Pumilio-Based RNA In Vivo Imaging

Tilsner, Jens

doi:10.1007/978-1-4939-1523-1_20

Cited by 5 publications

(3 citation statements)

References 52 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Previous works had demonstrated, using proteins that bind to specific RNA sequences, the measurement of mRNA expression level (23,24), imaging of mRNA dynamics (23)(24)(25)(26)32), and enhancement and suppression of mRNA translation (6,30,31,33) with variants of natural RNA-binding proteins. We demonstrated that our Pumby architecture, which uses a single repeated module to support protein generation (analogous to the TALE design), enables performance equivalent to the original Pumilio protein.…”

Section: Discussionmentioning

confidence: 99%

Programmable RNA-binding protein composed of repeats of a single modular unit

Adamala

Martin-Alarcon

Boyden

2016

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

The ability to monitor and perturb RNAs in living cells would benefit greatly from a modular protein architecture that targets unmodified RNA sequences in a programmable way. We report that the RNA-binding protein PumHD (Pumilio homology domain), which has been widely used in native and modified form for targeting RNA, can be engineered to yield a set of four canonical protein modules, each of which targets one RNA base. These modules (which we call Pumby, for Pumilio-based assembly) can be concatenated in chains of varying composition and length, to bind desired target RNAs. The specificity of such Pumby-RNA interactions was high, with undetectable binding of a Pumby chain to RNA sequences that bear three or more mismatches from the target sequence. We validate that the Pumby architecture can perform RNA-directed protein assembly and enhancement of translation of RNAs. We further demonstrate a new use of such RNA-binding proteins, measurement of RNA translation in living cells. Pumby may prove useful for many applications in the measurement, manipulation, and biotechnological utilization of unmodified RNAs in intact cells and systems.

show abstract

Section: Discussionmentioning

confidence: 99%

Programmable RNA-binding protein composed of repeats of a single modular unit

Adamala

Martin-Alarcon

Boyden

2016

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

show abstract

“…Pumilio homology domain (PUMHD) based BiFC systems can directly image endogenous RNAs since the PUMHD with different structures 151 can be designed according to the target sequences. Tilsner et al 152 fused PUMHD3794 and PUMHD3809 to N- or C-terminal halves of split mCitrine and successfully imaged the genomic RNA of the tobacco mosaic virus (TMV).…”

Section: Probes Imaging Endogenous Rnasmentioning

confidence: 99%

Recent advances in high-performance fluorescent and bioluminescent RNA imaging probes

et al. 2017

View full text Add to dashboard Cite

RNA plays an important role in life processes. Imaging of messenger RNAs (mRNAs) and micro-RNAs (miRNAs) not only allows us to learn the formation and transcription of mRNAs and the biogenesis of miRNAs involved in various life processes, but also helps in detecting cancer. High-performance RNA imaging probes greatly expand our view of life processes and enhance the cancer detection accuracy. In this review, we summarize the state-of-the-art high-performance RNA imaging probes, including exogenous probes that can image RNA sequences with special modification and endogeneous probes that can directly image endogenous RNAs without special treatment. For each probe, we review its structure and imaging principle in detail. Finally, we summarize the application of mRNA and miRNA imaging probes in studying life processes as well as in detecting cancer. By correlating the structures and principles of various probes with their practical uses, we compare different RNA imaging probes and offer guidance for better utilization of the current imaging probes and the future design of higher-performance RNA imaging probes.

show abstract

“…Upon both PUM-HDs recognizing the two sequences of target RNA, the two split fragments of EGFP are fused close enough to recover fluorescence. Since two different PUM-HDs carrying 16 elements can specifically recognize 4*16 transcripts, it is sufficient to use this probe to label any target mRNA in a cell (scheme 1-3) [23][24][25] .…”

Section: Pumilio Imaging Systemmentioning

confidence: 99%

Development of chemical tools for imaging RNA and studying RNA and protein interactions

Zhang¹

View full text Add to dashboard Cite

Pumilio-Based RNA In Vivo Imaging

Cited by 5 publications

References 52 publications

Programmable RNA-binding protein composed of repeats of a single modular unit

Programmable RNA-binding protein composed of repeats of a single modular unit

Recent advances in high-performance fluorescent and bioluminescent RNA imaging probes

Development of chemical tools for imaging RNA and studying RNA and protein interactions

Contact Info

Product

Resources

About