Why do cells spend energy to strictly regulate the expression and localization of these non-coding RNA? What are the functions of these RNA molecules? With the development of RNA sequencing technology, people can get a glimpse of this mysterious molecule. Now, a lot of information about lncRNA can be found in new databases, such as the human body atlas LINCNA catalogue jointly developed by Broder Institute, Harvard University and MIT. However, what people know now is only the tip of the iceberg, and there are still a lot of functions of lncRNA to be explored by scientists.
LncRNA research tool
At present, one of the main challenges of lncRNA research is that research tools are still being developed and improved, including designing chips with different lncRNA detection probes. Agilent's SurePrint G3 gene expression V2 microarray is one of them. The probe design of this chip not only refers to the mRNA in major public databases, but also refers to the databases of lincRNA and TUCP (transcripts with uncountable coding potential) developed by Broder Institute, which can simultaneously detect encoded RNA and noncoding RNA. According to Corinna Nunn, Agilent's gene expression product manager, the expression level of lncRNA is lower than that of coding RNA. "Therefore, it is very important for the chip to have a wide dynamic range, so as to ensure the detection of low-expression genes."
Affymetrix also launched a new version of the human full transcription expression profile chip GeneChip? Gene 2.0 array can detect mRNA and lincRNA simultaneously on one chip. The design of the chip combines several database resources, including RefSeq, Ensemble, the human body map lincRNAs of Broder Institute and TUCP catalogue. "Our ultra-high density chip has a unique probe, which can detect multiple sites on each exon of each transcript to ensure that relevant biological information is captured to the maximum extent," said Tsetska Takova of Affymetrix. Biology Tong www.ebiotrade.com
Arraystar has been designing lncRNA chips since 2009. Recently, the company has just released the third generation lncRNA chip human lncRNA microarray V3.0, which can detect mRNA and LNC RNA. Ed davis, a technical support expert of Arraystar, said that expression profiling is often the first step to study lncRNA, but developing lncRNA expression chips is still very complicated, and the coexistence of multiple lncRNA databases is a complicated factor. "To this end, we have established a reliable comprehensive LNCNA database by combining the public database with the information in LNCNA's important papers," Davis said. In addition, it is not easy to design lncRNA probes, because lncRNA often overlaps with nearby protein coding genes. Davis introduced, "The traditional chip probe is' gene-specific', in other words, it is the 3' end of the probe target transcript, so it is impossible to distinguish multiple transcripts formed by variable transcription start sites or splicing methods. But Arraystar's probe is "transcript-specific" and can detect different transcripts of a single gene for exons and splicing points. "
Function of lncRNA
It is not easy to clarify the function of lncRNA. Davis said, "Unlike microRNA, lncRNA can function through many mechanisms, and it is difficult to infer its function from its sequence." According to Affymetrix company Takova, in fact, the lncRNA with known function is less than 1%. However, more and more studies show that lncRNA plays an important role in normal cell differentiation and tumorigenesis. As people gradually understand the difference between normal state and disease state, scientists believe that non-coding RNA can be used as a biological index for disease diagnosis and prediction.
How to study the function of lncRNA? According to experts, in addition to the study of expression profile, protein coding genes related to specific lncRNA can also provide valuable information about the function of lncRNA. Chris Streck, marketing manager of RNA and epigenetics in Illumina, also believes that analyzing the whole transcriptome is undoubtedly more valuable than just studying the coding RNA. He pointed out that under the impetus of the ENCODE (Encyclopedia of DNA Components) program, researchers now pay more attention to comprehensive research, including RNA, DNA and regulatory functions, among which non-coding RNA plays an increasingly prominent role. (The goal of the ENCODE project is to identify all transcription regions, transcription factor associations, chromatin structures and histone modifications in the human genome. ) Biology is www.ebiotrade.com.
Ivan Gibb of British Columbia Cancer Institute is studying the role of lncRNA in diseases. "Although many LNCNAs have been annotated with genomes, there is still a lack of evidence about the function of most LNCNAs," Gibb said. "I'm sure there are thousands of lncRNA that are functional, but we still need to pay attention to the fact that universal transcription does not mean universal function. It is very important to clarify the function of lncRNA from the transcription spectrum. " For example, the research team of Sapienza University in Rome expounded the function of lncRNA, which controls muscle differentiation as an endogenous competitive RNA. Gibb pointed out that another challenge of lncRNA research is to find the relationship between the structure and function of lncRNA. "Some studies indicate that the structure of lncRNA is domain-based, which is somewhat similar to the coding gene of protein," he said. "But how this organizational form is formed and how the structure of lncRNA is related to its function needs further study."
Role in cancer and other diseases
Obviously, lncRNA plays an important role in diseases. How does lncRNA have a strong influence on the disease process? Anne Bogestrom Lucas, a senior scientist at Agilent, introduced a new study by Broad Institute. P53 usually suppresses hundreds of genes, and if the level of p53-related lncRNA is down-regulated, the expression of these genes will be affected. "pointing out that lncRNA has a direct impact on tumor inhibition or carcinogenesis will lay the foundation for developing new cancer therapies," she said. In addition, the latest progress of the ENCODE project also shows that about 80% non-coding genomes play a role in gene regulation.
Gibb is studying the function of lncRNA abnormally expressed in human cancer. "Generally speaking, we can use a computer to analyze the data obtained by deep sequencing to determine the abnormal expression of lncRNA in diseases. Explaining the function of these lncRNA depends on traditional biochemical methods, "Gibb said. "analyzing the function of lncRNA in human cancer will not only greatly expand the target of cancer treatment, but also help people develop new cancer treatment methods. For example, gene regulation can be carried out through antisense RNA or target lncRNA- protein interaction. "
Many studies have shown that lncRNA is not only a regulatory factor, but also a biological indicator of diseases, such as lncRNA named HOTAIR. The expression of HOTAIR in primary and metastatic breast tumors will increase, and the expression level of HOTAIR in primary tumors can be used to effectively predict cancer metastasis and death. Another lncRNA called PCA3 (prostate cancer antigen 3) is highly overexpressed in prostate cancer. This kind of lncRNA exists in urine, and it is quite convenient for clinical detection. Recently, FDA approved a commercial test kit Progensa PCA3 test, which can be used in clinic. In addition, according to Davis of Arraystar, lncRNA-HEIH is also highly expressed in hepatocellular carcinoma, which can be detected by Arraystar's lncRNA chip.
In addition to cancer, the regulation of lncRNA also plays an important role in some genetic diseases. For example, the abnormal regulation of lncRNA is related to short finger/toe deformity and HELLP syndrome. In addition, studies have shown that lncRNA can stabilize the mRNA of key enzymes in Alzheimer's disease. Can lncRNA reveal the disease regulation mechanism beyond the coding gene for us? Davis of Arraystar said: "In my opinion, the most exciting development is that there is more and more evidence that lncRNA is closely related to major human diseases, and lncRNA can be better used for disease diagnosis and prognosis than RNA encoded by protein." I hope that one day, non-coding RNA can become a powerful weapon to help people resist diseases.