CRIT: Identifying RNA-binding protein regulator in circRNA life cycle via non-negative matrix factorization

Shao, Mengting; Hao, Shijia; Jiang, Leiming; Cai, Yujie; Zhao, Xing; Chen, Qiuyang; Gao, Xuefei; Xu, Jianzhen

doi:10.1016/j.omtn.2022.10.015

Cited by 6 publications

(2 citation statements)

References 63 publications

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“…Recently, circRNA regulator identification tool (CRIT) has utilized multiple datasets such as gene alteration, clinical significance, gene ontology (GO) similarity, and transcriptome data collected from twelve cancer types. All the data are subjected to being characterized and clustered using non-negative matrix factorization (NMF), resulting in 73 predicted candidates and 17 known candidates [ 217 ]. Therefore, CRIT might be another efficient tool for predicting circRNA–protein interactions, as it revealed both novel and known regulators.…”

Section: Conclusion and Future Perspectivesmentioning

confidence: 99%

Circular RNAs in Cell Cycle Regulation of Cancers

Thamjamrassri,

Ariyachet

2024

IJMS

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Cancer has been one of the most problematic health issues globally. Typically, all cancers share a common characteristic or cancer hallmark, such as sustaining cell proliferation, evading growth suppressors, and enabling replicative immortality. Indeed, cell cycle regulation in cancer is often found to be dysregulated, leading to an increase in aggressiveness. These dysregulations are partly due to the aberrant cellular signaling pathway. In recent years, circular RNAs (circRNAs) have been widely studied and classified as one of the regulators in various cancers. Numerous studies have reported that circRNAs antagonize or promote cancer progression through the modulation of cell cycle regulators or their associated signaling pathways, directly or indirectly. Mostly, circRNAs are known to act as microRNA (miRNA) sponges. However, they also hold additional mechanisms for regulating cellular activity, including protein binding, RNA-binding protein (RBP) recruitment, and protein translation. This review will discuss the current knowledge of how circRNAs regulate cell cycle-related proteins through the abovementioned mechanisms in different cancers.

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Section: Conclusion and Future Perspectivesmentioning

confidence: 99%

Circular RNAs in Cell Cycle Regulation of Cancers

Thamjamrassri,

Ariyachet

2024

IJMS

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“…For example, RBP Polypyrimidine tract binding protein 1 (PTBP1) is reported to repress the expression of circ_0076611, whose interaction with diverse proliferation-related transcripts (MYC and VEGFA mRNAs) augments cell proliferation and migration in triple-negative breast cancer cells, the RBP oncogenic splicing factor SRSF1 (Serine And Arginine Rich Splicing Factor 1) encourages this expression after the inactivation of PTBP1 protein by the long non-coding RNAs (lncRNA) MALAT1 (metastasis-associated lung adenocarcinoma transcript 1 [ 46 ]. Several novel RBPs regulating circRNA functions in tumorigenesis, such as SRSF5, HNRNPA2B1, HNRNPF, KHSRP, or PSIP1, have also been unveiled [ 47 ].…”

Section: General Roles Attributed To Rna-binding Proteinsmentioning

confidence: 99%

Roles of RNA-binding proteins in neurological disorders, COVID-19, and cancer

2022

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RNA-binding proteins (RBPs) have emerged as important players in multiple biological processes including transcription regulation, splicing, R-loop homeostasis, DNA rearrangement, miRNA function, biogenesis, and ribosome biogenesis. A large number of RBPs had already been identified by different approaches in various organisms and exhibited regulatory functions on RNAs’ fate. RBPs can either directly or indirectly interact with their target RNAs or mRNAs to assume a key biological function whose outcome may trigger disease or normal biological events. They also exert distinct functions related to their canonical and non-canonical forms. This review summarizes the current understanding of a wide range of RBPs’ functions and highlights their emerging roles in the regulation of diverse pathways, different physiological processes, and their molecular links with diseases. Various types of diseases, encompassing colorectal carcinoma, non-small cell lung carcinoma, amyotrophic lateral sclerosis, and Severe acute respiratory syndrome coronavirus 2, aberrantly express RBPs. We also highlight some recent advances in the field that could prompt the development of RBPs-based therapeutic interventions.

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RNA‐Binding Protein Hnrnpa1 Triggers Daughter Cardiomyocyte Formation by Promoting Cardiomyocyte Dedifferentiation and Cell Cycle Activity in a Post‐Transcriptional Manner

Li,

Chen,

Chen

et al. 2024

Advanced Science

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Stimulating cardiomyocyte (CM) dedifferentiation and cell cycle activity (DACCA) is essential for triggering daughter CM formation. In addition to transcriptional processes, RNA‐binding proteins (RBPs) are emerging as crucial post‐transcriptional players in regulating CM DACCA. However, whether post‐transcriptional regulation of CM DACCA by RBPs could effectively trigger daughter CM formation remains unknown. By performing integrated bioinformatic analysis of snRNA‐seq data from neonatal and adult hearts, this study identified Hnrnpa1 as a potential RBP regulating CM DACCA. Hnrnpa1 expression decreased significantly during postnatal heart development. With the use of α‐MHC‐H2B‐mCh/CAG‐eGFP‐anillin transgenic mice, Hnrnpa1 overexpression promoted CM DACCA, thereby triggering daughter CM formation and enhancing cardiac repair after myocardial infarction (MI). In contrast, CRISPR/Cas9 technology is used to generate CM‐specific Hnrnpa1 knockout mice. Hnrnpa1 knockout inhibited cardiac regeneration and worsened cardiac function in the neonatal MI model. Nanopore RNA sequencing, RIP assay, IP‐MS, MeRIP‐qPCR, PAR‐CLIP and luciferase reporter experiments showed that Hnrnpa1 induced Mettl3 post‐transcriptional splicing to inhibit m6A‐dependent Pbx1 and E2F1 degradation, thereby increasing Runx1, Ccne1, Cdk2 and Ccnb2 expression to promote CM DACCA. In conclusion, Hnrnpa1 triggered daughter CM formation by promoting CM DACCA in a post‐transcriptional manner, indicating that Hnrnpa1 might serve as a promising target in cardiac repair post‐MI.

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CRIT: Identifying RNA-binding protein regulator in circRNA life cycle via non-negative matrix factorization

Cited by 6 publications

References 63 publications

Circular RNAs in Cell Cycle Regulation of Cancers

Circular RNAs in Cell Cycle Regulation of Cancers

Roles of RNA-binding proteins in neurological disorders, COVID-19, and cancer

RNA‐Binding Protein Hnrnpa1 Triggers Daughter Cardiomyocyte Formation by Promoting Cardiomyocyte Dedifferentiation and Cell Cycle Activity in a Post‐Transcriptional Manner

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