lncRNA-Protein Interactions Analysis Service

lncRNAs (Long non-coding RNA) are usually 200-100000 nt in length and have 5' cap and 3' polyA tail structures. More and more studies focus on lncRNAs. lncRNA binding to proteins is one of their important regulatory modalities. Through binding to proteins, lncRNAs are involved in a variety of cellular processes. For example:

  • Regulating the activity of that binding protein
  • Altering the cellular localization of the bound protein
  • Binding a protein in competition with other RNAs/proteins to regulate the activity of other RNAs or proteins
  • Binding transcription factors to regulate the transcriptional activity of genes recruiting chromosome remodeling and modification complexes to specific sites, changing the modification status of DNA/RNA, chromosome structure, etc.

lncRNA mechanisms of actionlncRNA mechanisms of action (Sweta et al., 2019)

Types of lncRNA-protein interactions:

LncRNAs can interact with proteins in a variety of ways. The most intensively studied interaction is between lncRNAs and RNA binding proteins (RBPs), proteins that bind to RNA molecules and regulate their function.LncRNAs can interact with RBPs in a variety of ways, including

  • Recruitment of RBPs to specific genomic loci where they can regulate gene expression. For example, lncRNA Xist recruits the RBP PRC2 to the inactive X chromosome, resulting in silencing of genes on that chromosome.
  • Regulation of RBP activity. For example, lncRNA HOTAIR can interact with RBP EZH2 and enhance its histone methyltransferase activity, resulting in silencing of target genes.
  • Form complexes with RBPs, which can affect their stability, localization and function. For example, lncRNA NEAT1 forms a complex with the RBP Paraspeckle Protein 1 (PSP1), which is required for the formation of nuclear paraspeckles.

Human long non-coding RNAs (lncRNA) interactome, interaction of human lncRNA with cellular biomoleculesHuman long non-coding RNAs (lncRNA) interactome, interaction of human lncRNA with cellular biomolecules (Kazimierczyk et al., 2020)

In addition to RBPs, lncRNAs can also interact with other types of proteins, such as transcription factors and chromatin-modifying enzymes.

Creative Proteomics offers the identification and characterization of lncRNA-protein complexes and the study of the functional role of these complexes in a variety of cellular processes. We use a variety of techniques, including RNA immunoprecipitation (RIP) and RNA pull-down analysis, to identify lncRNA-protein interactions. We also use mass spectrometry-based proteomics to identify proteins that interact with lncRNAs.

lncRNA and Protein Interaction Analysis Technology in Creative Proteomics

Technology Type Exogenous RNA pull-down Endogenous RNA pull-down RIP
Technology Goals Finding or verifying proteins bound to target lncRNAs under in vitro conditions Find or verify the protein binding to target lncRNA under in vivo conditions Finding or verifying lncRNAs bound to target proteins under in vivo conditions
Principle of Technology In vitro transcription of biotin-labeled lncRNA and incubation with sample lysate, capture of target RNA-protein complexes bound under in vitro conditions using streptavidin magnetic beads, and identification of proteins in the complexes using Western Blot or mass spectrometry techniques Construct a fusion expression vector with the specific RNA tag and the target lncRNA, transfect the cells for fusion expression, purify the complex of RNA tag-lncRNA and protein by binding the specific RNA tag to the affinity medium, and identify the protein in the complex by Western Blot or mass spectrometry Capture decoy protein-RNA complexes under in vivo conditions with decoy protein antibodies and identify lncRNAs bound to decoy proteins using qPCR or high-throughput sequencing techniques


  1. Sweta, et al. "Importance of long non-coding RNAs in the development and disease of skeletal muscle and cardiovascular lineages." Frontiers in Cell and Developmental Biology 7 (2019): 228.
  2. Kazimierczyk, Marek, et al. "Human long noncoding RNA interactome: detection, characterization and function." International journal of molecular sciences 21.3 (2020): 1027.
* This service is for RESEARCH USE ONLY, not intended for any clinical use.