lncRNA-Protein Interaction Prediction

Identifying the interactions between long non-coding RNAs (lncRNAs) and proteins is very important to decipher the functional mechanisms of lncRNAs. CD Genomics provides next-generation sequencing (NGS)- and mass spectrometry (MS)-based methods for building in vitro or in vivo lncRNA-protein interaction network and providing vital insight into the functions and action mechanisms of lnRNA. Our solutions for lncRNA-protein interaction analysis include ChIRP-seq, CLIP-seq, RIP-seq, and ChIRP-MS.


Non-coding RNAs with a length of greater than 200 bases are referred to as lncRNAs, which have attracted a lot of attention in recent decades. Many studies have found that lncRNAs play an important role in post-transcriptional gene regulation and chromatin remodeling by targeting chromatin-modifying enzymes to distinct genomic sites. The mutations and malfunctions of lncRNAs are closely associated with a number of human diseases. As lncRNAs interact with various proteins, the prediction of lncRNA-protein interactions is a sufficient way to explore lncRNA functions and. A variety of assays have been developed to build lncRNA-protein interaction network. RNA pull-down assays use either bead-bound proteins or immobilized synthetic RNAs to capture lncRNA-protein interactions. RNA immunoprecipitation (RIP) assays use a protein of interest to capture interacting endogenous RNAs. Both the methods can be applied to material from proliferating and quiescent cells, thus providing insights into how lncRNA-protein interactions are altered between these two cellular states. As both RNA pull-down and RIP assays capture in vitro RNA-protein interactions. We also provide in vivo detection of lncRNA-protein interactions using ChIRP and CLIP, both of which use crosslinking to stabilize the protein-RNA complexes. These assays are further combined with NGS or MS to profile lncRNA-protein interactions and provide detailed insight into the functions and mechanisms of lncRNAs. Our services are devoted to offering accurate and reproducible data to support lncRNA research.


Rich ExperienceVarious MethodsValidated ProcessesQuality Control
Rich experience in lncRNA research and bioinformatics analysis.We provide ChIRP-seq, CLIP-seq, RIP-Seq, RAP-Seq, ChIRP-MS, RAP-MS for lncRNA studies. Perform advanced and validated experiments on NGS and MS instruments.Quality control is executed following every procedure.
Data Analysis Workflow

Data Analysis Workflow

In-depth data analysis:

  • Prediction of binding sequence signature(s)
  • GO Term enrichment
  • KEGG pathway analysis
  • lncRNA-associated ceRNA network analysis
  • Prediction of lncRNA-protein interaction networks
  • lncRNA and mRNA interaction network analysis
  • Measure the effect of lncRNA on global protein levels

Sample Requirements

(NGS platform) RNA sample (concentration ≥ 200 ng/uL, quantity ≥ 4 ug), 1.8 ≤ OD260/280 ≤ 2.2, OD260/230≥2.0, RIN ≥ 6.5, 28S:18S≥1.0. Please make sure that RNA is not significantly degraded.
(MS platform) We work with a wide range of sample types including protein solution, fresh tissue, cultured cells, blood, and microbial sample. Please feel free to contact us for sample size.

Sample Storage: The sample should be stored at -80°C. Avoid repeated freezing and thawing.

Shipping Method: When shipping the sample, it is stored in a 1.5 mL Eppendorf tube, sealed with a sealing film. Shipments are generally recommended to contain 5-10 pounds of dry ice per 24 hours.


(NGS analysis) FastQ, BAM, coverage summary, QC report, GO enrichment histogram, GO terms DAG (directed acyclic hierarchical graph), and KEGG enrichment scatter plot, and other designated report.
(MS analysis) Data QC report, MS results, integrated experimental report (materials, methodologies, and bioinformatics analysis).


  1. Zhang H, Liang Y, Han S, et al. Long noncoding RNA and protein interactions: from experimental results to computational models based on network methods. International journal of molecular sciences, 2019, 20(6): 1284.
  2. Bierhoff H. Analysis of lncRNA-protein interactions by RNA-protein pull-down assays and RNA immunoprecipitation (RIP). Cellular Quiescence. Humana Press, New York, NY, 2018: 241-250.
* For Research Use Only. Not for use in diagnostic procedures.


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