The RBPome: where the brains meet the brawn

Attar, Naomi

doi:10.1186/gb4153

Cited by 4 publications

(5 citation statements)

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“…Intensive attempts have been undertaken to better understand RNA-binding proteins (RBPs) and RNA–protein interactions ( 13 ). The advent of next-generation sequencing and relevant molecular techniques have allowed the development of systematic experimental protocols for the identiﬁcation of protein-binding sites on RNA using the immunoprecipitation of RBPs, with or without in vivo RNA–protein crosslinking, known as crosslinking immunoprecipitation sequencing (CLIP-seq) and RNA immunoprecipitation sequencing (RIP-seq), respectively ( 14 , 15 ).…”

Section: Introductionmentioning

confidence: 99%

“…Identifying changes in RBP binding induced by SNVs for a messenger RNA (mRNA) in vivo remains challenging because RBPs have much more scope to achieve specificity through the secondary structure of RNA and SNVs could change intramolecular bonds which may twist RNA molecules into hairpins, stem-loops and various other bumps and bulges ( 13 ). The impact of SNVs on RNA structure and gene regulation has been widely studied ( 1 – 4 ).…”

Section: Introductionmentioning

confidence: 99%

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RBP-Var: a database of functional variants involved in regulation mediated by RNA-binding proteins

Mao

Xiao

et al. 2015

Nucleic Acids Res

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Transcription factors bind to the genome by forming specific contacts with the primary DNA sequence; however, RNA-binding proteins (RBPs) have greater scope to achieve binding specificity through the RNA secondary structure. It has been revealed that single nucleotide variants (SNVs) that alter RNA structure, also known as RiboSNitches, exhibit 3-fold greater local structure changes than replicates of the same DNA sequence, demonstrated by the fact that depletion of RiboSNitches could result in the alteration of specific RNA shapes at thousands of sites, including 3′ UTRs, binding sites of microRNAs and RBPs. However, the network between SNVs and post-transcriptional regulation remains unclear. Here, we developed RBP-Var, a database freely available at http://www.rbp-var.biols.ac.cn/, which provides annotation of functional variants involved in post-transcriptional interaction and regulation. RBP-Var provides an easy-to-use web interface that allows users to rapidly find whether SNVs of interest can transform the secondary structure of RNA and identify RBPs whose binding may be subsequently disrupted. RBP-Var integrates DNA and RNA biology to understand how various genetic variants and post-transcriptional mechanisms cooperate to orchestrate gene expression. In summary, RBP-Var is useful in selecting candidate SNVs for further functional studies and exploring causal SNVs underlying human diseases.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

RBP-Var: a database of functional variants involved in regulation mediated by RNA-binding proteins

Mao

Xiao

et al. 2015

Nucleic Acids Res

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“…RBPs bind to the mRNA through a wide variety of intramolecular bonds in hairpins, stem loops, and other bumps and bulges (Attar 2014 ). Generally, RBPs associate with nascent mRNA both at the 5′- and 3′-ends.…”

Section: Rna-binding Proteins: Overviewmentioning

confidence: 99%

RNA-Binding Proteins: A Role in Neurotoxicity?

Ocharán-Mercado,

Loaeza-Loaeza,

Castro-Coronel

et al. 2023

Neurotox Res

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Despite sustained efforts to treat neurodegenerative diseases, little is known at the molecular level to understand and generate novel therapeutic approaches for these malignancies. Therefore, it is not surprising that neurogenerative diseases are among the leading causes of death in the aged population. Neurons require sophisticated cellular mechanisms to maintain proper protein homeostasis. These cells are generally sensitive to loss of gene expression control at the post-transcriptional level. Post-translational control responds to signals that can arise from intracellular processes or environmental factors that can be regulated through RNA-binding proteins. These proteins recognize RNA through one or more RNA-binding domains and form ribonucleoproteins that are critically involved in the regulation of post-transcriptional processes from splicing to the regulation of association of the translation machinery allowing a relatively rapid and precise modulation of the transcriptome. Neurotoxicity is the result of the biological, chemical, or physical interaction of agents with an adverse effect on the structure and function of the central nervous system. The disruption of the proper levels or function of RBPs in neurons and glial cells triggers neurotoxic events that are linked to neurodegenerative diseases such as spinal muscular atrophy (SMA), amyotrophic lateral sclerosis (ALS), fragile X syndrome (FXS), and frontotemporal dementia (FTD) among many others. The connection between RBPs and neurodegenerative diseases opens a new landscape for potentially novel therapeutic targets for the intervention of these neurodegenerative pathologies. In this contribution, a summary of the recent findings of the molecular mechanisms involved in the plausible role of RBPs in RNA processing in neurodegenerative disease is discussed.

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“…The RBPome can be defined as the interface where RNA and RBPs meet, for controlling many aspects of gene regulation [8,17]. RNA–protein complexes are very dynamic and can undergo extensive remodelling.…”

Section: Focus On the Rbpomementioning

confidence: 99%

Ribonomic approaches to study the RNA‐binding proteome

Faoro

Ataide

2014

FEBS Letters

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a b s t r a c tGene expression is controlled through a complex interplay among mRNAs, non-coding RNAs and RNA-binding proteins (RBPs), which all assemble along with other RNA-associated factors in dynamic and functional ribonucleoprotein complexes (RNPs). To date, our understanding of RBPs is largely limited to proteins with known or predicted RNA-binding domains. However, various methods have been recently developed to capture an RNA of interest and comprehensively identify its associated RBPs. In this review, we discuss the RNA-affinity purification methods followed by mass spectrometry analysis (AP-MS); RBP screening within protein libraries and computational methods that can be used to study the RNA-binding proteome (RBPome).

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The RBPome: where the brains meet the brawn

Cited by 4 publications

References 48 publications

RBP-Var: a database of functional variants involved in regulation mediated by RNA-binding proteins

RBP-Var: a database of functional variants involved in regulation mediated by RNA-binding proteins

RNA-Binding Proteins: A Role in Neurotoxicity?

Ribonomic approaches to study the RNA‐binding proteome

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