Zhang et al. 2019 (PRJNA419198)

General Details

Title Circular RNA profiling reveals the different distribution/characteristic and possible transport mechanism among the subcellular fractions
Organism
Number of Samples 2
Release Date 2017/11/20 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP125321
ENA SRP125321
GEO
BioProject PRJNA419198

Publication

Title
Authors Zhang J,Zhang X,Li C,Yue L,Ding N,Riordan T,Yang L,Li Y,Jen C,Lin S,Zhou D,Chen F
Journal RNA biology
Publication Date 2019 Feb
Abstract Circular RNA (circRNA) is a novel RNA molecule that has become a research focus recently. Although some research indicated that the circRNAs in different subcellular compartments could execute different regulatory functions, a panoramic analysis of the subcellular distribution and the transport mechanism of circRNA is still required. In this study, we comprehensively analyzed the subcellular distribution/characteristics and the transport mechanism, through systemically investigating the circRNA profiles among the subcellular fractions of HepG2 cell (nucleus, cytoplasm, mitochondria, ribosome, cytosol and exosome). CircRNAs were widely distributed among the subcellular fractions except in the mitochondria, with differences in the subcellular distribution/characteristics in terms of classification, length, GC content, alternative circularization and parental gene function. Further analysis indicated this might be due to the selective transportation mediated by the transport-related RNA binding proteins (RBPs). The circRNAs may follow the same transportation mechanism of linear RNAs, in which the RBPs specially recognize/transport the RNAs with the corresponding binding motifs. Interestingly, we found that the exosome could selectively package the circRNAs containing the purine-rich 5'-GMWGVWGRAG-3' motif, with the characteristic of 'garbage dumping' and 'intercellular signaling' functions. Besides, although we observed numerous circRNAs enriched in the ribosome, we did not reliably identify any unique-peptides from circRNAs using 3D-LC-MS/MS strategy. This suggests that circRNAs rarely function as translation templates in vivo like lincRNA. Our findings not only indicates the differential distributions/characteristics among the subcellular fractions, but also reveals the possible transportation mechanism. This provides an improved understanding of the life history and molecular behavior of circRNA in cells.
PMC PMC6380345
PMID 30614753
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR6309605 PRJNA419198 Homo sapiens HepG2 Ribo-Seq
SRR6309606 PRJNA419198 Homo sapiens HepG2 Ribo-Seq
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)

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