circRNA Modification Analysis

N6-methyladenosine (m6A) is a common abundant modification present in mRNAs and various non-coding RNAs (ncRNAs). Compared to mRNA m6A studies, little is known about m6A modifications to circular RNAs (circRNAs). CD Genomics provides next-generation sequencing (NGS) and mass spectrometry (MS)-based methods for circRNA modification analysis, allowing for the detection of m6A and other methylation modifications on circRNAs.

Overview

m6A is a widespread methylation modification in eukaryotic cells from yeast to humans. m6A is involved in all aspects of post-transcriptional RNA metabolism including RNA half-life, splicing, translational efficiency, RNA structure and nuclear export. According to previous studies, m6A is also present on circRNAs and has the potential to initiate cap-independent translation. And m6A RNA modification on human circRNAs can inhibit innate immunity by abrogating immune gene activation and adjuvant activity. The development of m6A mapping assays utilizing anti-m6A antibodies coupled to RNA sequencing (RNA-seq) or mass spectrometry (MS) after RNA fragmentation can reveal sites of m6A modification located on various mRNAs and ncRNAs. More than one thousand m6A circRNAs are found in human embryonic stem cells (hESCs) and are abundant in ESCs. And m6A circRNA displays cell-type specific expression patterns.

CD Genomics provides solutions for circRNA modification analysis, including MS and MeRIP-seq, also known as m6A-seq. MS can detect circRNA modifications and determine the types of modifications and their extent. MeRIP-seq represents methylated RNA immunoprecipitation sequencing, which utilizes m6A-specific antibodies to immunoprecipitate RNA. Please do not hesitate to contact us to discuss your circRNA project and we will assist you in the whole process from experimental design and operations to data preprocessing and analysis.

Features

Rich Experience Genome-Wide Integrative Solution Single Nucleotide Resolution
Rich experience in circRNA experiments and bioinformatics analysis. Transcriptome-wide identification of circRNA m6A modifications, either known or unknown. Integrative circRNA solution to reveal mechanisms underlying circRNA biology. Map m6A sites in the transcriptome at single nucleotide resolution.
circRNA Modification Analysis

Data Analysis Workflow

In-depth data analysis:

  • Data preprocessing
  • m6A peaks calling
  • Quantitative analysis of m6A circRNA sites
  • De novo motif analysis
  • Differential m6A level analysis

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. Zhou C, Molinie B, Daneshvar K, et al. Genome-wide maps of m6A circRNAs identify widespread and cell-type-specific methylation patterns that are distinct from mRNAs. Cell reports, 2017, 20(9): 2262-2276.
  2. Chen Y G, Chen R, Ahmad S, et al. N6-methyladenosine modification controls circular RNA immunity. Molecular cell, 2019, 76(1): 96-109. e9.
* For Research Use Only. Not for use in diagnostic procedures.


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