circRNA-miRNA Interaction Analysis

Circular RNAs (circRNAs) are a class of non-coding RNAs (ncRNAs), characterized by evolutionary conservation, structural stability and tissue specificity. cirRNAs have attracted wide attention in recent years, as they play important roles in human diseases such as tumors, nervous system disease and diabetes. CD Genomics provides RNA sequencing (RNA-seq), circRNA sequencing and CLIP-seq for identifying circRNA-miRNA interactions and circRNA-miRNA-mRNA network.

Overview

circRNAs are a class of endogenous ncRNAs that form a covalently closed continuous loop, resulting in a more stable structure than linear RNA. With advances in next-generation sequencing technology, recent studies have found that circRNAs in human cells might be involved in fetal development, myocardial infarction and carcinomas and some circRNAs might regulate miRNA function as miRNA sponges. The circRNA-miRNA-mRNA interactions may play a vital role in cancer-related or non-cancer pathways. Therefore, circRNA studies provide novel strategies for clinical diagnostics and treatment of human diseases, especially carcinomas. A major topic in the field of circRNA biology is their role in sequestering microRNAs (miRNAs). circRNAs can act on certain targeted miRNAs to regulate cellular processes such as cell invasion and apoptosis.

Next-generation sequencing provides several tools such as circRNA sequencing and CLIP-seq to discover circRNA-miRNA interactions. circRNA sequencing can be used to obtain the profile of circRNAs in a biological sample and detect differentially expressed circRNAs. Crosslinking immunoprecipitation (CLIP)-seq has been recently developed to reveal transcriptome-wide binding sites of RNA-binding proteins at single nucleotide level. CD Genomics comprehensively integrating CLIP-seq and RNA-seq data to reveal the regulatory networks involving miRNAs and circRNAs. We also conduct weighted gene co-expression network analysis (WGCNA), Gene Ontology (GO) functional annotations and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses to explore the underlying mechanisms of action of the circRNAs.

Interaction of different types of ncRNAs (miRNA, lncRNA, and circRNA).Figure 1. Interaction of different types of ncRNAs (miRNA, lncRNA, and circRNA).

Features

Rich Experience Genome-Wide Integrative Solution Quality Control
Rich experience in circRNA sequencing and bioinformatics analysis. Genome-wide identification of circRNA interactome such as miRNA, mRNA and protein. Provide integrative circRNA solution from target prediction, pathway prediction to function prediction. Quality control is executed following every procedure.
circRNA-miRNA Interaction Analysis

Data Analysis Workflow

In-depth data analysis:

  • Prediction of miRNA response elements (MERs)
  • Weighted gene co-expression network analysis (WGCNA)
  • Gene Ontology (GO) functional annotations
  • KEGG pathway analysis
  • Identification of circRNA-miRNA associations
  • Creation of circRNA–miRNA–mRNA network

Sample Requirements

(NGS platform) RNA sample (concentration ≥ 200 ng/uL, quantity ≥ 4 ug), 1.8 ≤ OD260/280 ≤ 2.2, OD260/230 ≥ 2.0, RIN ≥ 6.5, 28S:18S ≥ 1.0. Please make sure that RNA is not significantly degraded.
(MS platform) We work with a wide range of sample types including protein solution, fresh tissue, cultured cells, blood, and microbial sample. Please feel free to contact us for sample size.

Sample storage: The sample should be stored at -80°C. Avoid repeated freezing and thawing.

Shipping Method: When shipping the sample, it is stored in a 1.5 mL Eppendorf tube, sealed with a sealing film. Shipments are generally recommended to contain 5-10 pounds of dry ice per 24 hours.

Deliverable:
(NGS analysis) FastQ, BAM, coverage summary, QC report, GO enrichment histogram, GO terms DAG (directed acyclic hierarchical graph), and KEGG enrichment scatter plot, and other designated report.
(MS analysis) Data QC report, MS results, integrated experimental report (materials, methodologies, and bioinformatics analysis).

References:

  1. Holdt L M, Kohlmaier A, Teupser D. Molecular functions and specific roles of circRNAs in the cardiovascular system. Non-coding RNA research, 2018, 3(2): 75-98.
  2. Rong D, Sun H, Li Z, et al. An emerging function of circRNA-miRNAs-mRNA axis in human diseases. Oncotarget, 2017, 8(42): 73271.
  3. Zhang X Q, Yang J H. Discovering circRNA-microRNA interactions from CLIP-Seq data. Circular RNAs. Humana Press, New York, NY, 2018: 193-207.
* For Research Use Only. Not for use in diagnostic procedures.


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