RNA-Binding Protein (RBP) Profiling Services for RNA–Protein Interaction Analysis

What Are RNA-Binding Proteins (RBPs)?

RNA-binding proteins (RBPs) are a diverse class of proteins that specifically recognize and bind RNA molecules to regulate nearly every step of RNA metabolism. These include RNA splicing, polyadenylation, export, localization, translation, and decay. The human genome encodes over 2,000 RBPs, many of which contain canonical RNA-binding domains (e.g., RRM, KH, DEAD-box) or intrinsically disordered regions that enable versatile and dynamic RNA interactions.

RBPs play essential roles in post-transcriptional gene regulation by interacting with various RNA species—including mRNAs, long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and microRNAs. Their dysregulation is implicated in a wide range of biological processes and disease mechanisms, such as:

• Cancer progression and metastasis
• Neurodevelopmental and neurodegenerative disorders
• Stem cell differentiation and aging
• Viral infection and host immunity

Understanding RBP-RNA interactions at high resolution provides critical insights into RNA regulatory networks and unveils novel targets for therapeutic intervention and biomarker discovery.

RBP Profiling Methods and Comparison

A variety of experimental strategies are available to study RNA–protein interactions. CD Genomics offers both RNA-centered and protein-centered approaches, tailored to your research goals—whether identifying RNA targets of a specific RBP or discovering proteins interacting with a specific RNA molecule.

We help you select the optimal method based on your biological question, desired resolution, and available reagents.

Overview of Available RBP Analysis Techniques

Tip: eCLIP-seq is ideal for mechanistic studies; RNA pulldown is preferred when investigating non-coding RNA interactomes.

Comparison of RIP-seq, iRIP-seq, eCLIP-seq, and RNA Pulldown methods for RBP profiling, showing input materials, experimental principles, and output data types.

Sequencing Platforms We Support

CD Genomics provides flexible platform options tailored to different RBP research needs—from bulk RNA profiling to high-resolution interaction mapping and transcript structure analysis.

Illumina NovaSeq™

• Ideal for RIP-seq, eCLIP-seq, and RNA-seq
• High throughput, low error rates, and mature analytical pipelines
• Suitable for large-scale discovery, motif enrichment, and peak calling

Oxford Nanopore PromethION™

• Enables full-length transcriptome sequencing
• Supports poly(A) tail analysis, isoform-level RBP regulation, and RNA modifications
• Direct RNA sequencing without amplification or fragmentation

BD Rhapsody™ Platform

• Compatible with RBP expression profiling and transcriptomic integration
• Resolves cell-type–specific RBP activity and regulatory networks
• Ideal for heterogeneous tissues or rare cell populations

Bioinformatics Analysis

Industry Case Study: iRIP-seq Identifies CSDE1 Variants Impairing Neuronal Development

Science Advances (2019), "Disruptive variants of CSDE1 associate with autism and interfere with neuronal development and synaptic transmission"

DOI: 10.1126/sciadv.aax2166

Frequently Asked Questions

• • What types of samples are acceptable for RBP profiling?
    • We accept a variety of input materials including cultured cells (fresh or frozen), tissue samples, total RNA or protein lysates, and purified RNA/protein. Some methods like RIP-seq, iRIP-seq, and eCLIP-seq require crosslinking, while RNA pulldown and long-read sequencing methods do not.
• • Which method should I choose to map RNA–protein binding at single-nucleotide resolution?
    • For precise binding site resolution, eCLIP-seq and iRIP-seq are optimal. eCLIP offers single-nucleotide resolution of direct binding sites; iRIP-seq provides high-resolution motif mapping, including indirect interactions.
• • How can I discover proteins that bind a specific RNA?
    • Use RNA Pulldown. This method captures proteins that interact with a specific RNA, such as lncRNA, circRNA, miRNA, or mRNA transcripts, with high specificity and simplicity.
• • Can we analyze transcript isoforms or poly(A) tail lengths in the same workflow?
    • Absolutely. Long-read platforms like ONT-IrRNA-seq and ONT-PAIrRNA-seq allow full-length isoform profiling and measurement of poly(A) tail lengths, enabling direct connection between RBP binding and splicing, APA, or tail dynamics.
• • Is it possible to detect RNA modifications and RBP interactions simultaneously?
    • Yes, ONT-DRS (Direct RNA Sequencing) can detect the full transcriptome structure, poly(A) tail, and modifications (e.g., m⁶A), revealing how RBPs recognize or regulate epitranscriptomic marks.
• • Can RBP binding be mapped while preserving tissue spatial context?
    • Yes—Spatial Transcriptomics methods allow mapping of RBP interactions within tissue architecture, such as tumor margins or specific brain regions, providing spatially resolved insights into functional regulation.
• • What if I have limited or rare sample material?
    • For low-input or limited samples, options like ARTR-seq and LACE-seq capture RBP-RNA binding from as few as 20 cells or a single tissue section. They avoid UV crosslinking and immunoprecipitation.
• • How are data delivered and what analysis support is provided?
    • You receive raw and processed data (FASTQ, peak/annotation files), high-resolution visualizations, and an interactive report (HTML or PDF). Our bioinformatics team also includes motif discovery, GO/KEGG enrichment, and cross-platform integration analysis.
• • Can I integrate RBP profiling data with other omics datasets?
    • Absolutely. We specialize in integrative analysis, combining RBP binding data with RNA-seq, spatial transcriptomics, epitranscriptome maps, alternate splicing, and APA datasets to illuminate regulatory networks.
• • Do you assist with experimental design and troubleshooting?
    • Yes—we offer design consultation, sample prep guidance, method recommendations, and technical support to ensure your experiment meets publication or grant standards.

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