Reconstructing and quantifying the full-length transcripts of ring RNA.

On January 19th, the international academic journal Genome Medicine published the latest research results of the team of Zhao Fangqing of the Computational Genomics Laboratory of the Beijing Institute of Life Sciences of the Chinese Academy of Sciences entitled Reith of Full-length Circular RNAs enables the isoform - level quantification.
the study puts forward a new method of reconstructing and quantifying the ring transcript (CIRI-full), obtaining the full-length sequence through the characteristics of the reverse overlap area in the sequencing of the ring transcript, which not only effectively solves the problem of reconstruction of the internal structure of the ring transcript, but also provides a new way of thinking for the quantification of different shear products in the ring transcript.
the current function of the vast majority of ring RNA is not clear, and the existing method can not provide sufficient sequence characteristic information, this method can help researchers to more effectively screen out the potential function of the ring variable shear products, the function of the ring RNA and transcript level of differential expression analysis is of great significance.
in previous studies, the identification method of ring RNA is mainly by using the characteristics of the ring RNA-reverse splicing sequence.
However, due to the generally shorter read length of the second generation sequencing, the researchers, although they can obtain a large number of reverse shear sites, can not obtain high-throughput information on the complete internal structure of the ring RNA, and can not accurately quantify the different variable shear products.
to solve this problem, Zhao Fangqing's team first proposed a new ring RNA identification feature, reverse overlapping zones.
this feature usually appears in long-read ring RNA sequencing.
unlike all previous identification algorithms, this feature can be used not only to determine whether a pair of sequencing sequences in the transcript's double-ended sequencing came from ring RNA, but also to determine whether the sequence can cover the entire ring RNA. The researchers used this method to obtain a full-length sequence of more than 80% of the ring RNA from the brain tissue of different mammals. the full-length reconstruction of
ring RNA is the basis for its precise quantification.
for ring RNA with a variety of variable shear products, CIRI-full uses Monte Carlo method to simulate the distribution of read segments from different shear products on the full length sequence, and filters out the combination with optimal expression by gradient drop method.
, the sequencing coverage and variable shear events on each exon can be used to determine the difference between the prediction result and the real situation.
researchers used simulation and real-world data to verify the accuracy of this approach.
for producing multiple variable shear products at each BSJ site, CIRI-full not only sensitively reconstructs its full-length sequence, but also accurately predicts its relative abundance.
this study provides a new perspective for the study of the composition and function of the ring RNA, presents the more detailed internal structure of the ring transcript, and realizes the precise quantification of transcript level, which provides an important methodological tool for the subsequent screening of the potentially functional ring RNA molecules.
the work was mainly completed by Zheng Yi, a doctoral student of Zhao Fangqing's research group, and Zhai Peifeng, an assistant researcher, and received financial support from the National Natural Science Foundation of China, the Key Research and Development Program of the Ministry of Science and Technology and the Chinese Academy of Sciences.
related information: Multi-energy stem cell ring RNA has regulatory stem cell maintenance and differentiation function A study by scientists in Taiwan has found that the ring RNA in human pluripotent stem cells has the function of regulating stem cell maintenance and differentiation, this research is expected to promote regenerative medicine and innovative medical technology.
at a press conference held on the 3rd, Taiwan's "Chinese Academy of Sciences" Institute of Cell and Individual Biology, associate researcher Guo Weizhi introduced his team's findings.
Guo said that human pluripotent stem cells contain a large number of ring RNA, one of which is ring RNA-circBIRC6 to maintain the pluripotcity of stem cells.
by controlling the performance of circBIRC6, researchers can regulate pluripotent stem cells to maintain pluripotency or initiate differentiation, as if they had discovered a "switch" that controls pluripotent stem cells.
, the body's cells will be injured, aging, pluripotent stem cells are the opportunity to repair the body.
multi-energy stem cells can be differentiated into different cells to replace damaged or aging cells, bringing many hopes for regenerative medicine, developmental biology, disease-causing mechanisms and new drug development.
research institutions around the world are using such stem cells as a basis for clinical cell therapy and drug development.
Human pluripotent stem cells include embryonic stem cells and induced pluripotent stem cells (iPSC), guo said.
the former is taken from embryos and is not readily available; the latter can artificially induce human cells into pluripotent stem cells, and its discoverer, Japanese scientist Yukio Yamanaka, has won the Nobel Prize.
pluripotent stem cells offer hope for regenerative medicine, but it is not clear how pluripotency of such cells can be maintained and how they differentiate into various cells. The presence of
ring RNA is a new discovery in recent years.
genes are transcribed from DNA into linear RNA, which is then spliced to form a ring RNA." Ring RNA used to be thought to be a mistake in the gene transcription process, but current studies have shown that ring RNA regulates gene performance in cells, but is not wrong, but has important functions.
," Guo said. "In addition to opening up the potential for the application of pluripotent stem cells, ring RNA may also help develop innovative medical technologies in the future that will target the diagnosis or treatment of diseases,"
said.
" Guo believes that the study is expected to provide new solutions for early diagnosis and treatment of cancer, Parkinson's disease, Alzheimer's disease and other diseases, by controlling ring RNA, can regulate pluripotent stem cells to differentiate into specific somatic cells, or thus induce better quality iPSC, reduce the possible cancerous phenomenon after cell transplantation, improve the safety of cell therapy.
Source: Beijing Institute of Life Sciences, etc.