ChIRP-Seq & ChIRP-MS Services for RNA–Chromatin and RNA–Protein Interaction Mapping
CD Genomics provides expert ChIRP-Seq and ChIRP-MS services for researchers seeking to uncover the molecular interactions of long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) across the genome and proteome. Our platform is optimized for in vivo RNA–chromatin and RNA–protein interaction mapping, delivering high-resolution insights with unmatched specificity.
Whether you're investigating transcriptional regulation, chromatin remodeling, or RNA-driven protein networks, our services offer a comprehensive solution for functional RNA research. We empower your projects with end-to-end support—from probe design to bioinformatics analysis—tailored to meet the needs of RNA biology and epigenomics research.
Understanding how long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) exert their regulatory functions remains one of the most intriguing challenges in modern molecular biology. Unlike protein-coding genes, these RNAs often lack conserved sequences and predictable structural motifs, making it difficult to infer their biological roles using computational prediction alone.
What defines their function is where they bind—to chromatin or to proteins—and how they guide molecular complexes to influence transcription, chromatin accessibility, or spatial genome organization. This is where ChIRP (Chromatin Isolation by RNA Purification) becomes indispensable.
ChIRP bridges the gap between RNA sequence and RNA function.
ChIRP-Seq reveals genome-wide binding sites of specific RNAs on chromatin, uncovering cis- and trans-regulatory targets, enhancer interactions, and epigenetic marks they may influence.
ChIRP-MS identifies protein partners that directly interact with lncRNAs or circRNAs, providing mechanistic insights into RNA-guided complex formation, nuclear structure, or chromatin remodeling.
Together, these technologies enable researchers to ask not just where RNA goes, but what it does when it gets there—in a way that is cell-type specific, native, and scalable.
ChIRP is not just a technique. It's a lens through which regulatory RNA biology becomes visible, quantifiable, and actionable.
Platform
Our Dual-Tech Platform: Integrated RNA–Chromatin and RNA–Protein Mapping
At CD Genomics, we provide a fully integrated platform that combines ChIRP-Seq and ChIRP-MS, enabling comprehensive mapping of lncRNA or circRNA interactions across both chromatin and the proteome. These technologies can be used independently or in parallel for maximal insight.
ChIRP-Seq: Locate Where Your RNA Binds the Genome
ChIRP-Seq uses biotinylated antisense DNA probes tiled across the target RNA to pull down endogenous RNA–chromatin complexes. After stringent washing and reversal of cross-links, the co-purified DNA is sequenced to reveal high-resolution binding profiles across the genome.
Pinpoints promoter, enhancer, intragenic, or intergenic regions targeted by regulatory RNAs
Reveals cis- and trans-acting mechanisms of lncRNA or circRNA regulation
Supports annotation of non-coding regulatory hotspots, including R-loop–associated regions
ChIRP-MS applies the same probe hybridization strategy but focuses on the protein fraction co-purified with the RNA of interest. Cross-linked protein complexes are released and analyzed by LC–MS/MS, revealing the interactome that enables or is regulated by your RNA.
Identifies RNA-binding proteins (RBPs) and chromatin modifiers associated with your RNA
Detects nuclear structural proteins, transcription factors, or enzymes involved in RNA-guided remodeling
Helps infer functional modules and potential co-factors for downstream assays
Output: Quantified protein list, control comparison, GO/pathway annotation, PPI network
Dual Profiling for Deeper Discovery
Running ChIRP-Seq and ChIRP-MS in parallel from the same cross-linked input allows you to construct a multi-dimensional map of your RNA's influence in the nucleus:
Match protein partners with specific genomic binding loci
Discover RNA-centered regulatory circuits across chromatin states
Prioritize functionally relevant hits for follow-up validation or perturbation
Whether you aim to characterize a novel lncRNA or validate mechanistic hypotheses, our dual tech platform delivers the interaction landscape you need.
Service Workflow
How Our ChIRP-Seq & ChIRP-MS Services Work
Our optimized ChIRP workflows are built to deliver reproducible, high-specificity results across cell and tissue systems. Each step is handled with stringent controls to preserve true in vivo interactions.
Same crosslinking strategy as ChIRP-Seq, followed by nuclear extraction.
Probe Hybridization
Same tiling probe design applied to RNA–protein complexes.
Bead-Based Pull Down
Biotinylated complexes are captured and washed under denaturing conditions.
Protein Elution & Cleanup
Proteins are eluted, concentrated, and prepared for MS.
LC–MS/MS Proteomic Profiling
High-resolution identification and quantification of RBPs.
Bioinformatics & Pathway Mapping
Includes statistical filtering, GO/KEGG analysis, and PPI network building.
Run Both in Parallel
Our unified protocol enables simultaneous processing of ChIRP-Seq and ChIRP-MS from the same biological sample—minimizing input needs and ensuring consistency across modalities.
This dual-track approach is ideal for researchers seeking to connect RNA function to both chromatin context and protein machinery in a single study.
Bioinformatics
Data Processing & Bioinformatics for ChIRP-Seq / ChIRP-MS
We provide comprehensive bioinformatics pipelines tailored to the unique data types generated by ChIRP-Seq and ChIRP-MS, ensuring not only high-quality outputs but also actionable biological insights.
ChIRP-Seq Data Analysis Pipeline
Our ChIRP-Seq analysis captures the full chromatin-binding landscape of your target RNA. We process raw sequencing data into interpretable genomic maps and annotated peak sets.
Key analysis steps:
Quality Control
Trimming of adapters and low-quality bases (FastQC, Trimmomatic)
Read Alignment
Mapping to reference genome using Bowtie2 or BWA
Peak Calling
MACS2 or custom statistical models optimized for RNA-hybridized chromatin signals
Functional Annotation
Link peaks to nearest genes, promoters, enhancers, and intergenic elements
Enrichment Analysis
Gene Ontology (GO), KEGG, Reactome, and chromatin state annotations
Visualization Outputs
Genome browser tracks (IGV), coverage heatmaps, motif density plots
ChIRP-MS Data Analysis Pipeline
Our proteomics team uses robust mass spectrometry analysis tools to extract high-confidence RNA-associated protein profiles.
Integration of STRING or BioGRID databases to reconstruct protein complexes
Integrated Multi-Omics Mapping (Optional)
For projects using both ChIRP-Seq and ChIRP-MS:
RNA–Chromatin–Protein Interaction Networks
Cross-reference protein partners with genomic binding sites
Co-localization & Motif Enrichment
Investigate whether RBPs localize to regulatory DNA features
Functional Module Identification
Identify biologically relevant subnetworks for hypothesis generation or experimental validation
All data are delivered with clear visual outputs and interpretation-ready tables to help you quickly draw conclusions—or continue discovery with your next experiment.
Sample Requirements
Sample Submission Guidelines for ChIRP Experiments
We accept a variety of sample types for ChIRP-Seq and ChIRP-MS. Please refer to the simplified table below for essential submission guidelines.
Pellet in 1.5 mL tubes, flash-freeze in liquid nitrogen, store at –80 °C, ship on dry ice
Tissue Samples
50–100 mg
Mince and crosslink if possible, freeze immediately at –80 °C, ship on dry ice
Primary Cells / PBMCs
≥ 10⁷ cells
Isolate, pellet, freeze at –80 °C, ship on dry ice
Other / Custom Samples
Contact us
We'll advise optimal handling and conditions based on sample type
To maintain interaction integrity, avoid freeze–thaw cycles.
Always ship samples on dry ice in sealed tubes.
Engaging Researcher-First Experience
We understand that no two RNA targets—or research questions—are exactly alike. That's why our ChIRP-Seq and ChIRP-MS services are built around a collaborative, milestone-driven experience that puts your scientific goals at the center of everything we do.
Project Planning with Purpose
Before your project begins, we schedule a scientific consultation to align on:
Your target RNA and biological system
Experimental design options (e.g. probe coverage, number of replicates)
Feasibility based on expression level and sample input
Expected data types, deliverables, and timelines
This ensures we're building the right study—together.
Transparent Progress, Informed Adjustments
You'll receive key checkpoints during the process, including:
QC metrics after RNA pulldown and library prep or MS loading
Preliminary mapping rates or protein ID stats
Option to refine filtering thresholds or analysis priorities based on interim trends
These updates are collaborative—not just reports, but opportunities to steer the outcome.
Data That's Delivered with Insight
Once the data is ready, we provide more than a download link:
A technical debrief (via email or call) explaining key findings and their relevance to your RNA's mechanism
Discussion of potential follow-up strategies: CRISPR validation, RIP-seq confirmation, or extended pathway analysis
Optional integration with previous datasets or publications you've produced
We treat your RNA target like a research partner, not just a sequence. That's how we help turn interactions into insights—and results into direction.
Deliverables
What You'll Receive: ChIRP-Seq & ChIRP-MS Deliverables
We provide a full suite of deliverables designed to help you extract maximum insight from your ChIRP experiment—whether you're mapping genomic binding sites, identifying protein interactors, or integrating both.
ChIRP-Seq Deliverables
Category
Content
Raw Data
Cleaned FASTQ files (after QC and adapter trimming)
Aligned Reads
BAM files mapped to reference genome (e.g. hg38, mm10)
Peak Files
NarrowPeak or BED files for binding regions
Gene Association
Annotated peak-to-gene mapping tables
Functional Enrichment
GO and KEGG pathway analysis reports
Visualization
IGV-ready track files, coverage heatmaps, motif density plots
ChIRP-MS Deliverables
Category
Content
Raw Data
LC-MS/MS spectra and raw identification files
Protein List
Quantified protein tables with fold changes, p-values, and UniProt IDs
Control Comparison
Enrichment statistics against non-specific probe control
Functional Annotation
GO/KEGG pathway mapping and domain annotations
Interaction Mapping
PPI network diagrams (STRING-based or custom)
Optional: Joint Insights from Combined ChIRP-Seq & MS
For clients running both assays:
Integrated tables matching DNA peaks to co-binding proteins
Circos plots or RNA–DNA–protein network visualizations
Ranked candidate interactions for downstream validation
All data are delivered electronically with structured documentation and naming conventions. You are free to re-analyze, publish, or expand upon any results with full reproducibility.
Applications
Ideal Applications for ChIRP-Seq & ChIRP-MS
ChIRP-based technologies are uniquely suited for exploring the regulatory roles of non-coding RNAs in the nucleus. Whether you're studying gene expression, chromatin dynamics, or protein complex assembly, ChIRP Seq and ChIRP-MS offer direct, functional readouts of RNA activity.
Common Research Use Cases
Decoding Transcriptional Regulation
Map how lncRNAs or circRNAs guide transcription factors to target promoters or enhancers
Investigate RNA-mediated recruitment of chromatin modifiers (e.g., PRC2, HDACs)
Elucidating Nuclear RNA Functions
Study subnuclear structures like paraspeckles or nucleoli
Identify architectural RBPs involved in nuclear retention, scaffolding, or compartmentalization
Characterizing Novel Non-coding RNAs
Assign biological roles to uncharacterized lncRNAs based on their binding loci and protein partners
Use ChIRP-MS to infer functional modules even without prior knowledge of RNA mechanism
Exploring Chromatin–RNA–Protein Networks
Build interaction networks to connect RNA molecules with chromatin states and coregulators
Detect co-occupancy with R-loops, enhancer RNAs, or 3D chromatin domains
Especially Relevant For:
lncRNA/circRNA functional studies
Cancer epigenetics and cell fate regulation
Enhancer biology and long-range transcriptional control
Chromatin remodeling and nuclear architecture
RNA–protein interaction discovery in stress, development, or differentiation models
Not sure if your target RNA fits these categories? Contact us for a feasibility discussion—we're happy to evaluate your hypothesis and provide guidance.
Advantages
Why Choose CD Genomics for Your ChIRP Project
At CD Genomics, we don't just run ChIRP—we optimize it for your scientific questions. Our platform combines technical precision, flexible project design, and deep biological understanding to ensure your results are both reproducible and biologically meaningful.
Expertise That Goes Beyond Protocols
Custom Probe Design
Tiling antisense probes (20–30 nt) are designed to span your full RNA target with balanced GC content and odd/even group splitting—maximizing capture efficiency and specificity.
Rigorous QC and Controls
We include positive/negative controls in both sequencing and proteomic workflows, enabling confident interpretation and filtering of background signals.
Optimized Dual-Track Platform
Our ChIRP-Seq and ChIRP-MS workflows share upstream processing, minimizing sample input while generating parallel chromatin and protein interactomes.
Researcher-Centric Support
Pre-project design consultation to tailor probe layout, controls, and analysis depth
Interim progress updates so you can steer data priorities during the project
Post-analysis debrief that translates raw results into biological insights
Trusted by Researchers Worldwide
We work with academic labs, biotech teams, and discovery research groups across continents. Whether you're validating a known RNA or venturing into novel discovery, we adapt to your needs without compromising on data integrity or delivery quality.
