooperates with CXCR4 to specify hematopoietic stem cell localization to bone marrow niches. Cell Stem Cell 8: 72-83.
32. Spangrude GJ. 2008. Assessment of lymphocyte development in radiation bone marrow chimeras. Curr Protoc Immunol 81: 4.6.1-4.6.9.
33. Stepniak E, Radice GL, Vasioukhin V. 2009. Adhesive and signaling functions of cadherins and catenins in vertebrate development. Cold Spring Harb Perspect Biol 1: a002949
34. Takamatsu H, Takegahara N, Nakagawa Y, Tomura M, Taniguchi M, Friedel RH, Rayburn H, Tessier-Lavigne M, Yoshida Y, Okuno T, et al. 2010. Semaphorins guide the entry of dendritic cells into the lymphatics by activating myosin II. Nat Immunol 11: 594-600.
35. Takash W, Canizares J, Bonneaud N, Poulat F, Mattei MG, Jay P, Berta P. 2001. SOX7 transcription factor: Sequence, chromosomal localisation, expression, transactivation and interference with Wnt signalling. Nucleic Acids Res 29: 4274-4283
36. + lineage to primitive and definitive hematopoietic cells. Genesis 48: 563-567.