Methods to study the RNA-protein interactions

Popova, V. V.; Куршакова, М. М.; Копытова, Д. В.

doi:10.1134/s0026893315020107

Cited by 16 publications

(11 citation statements)

References 40 publications

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“…In the present study, the cytoplasmic localization of LINC00857 in CRC cells indicated the post-transcriptional effect of LINC00857 on gene expression. Furthermore, RBPs exert crucial effects by post-transcriptionally regulating gene expression (28), including pre-mRNA splicing, mRNA stabilization, mRNA localization and translation (17,38). The present study hypothesized the potential regulatory pattern of LINC00857 in which LINC00857 interacted with RBPs to stabilize mRNA.…”

Section: Discussionmentioning

confidence: 69%

LINC00857 promotes cell proliferation and migration in colorectal cancer by interacting with YTHDC1 and stabilizing SLC7A5

Shu

Liu

2021

Oncol Lett

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Colorectal cancer (CRC) is one of the most lethal malignances in humans. Hence, it is of great significance to identify regulatory molecules in CRC progression. Accumulating evidence has demonstrated that long non-coding RNAs (lncRNAs) are involved in cancer malignancy. It has been reported that long intergenic non-protein coding RNA 857 (LINC00857) acts as a vital oncogene in many types of cancer by promoting cell proliferation and migration. However, the role of LINC00857 in CRC remains unclear. In the present study, LINC00857 was upregulated in CRC tissue samples and cells. Next, in vitro loss-of-function experiments demonstrated that LINC00857 knockdown suppressed CRC cell viability, proliferation and migration, as well as epithelial-mesenchymal transition and increased cell apoptosis. Mechanistically, LINC00857 abundantly interacted with the RNA-binding protein YTH domain containing 1 (YTHDC1). YTHDC1 ultimately combined with solute carrier family 7 member 5 (SLC7A5) and increased SLC7A5 mRNA stability. Finally, a series of rescue experiments indicated that LINC00857 promoted the proliferation and migration of CRC cells by regulating mRNA stability. Thus, the present findings illustrated that LINC00857 functions as an oncogene in CRC cells via the YTHDC1/SLC7A5 axis.

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Section: Discussionmentioning

confidence: 69%

LINC00857 promotes cell proliferation and migration in colorectal cancer by interacting with YTHDC1 and stabilizing SLC7A5

Shu

Liu

2021

Oncol Lett

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“…To better understand the mechanistic basis of the RNA-binding-protein-mediated regulation of biological functions, including brain functions, it is important to identify target mRNAs for RNA-binding proteins. Various methods have been developed for this purpose [234,235].…”

Section: Methods For Identifying Rna-protein Interactionsmentioning

confidence: 99%

Cataloguing and Selection of mRNAs Localized to Dendrites in Neurons and Regulated by RNA-Binding Proteins in RNA Granules

Ohashi

Shiina

2020

Biomolecules

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Spatiotemporal translational regulation plays a key role in determining cell fate and function. Specifically, in neurons, local translation in dendrites is essential for synaptic plasticity and long-term memory formation. To achieve local translation, RNA-binding proteins in RNA granules regulate target mRNA stability, localization, and translation. To date, mRNAs localized to dendrites have been identified by comprehensive analyses. In addition, mRNAs associated with and regulated by RNA-binding proteins have been identified using various methods in many studies. However, the results obtained from these numerous studies have not been compiled together. In this review, we have catalogued mRNAs that are localized to dendrites and are associated with and regulated by the RNA-binding proteins fragile X mental retardation protein (FMRP), RNA granule protein 105 (RNG105, also known as Caprin1), Ras-GAP SH3 domain binding protein (G3BP), cytoplasmic polyadenylation element binding protein 1 (CPEB1), and staufen double-stranded RNA binding proteins 1 and 2 (Stau1 and Stau2) in RNA granules. This review provides comprehensive information on dendritic mRNAs, the neuronal functions of mRNA-encoded proteins, the association of dendritic mRNAs with RNA-binding proteins in RNA granules, and the effects of RNA-binding proteins on mRNA regulation. These findings provide insights into the mechanistic basis of protein-synthesis-dependent synaptic plasticity and memory formation and contribute to future efforts to understand the physiological implications of local regulation of dendritic mRNAs in neurons.

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“…As the characterization of physiological protein-RNA interactions is essential to understand how mRNA is transcribed and processed in cells, various methods have been developed to detect such transient and faint interactions, which has been reviewed in several articles [13][14][15]. These methods can be classified into protein-centric and RNA-centric methods.…”

Section: Figurementioning

confidence: 99%

Rapidly Growing Protein-Centric Technologies to Extensively Identify Protein–RNA Interactions: Application to the Analysis of Co-Transcriptional RNA Processing

Matsubara

Kawachi

Ohno

2021

IJMS

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During mRNA transcription, diverse RNA-binding proteins (RBPs) are recruited to RNA polymerase II (RNAP II) transcription machinery. These RBPs bind to distinct sites of nascent RNA to co-transcriptionally operate mRNA processing. Recent studies have revealed a close relationship between transcription and co-transcriptional RNA processing, where one affects the other’s activity, indicating an essential role of protein–RNA interactions for the fine-tuning of mRNA production. Owing to their limited amount in cells, the detection of protein–RNA interactions specifically assembled on the transcribing RNAP II machinery still remains challenging. Currently, cross-linking and immunoprecipitation (CLIP) has become a standard method to detect in vivo protein–RNA interactions, although it requires a large amount of input materials. Several improved methods, such as infrared-CLIP (irCLIP), enhanced CLIP (eCLIP), and target RNA immunoprecipitation (tRIP), have shown remarkable enhancements in the detection efficiency. Furthermore, the utilization of an RNA editing mechanism or proximity labeling strategy has achieved the detection of faint protein–RNA interactions in cells without depending on crosslinking. This review aims to explore various methods being developed to detect endogenous protein–RNA interaction sites and discusses how they may be applied to the analysis of co-transcriptional RNA processing.

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Methods to study the RNA-protein interactions

Cited by 16 publications

References 40 publications

LINC00857 promotes cell proliferation and migration in colorectal cancer by interacting with YTHDC1 and stabilizing SLC7A5

LINC00857 promotes cell proliferation and migration in colorectal cancer by interacting with YTHDC1 and stabilizing SLC7A5

Cataloguing and Selection of mRNAs Localized to Dendrites in Neurons and Regulated by RNA-Binding Proteins in RNA Granules

Rapidly Growing Protein-Centric Technologies to Extensively Identify Protein–RNA Interactions: Application to the Analysis of Co-Transcriptional RNA Processing

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