RNA molecules undergo a number of chemical modifications whose effects can alter their structure and molecular interactions. Previous studies have shown that RNA editing can impact the formation of ribonucleoprotein complexes and influence the assembly of membrane-less organelles such as stress granules. For instance, N6-methyladenosine (m6A) enhances SG formation and N1-methyladenosine (m1A) prevents their transition to solid-like aggregates. Yet, very little is known about adenosine to inosine (A-to-I) modification that is very abundant in human cells and not only impacts mRNAs but also noncoding RNAs. Here, we introduce the CROSSalive predictor of A-to-I effects on RNA structure based on high-throughput in-cell experiments. Our method shows an accuracy of 90% in predicting the single and double-stranded content of transcripts and identifies a general enrichment of double-stranded regions caused by A-to-I in long intergenic noncoding RNAs (lincRNAs). For the individual cases of NEAT1, NORAD, and XIST, we investigated the relationship between A-to-I editing and interactions with RNA-binding proteins using available CLIP data and catRAPID predictions. We found that A-to-I editing is linked to the alteration of interaction sites with proteins involved in phase separation, which suggests that RNP assembly can be influenced by A-to-I. CROSSalive is available at http://service.tartaglialab.com/new_submission/crossalive.
Download full-text PDF |
Source |
---|---|
http://dx.doi.org/10.1002/iub.2673 | DOI Listing |
Mol Biol Rep
January 2025
Centre for Research Impact & Outcome-Chitkara College of Pharmacy, Chitkara University, Punjab, India.
Chemotherapy resistance (CR) represents one of the most important barriers to effective oncological therapy and often leads to ineffective intervention and unfavorable clinical prognosis. Emerging studies have emphasized the vital significance of extracellular RNA (exRNA) in influencing CR. This thorough assessment intends to explore the multifaceted contributions of exRNA, such as exosomal RNA, microRNAs, long non-coding RNAs, and circular RNAs, to CR in cancer.
View Article and Find Full Text PDFJ Cell Biochem
January 2025
Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China.
tRNA-derived fragments (tRFs) are a newly recognized class of small noncoding RNAs (sncRNAs) that play significant roles in various diseases. The Wnt pathway plays a key role in various physiological processes such as embryonic development, tissue renewal and regeneration. In the regulation of Wnt/β-catenin, Forkhead box k1(FOXK1), Frizzled class receptor 3 (FZD3), and Wnt5b can be targeted and inhibited by three tRFs: tRF3008A targets FOXK1 to inhibit colorectal cancer (CRC), 5'-tiRNAVal targets FZD3 to inhibit breast cancer (BrC), and tRF-22-8BWS7K092 targets Wnt5b to induce ferroptosis in lung cells.
View Article and Find Full Text PDFInt J Rheum Dis
January 2025
Department of Orthopaedics, Shaanxi Rehbilitation Hospital, Xi'an, Shaanxi, China.
Background: Osteoarthritis (OA) is one of the most common bone disorders and has a serious impact on the quality of life of patients. LncRNA-HCP5 (HCP5) is downregulated in OA tissues. However, the latent function and regulatory mechanisms of HCP5 in OA are unclear.
View Article and Find Full Text PDFEnviron Sci Process Impacts
January 2025
Department of Otorhinolaryngology, No. 971 Hospital of People's Liberation Army Navy, Qingdao 266000, Shandong Province, China.
Hearing loss (HL) is an otolaryngology disease susceptible to environmental pollutants. Volatile organic compounds (VOCs), as a class of chemical pollutants with evaporation propensity, pose a great threat to human health. However, the association between VOCs and HL remains unclear.
View Article and Find Full Text PDFCirc Res
January 2025
Division of Cardiology, Department of Medicine, Pittsburgh Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, PA. (R.A.C., C.C.C., R.W., A.C., C.B., C.R., W.J.M., M.J. Bashline, A.P., A.M.P., P.B., M.J. Brown, C.S.H.).
Background: Calcific aortic valve disease is the pathological remodeling of valve leaflets. The initial steps in valve leaflet osteogenic reprogramming are not fully understood. As TERT (telomerase reverse transcriptase) overexpression primes mesenchymal stem cells to differentiate into osteoblasts, we investigated whether TERT contributes to the osteogenic reprogramming of valve interstitial cells.
View Article and Find Full Text PDFEnter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!