RNA N4-Acetylcytidine (ac4C) Analysis

N4-acetylcytidine (ac4C) is a dynamic and reversible RNA modification that adds a critical regulatory dimension to the transcriptome, influencing RNA stability and translation efficiency. CD BioSciences provides comprehensive and highly reliable RNA ac4C analysis services, empowering researchers to precisely map this modification and decipher its role in gene regulation, development, and disease.

Overview of N4-Acetylcytidine (ac4C)

N4-acetylcytidine (ac4C) is a conserved epigenetic mark where an acetyl group is added to the N4 position of cytidine in RNA molecules. Traditionally recognized for its role in stabilizing transfer RNA (tRNA), ac4C has emerged as a significant regulator within messenger RNA (mRNA), where it is deposited by the writer enzyme NAT10. This modification profoundly impacts RNA biology by enhancing mRNA stability and promoting efficient translation, thereby directly modulating protein output. Dysregulation of ac4C is increasingly linked to a spectrum of human diseases, including various cancers, neurological disorders, and metabolic conditions. Consequently, precise mapping and quantification of ac4C sites are essential for uncovering novel disease mechanisms, identifying potential therapeutic targets, and advancing our fundamental understanding of epitranscriptomic regulation.

Fig.1 (a) N4-acetylcytidine (ac4C). (b) Schematic of ac4C-G base pair. (c) Sites of ac4C that have been identified using nucleotide resolution methods in human RNA. (Bartee D, et al., 2022)

Our Services

CD BioSciences provides end-to-end, expert-driven RNA N4-acetylcytidine (ac4C) analysis services. We transform your complex epitranscriptomic questions into clear, actionable data. Our team guides you from initial experimental design through rigorous data analysis, leveraging cutting-edge, validated technologies to deliver precise mapping and quantification of ac4C across your RNA samples. We are committed to providing not just raw data, but deep biological insights that accelerate your research in gene regulation, disease etiology, and biomarker discovery.

Customized ac4C Analysis Solution

To meet the diverse and evolving needs of epitranscriptomics research, CD BioSciences offers highly flexible and customized ac4C analysis solutions. We move beyond standardized packages to collaborate closely with you, designing a project that seamlessly integrates with your specific biological questions, sample types, and research objectives.

1. ac4C Immunoprecipitation Sequencing (ac4C-IP-seq): Profile and map transcriptome-wide ac4C sites by sequencing RNA fragments immunoprecipitated with an ac4C-specific antibody.
2. Chemical Crosslinking and Immunoprecipitation Sequencing (ac4C-CLIP-seq): Identify ac4C modification sites at single-nucleotide resolution by sequencing RNA that is crosslinked in vivo to an ac4C-specific antibody.
3. Global RNA Methylation Quantification by LC-MS/MS: Quantify the absolute, global level of ac4C modification in bulk RNA samples with high precision using liquid chromatography-tandem mass spectrometry.
4. Custom Multi-Omics Integration: Decipher the functional impact of ac4C by integrating its mapping data with parallel transcriptomic or translatomic profiles to reveal correlations with RNA stability and translation.

Workflow of RNA ac4C Analysis Service

Our standardized, quality-controlled workflow ensures reproducibility and delivers publication-ready results through transparent collaboration. Based on the ac4C-IP-seq service, below is an introduction to our workflow.

Project Consultation & Design

Our project specialists will collaborate with you to define research objectives and sample specifications. Based on this, we will recommend the optimal technical path (genome-wide mapping or targeted validation) and co-develop a customized project plan detailing the experimental design, quality controls, and deliverables.

Sample Preparation & Stringent QC

Upon receipt of your RNA samples, we perform rigorous quality assessment using Bioanalyzer, spectrophotometry, and fluorometry to evaluate integrity (RIN), purity, and concentration. Samples must pass predefined QC thresholds to proceed to library construction.

ac4C Enrichment & Library Construction

We employ optimized, antibody-based protocols (e.g., ac4C-IP) to specifically immunoprecipitate ac4C-modified RNA fragments. The enriched RNA is then converted into high-quality, strand-specific sequencing libraries using industry-standard preparation kits, ready for next-generation sequencing.

High-Throughput Sequencing

The prepared libraries are sequenced on Illumina platforms to generate deep, high-coverage data. We monitor sequencing metrics in real-time to ensure sufficient depth and quality for robust downstream bioinformatic analysis.

Bioinformatics Analysis & Interpretation

Our dedicated bioinformatics pipeline processes raw data for alignment, peak calling, and motif discovery. We perform differential ac4C analysis across samples and integrate results with RNA-seq data to correlate modification changes with gene expression and functional pathways.

Comprehensive Reporting & Delivery

You will receive a final report containing all raw data, processed results, and publication-ready visualizations (e.g., peak tracks, heatmaps). The report includes a clear biological interpretation of key findings, highlighting significant ac4C dynamics and their potential functional implications.

Our Advantages

1. Integrated Multi-Omics Approach: We uniquely correlate ac4C modification data with parallel RNA-seq or Ribo-seq datasets, providing a holistic view of how ac4C impacts RNA stability and translation.
2. Single-Base Resolution Mapping: The advanced ac4C-CLIP-seq service enables precise identification of ac4C sites at single-nucleotide resolution, eliminating ambiguity.
3. Expert Epitranscriptomics Focus: Our dedicated scientific team possesses deep specialization in RNA modifications, ensuring expert guidance on experimental design and data interpretation beyond standard pipelines.
4. Flexible & Customizable Solutions: CD BioSciences tailors services from genome-wide discovery to focused validation studies, accommodating diverse sample types (cells, tissues, liquid biopsies) and species.
5. Rigorous Quality & Validation: Every step incorporates stringent controls, and we offer downstream functional validation assays to confirm the biological impact of key ac4C sites.

At CD BioSciences, our expertise in epitranscriptomics extends beyond ac4C. We provide a comprehensive suite of services for analyzing other crucial RNA modifications and editing events, including m6A, m5C, Ψ, m6Am, m7G, m1A, and RNA adenosine-to-inosine (A-to-I) editing analysis. Whether your research aims at mechanistic discovery, biomarker identification, or drug target validation, we offer fully customized, end-to-end solutions to meet your specific goals. If you are interested in learning more about our services, please do not hesitate to contact us for additional details and pricing information.

Reference

1. Bartee D, Nance K D, Meier J L. Site-specific synthesis of N 4-acetylcytidine in RNA reveals physiological duplex stabilization[J]. Journal of the American Chemical Society, 2022, 144(8): 3487-3496.