LncRNAs are key in CNS gene regulation, with dysregulation linked to neurological disorders, mediating effects via chromatin and RBP interactions. ChIRP-based analysis precisely maps these interactions, delivering mechanistic proof for therapeutic translation. Creative Biolabs specializes in ChIRP coupled with high-resolution sequencing and MS, accelerating drug discovery, providing definitive MOA insights, and validating CNS therapeutic targets to advance lncRNA candidates.
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The Chromatin Isolation by RNA Purification (ChIRP) method is an advancement in genomic technology, specifically engineered to map the interaction sites of lncRNAs across the genome.
Our service leverages the split-sample capability of ChIRP to deliver two distinct, yet complementary, data sets from a single initial sample:
We follow a meticulously controlled, scalable workflow designed for minimal sample input and maximal data fidelity, making it suitable for delicate neurological samples.
| Step | Activity |
|---|---|
| Probe Design & Synthesis | Design and synthesize a customized, high-affinity set of biotinylated antisense probes specific to the client's lncRNA sequence. |
| Sample Preparation & Cross-linking | Utilize client-provided cell or tissue samples (e.g., primary neurons, iPSC-derived neural cells) and perform optimal cell fixation (cross-linking) to preserve native lncRNA-DNA and lncRNA-Protein complexes. |
| ChIRP Assay & Purification | Perform targeted RNA purification using the custom probes and streptavidin beads. The sample is divided to purify associated DNA (for ChIRP-seq) and associated proteins (for ChIRP-MS). |
| Sequencing/Mass Spec | Prepare next-generation sequencing libraries (ChIRP-seq) and perform high-resolution liquid chromatography-tandem mass spectrometry (ChIRP-MS). |
| Bioinformatics & Analysis | Process raw data against control (e.g., LacZ probe) and input samples. Identify statistically significant peaks, annotate genomic regions, and perform pathway enrichment analysis for both DNA and protein targets. |
Required Starting Materials:
Final Deliverables:
Estimated Timeframe: The typical timeframe for this service ranges from 8 to 12 weeks, depending on the initial cell type, sample quality, and the complexity of the lncRNA structure (which influences probe optimization).
As a biology expert, you understand that non-coding RNA research demands unparalleled precision and flexibility. At Creative Biolabs, we don't just run an assay; we deliver a complete, customized mechanistic solution that stands up to the most rigorous peer review and regulatory scrutiny.
Custom Probe Design
Our in-house bioinformatics team designs and synthesizes proprietary, high-affinity, tiled probe sets perfectly optimized for the unique sequence and structure of your lncRNA of interest, guaranteeing maximum capture efficiency even for low-abundance transcripts.
Integrated Dual-Output Analysis (ChIRP-seq and ChIRP-MS)
We provide the simultaneous, gold-standard solution for achieving complete Molecular Mechanism of Action (MOA)—resolving both genomic DNA targets and protein partners from a single, precious sample.
Protocol Optimization for Complex Samples
We offer custom protocol adjustments for challenging, low-input samples, including primary neuronal cultures, specific brain microdissections, and iPSC-derived cells, ensuring successful data generation where standard methods fail.
Expert Bioinformatics and Interpretive Reporting
Beyond raw data, you receive a detailed, interpretive report that includes functional pathway enrichment and network visualization, translating raw peaks and spectra into actionable biological insights for your R&D pipeline.
End-to-End Scientific Consultation
Our service includes direct access to our Ph.D.-level specialists to assist with experimental design, result interpretation, and strategic planning for subsequent therapeutic development steps, ensuring a seamless journey from discovery to drug candidate.
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Long non-coding RNAs (lncRNAs) are widely present in the genome and have become important transcriptional regulatory factors, influencing all aspects of transcriptome regulation, including RNA transcription, splicing, and metabolism. In this study, the ChIRP strategy was adopted, combined with single-ended high-throughput DNA sequencing and subsequent bioinformatics tools. The binding map of Ppp1r1b-lncRNA on a genomic scale was drawn. Sequencing libraries of Ppp1r1b-lncRNA-ChIRP and control DNA fragments were constructed, and single-ended high-throughput sequencing with a reading length of 50 bp was performed.
Fig.1 The whole-genome chromatin placeholder map expressing endogenous Ppp1r1b-lncRNA was detected by ChIRP-Seq.1
We understand the limitations of working with primary neuronal cells. Our established, low-input protocol is highly optimized, requiring significantly less starting material than traditional methods. We typically recommend consultation for samples below 107 cells to ensure optimal probe and protocol adjustments.
ChIRP is superior for lncRNA studies because it directly targets the RNA itself, whereas ChIP-seq targets a protein (e.g., a histone mark) and RIP-seq targets an RBP. Only ChIRP allows you to simultaneously map both the lncRNA's DNA targets (ChIRP-seq) and its protein partners (ChIRP-MS) in one integrated workflow, providing unmatched mechanistic clarity.
Our team specializes in optimizing probe hybridization and signal amplification, making our platform one of the most sensitive available for detecting low-abundance transcripts. We utilize proprietary, tiled probe sets to maximize capture efficiency, successfully validating transcripts that fail with less optimized protocols.
Absolutely. Knowing the exact protein-binding domain and the genomic target site from our ChIRP data is essential for rational ASO design. This information allows you to design ASOs that precisely block a specific functional interaction, leading to higher specificity and reduced off-target effects.
Creative Biolabs is your dedicated partner for accelerating RNA-based therapeutic discovery in the complex field of neuroscience. Our ChIRP based RNA-Protein Interaction Analysis Service delivers the gold-standard mechanistic data—providing certainty in genomic targets and protein partners—that drives successful regulatory and clinical advancement.
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