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RiboCluster Profiler: Novel Gene Expression Analysis Tools

Gene expression is a tightly controlled process by several mechanisms in each stage of transmission of genetic information from DNA to mRNA and to proteins. Thus far, research on the control of gene expression has been conducted with a focus on transcription, wherein mRNA is synthesized from DNA, and the regulatory mechanisms involving transcription factors and DNA methylation have been elucidated. However, because changes at the transcriptional level do not necessarily reflect protein synthesis in a direct manner, ongoing research is conducted with an emphasis on the post-transcriptional regulation of gene expression, i.e., on the mechanisms that regulate events from mRNA transcription and translation to protein synthesis. Pre-mRNA, which is transcribed from DNA, is processed in the nucleus (capping, splicing, and addition of poly(A) tail), and becomes a mature mRNA. Subsequently, the mRNA is exported from the nucleus to the cytoplasm, is translated locally in the cell on an as-needed basis, and will be decomposed after having completed its mission. RNA-binding proteins (RBPs) play important roles in this series of reactions involved in the "life of the mRNA." RBPs bind selectively to functionally-related mRNAs, and form unique complexes called ribonucleoproteins (RNPs). Specific mRNA contained in the RNPs can be obtained by performing RNP immunoprecipitation (RIP) using antibodies against RBPs. The method consists of performing RIP analysis and identifying the resultant mRNA by using microarrays or high-throughput sequencing, is termed "RIP-Chip analysis" and "RIP-Seq analysis" respectively. RIP-Chip and RIP-Seq analysis are expected to provide information that has been hitherto impossible to obtain using existing methods, and it can be helpful for the development of pharmaceutical products targeting specific responses in specific cells. Most patents related to RIP analysis are owned jointly by our company and the family company Ribonomics, Inc. (Massachusetts, USA).

RiboChip Analysis

RiboChip analysis of RBP genes reveals changes in the expression level or pattern of mRNAs encoding RBPs in specific cells, tissues, or diseases.

RIP-Assay Kit

In 2009, we started distributing kits for the immunoprecipitation of RBP in RNP, and for RNP mRNA isolation and purification. In addition, we provide products such as RIP-certified antibodies and anti-RBP antibodies. The expression profile of the mRNA obtained from the RIP analysis can be examined using microarray, sequencing, and RT-PCR. Recent studies have revealed that over 90% of the RNA transcribed from DNA does not get translated into proteins (non-coding RNA: ncRNA). It has been elucidated that among ncRNAs, small or microRNA (miRNA) are expressed in specific cells and tissues in the same manner as mRNA, and this miRNA is involved in translational control. miRNA is beyond the frame of RNA research, and it has been receiving increasing attention in various fields of research such as immunity, development, and oncology. Since 2010, MBL distributes RIP analysis kits that enable isolation and purification of mRNAs and small ncRNAs, including miRNAs. In response to the market demands, we are further developing the technology pertaining to RIP analysis.

RiboTrap Kit

RiboTrap is a technology that allows identification of RBPs that bind to a specific RNA. RNA binds to several RBPs, from the time of its birth until its maturation, translation, and degradation. If we can elucidate the full spectrum of RBP binding to RNA, RBP-RNA interaction networks can facilitate the determination of the majority of all the processes involved in protein expression from specific genes. Since 2010, MBL distributes RiboTrap kit, which artificially generates RNPs by inducing a reaction between labeled RNA and cell extracts, allowing isolation of RBPs, which in turn bind to the labeled RNA from the reaction mixture.

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