RIC-seq Service

RIC-seq Service

RIC-seq (RNA In situ conformation sequencing) is a new technique that can capture the advanced structure of RNA and molecular interaction sites at the cellular in situ level. RlC-seq is able to map genome-wide enhancer-promoter regulatory networks on the conformational and organizational patterns of mRNA and non-coding RNAs in cells, and to elucidate novel mechanisms of enhancer-activated oncogene transcription. The RlC-seq technology can also be used to systematically analyze the effects of major disease-associated mutations on the advanced structure and action targets of RNA, which will hopefully reveal the pathogenic mechanisms of mutations in non-coding regions and lay the foundation for clinical diagnosis and treatment.

Creative Proteomics offers RIC-seq services that capture all direct RNA-RNA pairings, or protein-mediated interproximity RNA-RNA interactions, in a single pass while maintaining cellular integrity.

Principle of RIC-seq Technology

The basic procedure of the RlC-seq technique is to cross-link cells with formaldehyde to fix protein-mediated RNA-RNA interactions in situ, followed by membrane perforation while maintaining cellular integrity and treatment with micrococcal nuclease to remove free RNA fragments. Then pCp-biotin labeling is performed at the 3' end of the RNA and proximal ligation is performed in situ. Finally, cells are lysed, total RNA is extracted, and chimeric RNA fragments containing the C-biotin marker are purified for library sequencing.

Schematic of RIC-seq technologySchematic of RIC-seq technology (Cai et al., 2020).

Application of RIC-seq

Identify rna-rna interactions in the nucleus

Systematically analyze the high-level structure and targets of non-coding RNAs in the nucleus

Mapping the advanced structure of RNA molecules

Constructing a three-dimensional RNA action map

Reveal the pathogenic mechanism of non-coding region mutations

Analysis Content

Basic analysis Advanced analysis

Sequence alignment analysis

RNA expression analysis and reciprocal frequency ranking

Construction of reciprocal group matrix

Construction of enhancer-promoter regulatory network

Analysis of differential reciprocal relationships

Association analysis of differential interactions with differentially expressed genes

Analysis of differentially interacting regions or differentially interacting RNAs with GWAS

Three-dimensional genomic regulatory network mapping

Advanced structure mapping of specific RNA molecules

Sample Requirements

  • Cell samples >10 million/sample
  • Animal tissue >100 mg. It is recommended to rinse with saline after sampling to remove blood stains and dirt, and to remove non-study tissues such as connective tissue.
  • Plant tissue >5 g. Prepared into protoplasts >2×107

If you would like to learn more about RlC-seq services or have other needs, please contact us. We look forward to cooperating with you.

Reference

  1. Cai, Z., Cao, C., et al. (2020). RIC-seq for global in situ profiling of RNA–RNA spatial interactions. Nature, 582(7812), 432-437.
* This service is for RESEARCH USE ONLY, not intended for any clinical use.