Emerging evidence suggests that some lncRNAs and circRNA have the ability to encode peptides (some have important biological functions) or proteins. Hence, we provide an optimized mass spectrometry (MS)-based method for rapid and accurate screening of theses lncRNAs and circRNA that can encode peptides or proteins.
Overview
Long non-coding RNAs (lncRNAs) are a large class of non-coding RNA molecules with a length exceeding 200 nucleotides that do not encode proteins. circular RNAs (circular RNAs) consist of a large class of non-coding RNAs that are produced by backsplicing. According to the denifition, lncRNAs and circRNAs were believed that cannot be translated into peptides or proteins. However, some studies demonstrated that some non-coding RNA species do encode peptide or even proteins. For example, lncRNA LINC00948 is a skeletal muscle-specific RNA molecule in humans that encodes a conserved 46-aa peptide named MLN that bears a function. The combination of MS data and computational tools have been successful in detecting small open reading frames (sORF) that could code for a peptide with biological functions, enabling the determination of coding potential in RNAs. CD Genomics has developed an optimized MS-based quantitative platform for encoding activity analysis of lncRNAs and circRNAs. Our platform truly detects the sORFs of non-coding RNAs to demonstrate their translatability, and reveal the clinical implications of theses translated products and their host lncRNAs or circRNAs. We also provide ribosome profiling (ribo-seq) combined with computational analyses for this purpose.
Features
Transcriptome-Wide
Bioinformatics Analysis
High Performance
Seamless Integration
Transcriptome-wide profiling of lncRNAs and circRNAs with coding potential
Data QC; encoding activity analysis; validation and functional analysis
Optimized experimental procedures, advanced LC-MS system, expertise in operation.
Provide MS- and NGS-based encoding activity analysis
Project Workflow
1. Create Database
Ribosome isolation; isolation of RNA-protein complex; lncRNA / circRNA sequencing; ORF prediction; creation of peptide or protein database.
2. Mass Spectrometry
Total protein; protein screening; mass spectrometry; data matching.
3. Screening of lncRNA/circRNA with Coding Potential
Detection of sORF and lncRNA/circRNA with coding potential based on data from 1 & 2.
4. Validation & Function Analysis
Validation of peptide/protein encoded by lncRNA/circRNA.
Sample Requirements
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: extracted protein 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.
Deliverable: data QC report, MS results, integrated experimental report (materials, methodologies, and bioinformatics analysis).
References:
Pang Y, Mao C, Liu S. Encoding activities of non-coding RNAs. Theranostics, 2018, 8(9): 2496.
Choi S W, Kim H W, Nam J W. The small peptide world in long noncoding RNAs. Briefings in bioinformatics, 2019, 20(5): 1853-1864.
Giambruno R, Mihailovich M, Bonaldi T. Mass spectrometry-based proteomics to unveil the Non-Coding RNA world. Frontiers in Molecular Biosciences, 2018, 5: 90.
* For Research Use Only. Not for use in diagnostic procedures.
