CHIRP-Seq Service for lncRNA and circRNA Binding Analysis Across the Genome

Introduction

Non-coding RNAs represent more than 80% of the human transcriptome, yet their molecular mechanisms remain poorly understood. Deciphering the roles of lncRNAs and circRNAs requires precise mapping of their interaction partners at the chromatin level. Traditional methods often lack resolution or reproducibility, leaving researchers with incomplete pictures of RNA regulatory networks.

CHIRP-Seq (Chromatin Isolation by RNA Purification sequencing) directly addresses this challenge. By capturing RNA molecules and their associated DNA and RNA partners in situ, CHIRP-Seq enables researchers to study RNA-DNA interactions and RNA-RNA interactions across the entire genome. This provides essential insights into transcriptional regulation, chromatin remodelling, and the functional biology of non-coding RNAs.

Why Choose CHIRP-Seq – Advantage

High Specificity with Odd/Even Probe Design

CHIRP-Seq uses biotin-labelled probes divided into odd and even groups. Only overlapping enrichment signals are counted as true binding sites, which significantly reduces background noise and ensures reproducibility.

Broad Applicability for lncRNAs and circRNAs

Unlike methods that require structural information, CHIRP-Seq can be applied to any lncRNA or circRNA sequence. This makes it highly flexible for projects targeting newly discovered or poorly characterised non-coding RNAs.

Multi-Omics Integration

Our platform supports CHIRP-Seq for RNA-DNA mapping and CHIRP-MS for RNA-protein profiling. By combining sequencing and proteomics, researchers gain a complete view of RNA-mediated regulatory networks.

Comprehensive Bioinformatics Support

CD Genomics delivers end-to-end chirp seq analysis, including binding site detection, functional annotation, GO/Pathway enrichment, and visualisation in genome browsers. This integrated pipeline transforms sequencing data into interpretable biological insights.

Strict Quality Control

Every experiment is run with positive and negative controls to confirm probe performance and enrichment reliability. This ensures that results are both accurate and publication-ready.

CHIRP-Seq workflow

Deliverables & Demo

FAQs

• • Q: What can CHIRP-Seq reveal that solves my research challenge?
    • CHIRP-Seq maps where lncRNAs or circRNAs bind across the genome—such as promoters, enhancers, intragenic or intergenic regions—uncovering both cis and trans regulatory sites, enhancer interactions, and epigenetic marks it may influence. It answers not just "where does this RNA go?" but "what might it regulate?"—enabling you to link RNA localization with function directly.
  • Q: How does CHIRP-Seq compare with ChIP-Seq or other interaction mapping methods?
    • Unlike ChIP-Seq, which profiles protein-DNA interactions via antibodies, CHIRP-Seq uses biotinylated probes complementary to your target RNA to pull down endogenous RNA–chromatin complexes, enabling direct detection of RNA-guided interactions and multi-omics integration.
  • Q: Can CHIRP-Seq work if I know little about my target lncRNA structure?
    • Yes—its probe tiling strategy does not require knowledge of RNA secondary structure or domains. You only need the sequence. The "odd/even probe pools" act as internal controls: only overlapping signals from both pools are accepted as specific, reducing noise.
  • Q: What analysis outputs should I expect from CHIRP-Seq?
    • After sequencing, you'll receive binding peak lists with annotations, genome browser tracks, GO/pathway enrichment results, and support for integrative analysis—transforming raw reads into biologically meaningful insights.
  • Q: Can CHIRP-MS run alongside CHIRP-Seq in one experiment?
    • Yes—CD Genomics offers integrated CHIRP-Seq and CHIRP-MS profiling from the same cross-linked input. You'll get paired data that links RNA-protein and RNA-DNA interactions for multidimensional insight.