RNA-centric approaches to study RNA-protein interactions in vitro and in silico

Dasti, Alessandro; Cid-Samper, Fernando; Bechara, Elías; Tartaglia, Gian Gaetano

doi:10.1016/j.ymeth.2019.09.011

Cited by 15 publications

(12 citation statements)

References 69 publications

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“…The success in discovering new findings is influenced by the technical capacity to preserve the natural characteristics of the protein-RNA partners, such as the secondary and tertiary structure, electrostatic and hydrophobic interactions, hydrogen bonding, rate of transcription of RNA and translation of protein, etc. We refer the reader to advanced reviews for details related to the experimental methods (Dasti et al, 2019).…”

Section: In Vitro Approaches To Predict Molecular Interactions Occurrmentioning

confidence: 99%

In silico, in vitro, and in vivo Approaches to Identify Molecular Players in Fragile X Tremor and Ataxia Syndrome

Haify

Botta-Orfila

Hukema

et al. 2020

Front. Mol. Biosci.

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Fragile X-associated tremor/ataxia syndrome (FXTAS) is a late-onset neurodegenerative monogenetic disorder affecting carriers of premutation (PM) forms of the FMR1 gene, resulting in a progressive development of tremors, ataxia, and neuropsychological problems. This highly disabling disease is quite common in the general population with an estimation of about 20 million PM carriers worldwide. The chances of developing FXTAS increase dramatically with age, with about 45% of male carriers over the age of 50 being affected. Both the gene and pathogenic trigger, a mutant expansion of CGG RNA, causing FXTAS are known. This makes it an interesting disease to develop targeted therapeutic interventions for. Yet, no such interventions are available at this moment. Here we discuss in silico, in vitro, and in vivo approaches and how they have been used to identify the molecular determinants of FXTAS pathology. These approaches have yielded substantial information about FXTAS pathology and, consequently, many markers have emerged to play a key role in understanding the disease mechanism. Integration of the different approaches is expected to provide crucial information about the value of these markers as either therapeutic target or biomarker, essential to monitor therapeutic interventions in the future.

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Section: In Vitro Approaches To Predict Molecular Interactions Occurrmentioning

confidence: 99%

In silico, in vitro, and in vivo Approaches to Identify Molecular Players in Fragile X Tremor and Ataxia Syndrome

Haify

Botta-Orfila

Hukema

et al. 2020

Front. Mol. Biosci.

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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%

“…Differential analysis of these changes compared with control cells and animals, using microarrays, RNA-seq, ribosome footprints, and their combination with the isolation of specific regions of cells, can identify mRNAs regulated by RNA-binding proteins. There are also various other methods to analyze RNA-protein associations, such as sequence-and structure-based methods using computational approaches [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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“…A most accurate validation should start from the screening of potential binders, followed by the precise determination of binding sites and kinetic and thermodynamic parameters, and completed with structural insights into the drivers of the interaction ( Figure 1 ). A comprehensive review of the methodology is beyond the scope of this article and for more details we refer to a number of recent reviews of the field [ 16 , 17 , 84–86 ].…”

Section: In Vitro Validation Of Predicted Rbp–rna Interactiomentioning

confidence: 99%

“…Large-scale identification of new potential RBPs can reveal unexpected biological and pathological functions and, when confronted with a novel RBP, the identification of its RNA binding partners is a critical step to define the protein's cellular and molecular roles. To achieve this goal, increasingly sophisticated highthroughput methodologies have been developed, spanning from methods that aim to preserve the native cellular RNA-RBP interactions [13][14][15] to finely-controlled in vitro techniques that allow to define kinetics and dynamic parameters for each binding pair [16,17]. However, the field that has probably seen the biggest evolution in the shortest time span is the one of computational prediction algorithms [18][19][20][21][22].…”

Section: Introductionmentioning

confidence: 99%

Zooming in on protein–RNA interactions: a multi-level workflow to identify interaction partners

Colantoni

Rupert

Vandelli

et al. 2020

Biochemical Society Transactions

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Interactions between proteins and RNA are at the base of numerous cellular regulatory and functional phenomena. The investigation of the biological relevance of non-coding RNAs has led to the identification of numerous novel RNA-binding proteins (RBPs). However, defining the RNA sequences and structures that are selectively recognised by an RBP remains challenging, since these interactions can be transient and highly dynamic, and may be mediated by unstructured regions in the protein, as in the case of many non-canonical RBPs. Numerous experimental and computational methodologies have been developed to predict, identify and verify the binding between a given RBP and potential RNA partners, but navigating across the vast ocean of data can be frustrating and misleading. In this mini-review, we propose a workflow for the identification of the RNA binding partners of putative, newly identified RBPs. The large pool of potential binders selected by in-cell experiments can be enriched by in silico tools such as catRAPID, which is able to predict the RNA sequences more likely to interact with specific RBP regions with high accuracy. The RNA candidates with the highest potential can then be analysed in vitro to determine the binding strength and to precisely identify the binding sites. The results thus obtained can furthermore validate the computational predictions, offering an all-round solution to the issue of finding the most likely RNA binding partners for a newly identified potential RBP.

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RNA-centric approaches to study RNA-protein interactions in vitro and in silico

Cited by 15 publications

References 69 publications

In silico, in vitro, and in vivo Approaches to Identify Molecular Players in Fragile X Tremor and Ataxia Syndrome

In silico, in vitro, and in vivo Approaches to Identify Molecular Players in Fragile X Tremor and Ataxia Syndrome

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

Zooming in on protein–RNA interactions: a multi-level workflow to identify interaction partners

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