Membraneless organelles (MLOs), also known as “biomolecular condensates,” are formed by the biological process of liquid-liquid phase separation (LLPS). MLOs are dynamic bodies that contain proteins and nucleic acids.
While the role of LLPS proteins has been widely investigated, there is a growing interest in the scientific community to understand the role of RNAs—the nucleic acids responsible for countless biological functions including coding, decoding, regulation, and expression. of genes, and finally. protein-phase separation.
Recent studies have revealed that MLOs are rich in RNAs that are poorly extracted by conventional methods but can be recovered using improved methods such as needle shearing and heating, a property known as semi-extractability. These semi-extractable RNAs may be important biomarkers and drug targets in disease diagnosis and treatment. However, very few studies have succeeded in identifying and characterizing these RNAs.
To address this gap, Dr. Chao Zeng, assistant professor at Waseda University, in collaboration with Dr. Michiaki Hamada from Waseda University, Dr. Takeshi Chujo from Kumamoto University, and Dr. Tetsuro Hirose from Osaka University, has developed a novel bioinformatic pipeline to identify semi-extractable RNAs in human cell lines. Their findings are published in the journal Nucleic Acid Research on July 19, 2023.
The team conducted cellular RNA extraction and sequencing of five human cell lines, namely, A10, A549, HEK293, HeLa, and HAP1 cells. They further analyzed the RNA sequencing data using different computational methods. Differential expression analysis was performed between the samples taken using the conventional RNA extraction method and the improved extraction method. The researchers identified RNA transcripts that were consistently semi-extractable in all five cell lines.
Repeat density and sequence motif analysis were also performed to investigate potential factors influencing semi-extractability. In addition, the researchers conducted k-mer analysis using the SEEKR algorithm to be used to classify semi-extractable RNAs based on their k-mer content.
Sharing the highlight of their study, Chao Zeng explained, “Using a newly developed bioinformatic analysis pipeline, we analyzed original experimental data from cultured human cell types and successfully identified and characterized 1,074 which is semi-extractable RNA that may be involved in the formation of membrane-free phase-separated. organelles.”
Investigating the localization of semi-extractable RNAs in chromatin as well as inside the cell, the team found that these RNAs were enriched in restricted and repetitive heterochromatin (darkly staining) regions, especially in Polycomb-repressed sites. Inside the cells, RNAs are concentrated in the nucleus, including the nucleolus, but separated from the chromatin.
In addition, researchers postulate that semi-extractable RNAs can act as a platform for communicating with other RNAs. To prove their hypothesis, they compared semi-extractable RNAs with nearly 600 hub RNAs that form protein-mediated RNA-RNA interactions with many other RNAs. They found that semi-extractable RNAs actually act as hubs and are important in the formation of RNA-RNA interactions.
Further analysis of semi-extractable RNA revealed a marked preference for RNA-binding proteins to bind to AU-rich regions associated with RNAs. While messenger RNAs usually display AU-rich regions at the 3′ end, which regulate RNA stability, semi-extractable RNAs display a concentration of AU regions at the 5′ end, indicating potential involving undiscovered functions.
The study provides the first dataset of semi-extractable RNAs in human cell lines, which is a valuable resource for investigating RNA-based phase separations. “Future integration of semi-extractable RNAs with RNA interaction studies will provide insights into the molecular mechanisms underlying RNA-induced compartmentalization of cells,” concluded Michiaki Hamada.
The findings of the study provide new insights to investigate the involvement of RNA in biological processes such as cancer development and progression, viral RNA degradation, and stress responses in cellular, and may drive the development of therapeutic strategies for cancer and infectious diseases.
Chao Zeng et al, Landscape of semi-extractable RNAs in five human cell lines, Nucleic Acid Research (2023). DOI: 10.1093/nar/gkad567
Provided by Waseda University
Citation: Unraveling the mystery of semi-extractable RNAs from human cell lines (2023, July 18) retrieved on July 18, 2023 from https://phys.org/news/2023-07-unraveling-mystery-semi -extractable-rnas-after. html
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