Temporally and Spatially Restricted Gene Expression Profiling
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.
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.
Rights & PermissionsPrintExport