Ago HITS-CLIP expands microRNA-mRNA interactions in nucleus and cytoplasm of gastric cancer cells

Intensive investigations have identified a collection of microRNAs (miRNAs) and their functional machineries in cytoplasm. However, a comprehensive view of miRNAs and mRNAs in cytoplasm and nucleus has not been explored. This study aims to reveal the mechanisms of miRNA-RNA interactions in nucleus a...

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Bibliographic Details
Published in:BMC cancer 2019-01, Vol.19 (1), p.29-29, Article 29
Main Authors: Zhang, Xinyi, Shen, Bo, Cui, Yalei
Format: Article
Language:English
Subjects:
Ago HITS-CLIP
Analysis
Argonaute 2 protein
Cancer
Cancer cells
Cell differentiation
Cell growth
Cell proliferation
Cytoplasm
Gastric cancer
Gastric cancer cell
Gene expression
Genes
Genetic aspects
Genetic research
Genomes
Genomics
High-throughput screening (Biochemical assaying)
Immune response
Immunoprecipitation
Innate immunity
Messenger RNA
MicroRNA
MicroRNAs
miRNA
miRNA-RNA interaction
mRNA
Next-generation sequencing
Nucleus and cytoplasm
Ontology
Polymer crosslinking
Proteins
RNA
Stomach cancer
Tumorigenesis
Tumors
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Summary:Intensive investigations have identified a collection of microRNAs (miRNAs) and their functional machineries in cytoplasm. However, a comprehensive view of miRNAs and mRNAs in cytoplasm and nucleus has not been explored. This study aims to reveal the mechanisms of miRNA-RNA interactions in nucleus and cytoplasm. In this study, the miRNAs and their target mRNAs in the Argonaute2 (Ago2) complex of nucleus and cytoplasm of gastric cancer cells were characterized using high-throughput sequencing of RNAs isolated by crosslinking immunoprecipitation (HITS-CLIP). Then, the selected miRNAs were verified by Northern blot. The target mRNAs in the Argonaute2 (Ago2) complex of nucleus and cytoplasm of gastric cancer cells were analyzed through Gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) analysis. The results revealed that there were 243 miRNAs and 265 miRNAs in the Ago2 complexes of nucleus and cytoplasm, respectively. The majority of mature miRNAs existed in cytoplasm. The analysis of miRNA targetome from the Ago2 complexes indicated that a lot of mRNAs with high expression level existed in nucleus. The target genes of miRNAs in the Ago2 complexes of nucleus and cytoplasm played important roles in cell proliferation, cell differentiation, innate immune response and tumorigenesis. microRNA-mRNA interactions occur in nucleus and cytoplasm of gastric cancer cells. Therefore, our study demonstrated that miRNA-mRNA interactions not only took place in cytoplasm but also in nucleus.
ISSN:1471-2407
1471-2407
DOI:10.1186/s12885-018-5246-0