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Current Genomics
ISSN (Print): 1389-2029
ISSN (Online): 1875-5488
VOLUME: 15
ISSUE: 4
DOI: 10.2174/1389202915666140602230106









Temporally and Spatially Restricted Gene Expression Profiling

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Author(s): Alexandra Tallafuss, Philip Washbourne and John Postlethwait
Pages 278-292 (15)
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.
Graphical Abstract:
Keywords:
4tU-tagging, Gene expression profiling, INTACT, RNA-seq, Transcriptome, Translatome, TRAP.
Affiliation:
Institute of Neuroscience, 1254-University of Oregon, 1425 E. 13th Avenue, Eugene, OR-97403, USA.