Current Genomics

Christian Néri
Institute of Biology Paris-Seine
CNRS UMR 8256 and UPMC
Paris, 75005
France

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Temporally and Spatially Restricted Gene Expression Profiling

Author(s): Alexandra Tallafuss, Philip Washbourne and John Postlethwait

Affiliation: Institute of Neuroscience, 1254-University of Oregon, 1425 E. 13th Avenue, Eugene, OR-97403, USA.

Keywords: 4tU-tagging, Gene expression profiling, INTACT, RNA-seq, Transcriptome, Translatome, TRAP.

Graphical Abstract:


Abstract:

Identifying gene function in specific cells is critical for understanding the processes that make cells unique. Several different methods are available to isolate actively transcribed RNA or actively translated RNA in specific cells at a chosen time point. Cell-specific mRNA isolation can be accomplished by the expression of transgenes in cells of interest, either directly from a specific promoter or using a modular system such as Gal4/UAS or Cre/lox. All of the methods described in this review, namely thiol-labeling of RNA (TU-tagging or RABT), TRAP (translating ribosome affinity purification) and INTACT (isolation of nuclei tagged in specific cell types), allow next generation sequencing, permitting the identification of enriched gene transcripts within the specific cell-type. We describe here the general concept of each method, include examples, evaluate possible problems related to each technique, and suggest the types of questions for which each method is best suited.

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Article Details

VOLUME: 15
ISSUE: 4
Page: [278 - 292]
Pages: 15
DOI: 10.2174/1389202915666140602230106