RIC-seq Service for In Situ RNA-RNA Interaction Mapping

In Situ Mapping of RNA-RNA Interactions and Higher-Order RNA Structures

RIC-seq (RNA in situ conformation sequencing) is a next-generation technology that captures RNA-RNA interactions and tertiary structures directly inside intact cells. By preserving spatial RNA conformation and molecular proximity, this method enables genome-wide profiling of both mRNA and non-coding RNA structures — offering new insights into RNA function, enhancer-promoter regulation, and gene expression dynamics.

At CD Genomics, we provide a full-suite RIC-seq service, from library preparation to sequencing and data interpretation, designed to empower your research into RNA structure-function relationships and 3D regulatory networks.

Service Package

Service	Description
RIC-seq	Library Construction
	Sequencing
	Data Analysis

Service Highlights

Transcriptome-wide RNA-RNA interaction mapping
Identify spatial RNA proximity events across thousands of genes and ncRNAs.
In situ RNA structure capture
Preserve native RNA folding states in the nuclear or cytoplasmic environment.
eRNA–uaRNA–promoter interaction profiling
Predict enhancer-promoter relationships using RNA-level contacts.
High-resolution detection of structural variants
Analyze how mutations alter RNA conformation and regulatory targets.

Advanced Bioinformatics

We offer customizable bioinformatics pipelines tailored to your project's complexity:

Basic Analysis	Advanced Interpretation
RNA-seq alignment	RNA 3D structure reconstruction
Interaction frequency matrix	Differential interaction analysis
Enhancer-promoter contact modeling	GWAS-linked RNA structure mapping
Domain and hub-RNA identification	Chromatin structure correlation (e.g., TADs, eRNAs, super-enhancers)

Application Areas

Cancer research: Understand how super-enhancer RNAs (e.g., CCAT1-5L) regulate oncogene transcription (e.g., MYC).
Neurobiology: Explore long-range ncRNA interactions in neuron-specific gene regulation.
Developmental biology: Study how RNA structure shapes transcript fate in early development.
Viral research: Map viral RNA structure and host target engagement.

Sample Requirements:

Fresh cells only (≥1×10⁷ per sample)

Supported species: Human, mouse, rat (others upon request)

Sample Guideline

Frequently Asked Questions

- What is RIC-seq and how does it work?
  - RIC-seq (RNA In Situ Conformation Sequencing) is a sequencing-based method used to detect RNA-RNA interactions and 3D RNA structures within intact cells. It combines crosslinking, nuclease digestion, end labeling, and in situ RNA ligation to capture spatial RNA conformations at a transcriptome-wide scale.
- What biological questions can RIC-seq help answer?
  - RIC-seq enables researchers to:
    - Identify endogenous RNA-RNA interactions
    - Map structural domains of mRNA and ncRNA
    - Reconstruct enhancer–promoter interaction networks via eRNAs
    - Analyze the functional impact of non-coding mutations
    - Discover RNA hubs and regulatory hotspots across the genome
- How is RIC-seq different from other RNA-RNA interaction methods?
  - Unlike in vitro methods, RIC-seq captures RNA structures in situ under native cellular conditions. Compared to techniques like PARIS, SPLASH, or LIGR-seq, RIC-seq offers improved signal-to-noise ratio, broader transcript coverage, and the ability to infer functional spatial proximity between RNAs.
- What types of RNA can be studied using RIC-seq?
  - RIC-seq detects both coding and non-coding RNAs, including:
    - mRNA
    - lncRNA
    - eRNA
    - snRNA and snoRNA
    - pre-mRNA and partially processed transcripts
    - viral RNAs (in host cells)
- Can RIC-seq be used to study enhancer-promoter interactions?
  - Yes. RIC-seq detects spatial interactions between enhancer RNAs (eRNAs) and promoter-associated transcripts (uaRNAs), which allows researchers to predict enhancer–promoter relationships and reconstruct regulatory networks at the RNA level.
- What sample types are accepted for RIC-seq?
  - We currently support:
    - Fresh human, mouse, or rat cells (minimum: 1×10⁷ cells per sample)
    - Other species may be evaluated upon request
    - Frozen samples, tissues, or FFPE material are not recommended due to protocol constraints.
- What deliverables are included in your RIC-seq service?
  - Our RIC-seq service typically includes:
    - Library preparation and Illumina sequencing
    - Raw FASTQ files
    - Interaction matrices and structural annotation reports
    - Optional: RNA 3D structure modeling, enhancer-promoter network reconstruction, or GWAS integration (advanced analysis packages)
- How can I get started with a RIC-seq project?
  - You can contact our scientific team to discuss your research goals. We'll help you design a study based on your cell type, biological question, and data analysis needs. Custom quotes are available upon request.

Industry Case Analysis: Profiling Virus-to-Host RNA–RNA Interactions Using RIC-seq

STAR Protocols (2024), "Protocol for profiling virus-to-host RNA-RNA interactions in infected cells by RIC-seq"

DOI: 10.1016/j.xpro.2024.103149

Background & Rationale

Understanding how viruses hijack host-cell functions often hinges on decoding direct RNA–RNA interactions between viral genomes/transcripts and host RNAs. These interactions can modulate host mRNA stability and viral replication. Traditional approaches like CLIP-seq or co-immunoprecipitation cannot capture RNA–RNA contacts in situ or at scale. This paper introduces a RIC-seq–based protocol tailored to map high-confidence, native virus–host RNA interactions in infected cells.

Core Analytical Dimensions and Technical Findings

In situ crosslinking of infected cells with formaldehyde preserves native RNA–RNA proximity before any cell lysis.
pCp-biotin labeling and in situ RNA ligation on permeabilized cells enable biotin-tagged RNA fragments to be covalently linked based on spatial adjacency.
Chimeric RNA enrichment and strand-specific library construction ensures accurate identification of both viral and host RNA fragments in a single sequencing read.
Sequencing and analysis deliver transcriptome-wide maps of virus–host RNA interactions, applicable across RNA viruses—even potentially DNA-virus transcripts.

Interpretation and Industry Relevance

Holistic virus–host interaction profiling: RIC-seq reveals physical associations between viral and host RNAs—knowledge crucial for understanding viral lifecycle and pathogenesis.
Functional insight into viral manipulation of host stability: For example, SARS-CoV-2 RNA was found to form >2000 duplexes with host 3′-UTRs, stabilizing host transcripts via YBX3 recruitment in A549 cells.
Broad applicability across virus types: The protocol works for diverse RNA viruses and may extend to transcripts from DNA viruses, offering a versatile tool for infectious disease research.

Strategic Takeaway

Expand virology services: Offering RIC-seq for virus–host interaction mapping signals a move beyond conventional transcriptomics or protein-centric assays.
Build partnerships with antiviral R&D: This method supports early drug discovery by revealing direct RNA targets for therapeutic intervention.
Diversify assay portfolio: RIC-seq complements other modular sequencing solutions (e.g., RNA-seq, CLIP-seq), enhancing CRO/CDMO competitiveness.
Capture high-demand workflows: Services grounded in RIC-seq align with urgent pathogen-response needs, making them attractive to clients in biodefense and infectious disease.

High-Resolution RIC-seq Service: Profile RNA-RNA Interactions In Situ

In Situ Mapping of RNA-RNA Interactions and Higher-Order RNA Structures

What is RIC-seq?

Service Package

Service Highlights

RIC-seq Workflow

Sample crosslinking and digestion

End modification & in situ RNA ligation

RNA purification and library construction

High-throughput sequencing

Data analysis