ArticleGenome biology2014
Constitutive patterns of gene expression regulated by RNA-binding proteins.
Article in Genome biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- The cryptic lncRNA-encoded microprotein TPM3P9 drives oncogenic RNA splicing and tumorigenesis.Signal transduction and targeted therapy · 2025Article
- Prediction of protein-RNA interactions from single-cell transcriptomic data.Nucleic acids research · 2024Article
- Exosomal circLPAR1 functions in colorectal cancer diagnosis and tumorigenesis through suppressing BRD4 via METTL3-eIF3h interaction.Molecular cancer · 2022Article
- catRAPID omics v2.0: going deeper and wider in the prediction of protein-RNA interactions.Nucleic acids research · 2021Article
- RNA-binding and prion domains: the Yin and Yang of phase separation.Nucleic acids research · 2020Article
- Zooming in on protein-RNA interactions: a multi-level workflow to identify interaction partners.Biochemical Society transactions · 2020Review
- NRF1-enhanced miR-4458 alleviates cardiac hypertrophy through releasing TTP-inhibited TFAM.In vitro cellular & developmental biology. Animal · 2020Article
- RNA structure drives interaction with proteins.Nature communications · 2019Article
- RNA-protein interactions: disorder, moonlighting and junk contribute to eukaryotic complexity.Open biology · 2019Review
- Post-transcriptional regulatory patterns revealed by protein-RNA interactions.Scientific reports · 2019Article
- Genomic and regulatory characteristics of significant transcription factors in colorectal cancer metastasis.Scientific reports · 2018Article
- Discovering the 3' UTR-mediated regulation of alpha-synuclein.Nucleic acids research · 2017Article
- The hnRNP RALY regulates transcription and cell proliferation by modulating the expression of specific factors including the proliferation marker E2F1.The Journal of biological chemistry · 2017Article
- Whole-transcriptome microarray analysis reveals regulation of Rab4 by RBM5 in neurons.Neuroscience · 2017Article
- Advances in the characterization of RNA-binding proteins.Wiley interdisciplinary reviews. RNA · 2016Review
- Molecular Pathophysiology of Fragile X-Associated Tremor/Ataxia Syndrome and Perspectives for Drug Development.Cerebellum (London, England) · 2016Review
- Non-random distribution of homo-repeats: links with biological functions and human diseases.Scientific reports · 2016Article
- Dissecting the expression relationships between RNA-binding proteins and their cognate targets in eukaryotic post-transcriptional regulatory networks.Scientific reports · 2016Article
- The Grand Challenge of Characterizing Ribonucleoprotein Networks.Frontiers in molecular biosciences · 2016Article
- Protein aggregation, structural disorder and RNA-binding ability: a new approach for physico-chemical and gene ontology classification of multiple datasets.BMC genomics · 2015Article
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6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundRNA-binding proteins regulate a number of cellular processes, including synthesis, folding, translocation, assembly and clearance of RNAs. Recent studies have reported that an unexpectedly large number of proteins are able to interact with RNA, but the partners of many RNA-binding proteins are still uncharacterized.
resultsWe combined prediction of ribonucleoprotein interactions, based on catRAPID calculations, with analysis of protein and RNA expression profiles from human tissues. We found strong interaction propensities for both positively and negatively correlated expression patterns. Our integration of in silico and ex vivo data unraveled two major types of protein-RNA interactions, with positively correlated patterns related to cell cycle control and negatively correlated patterns related to survival, growth and differentiation. To facilitate the investigation of protein-RNA interactions and expression networks, we developed the catRAPID express web server.
conclusionsOur analysis sheds light on the role of RNA-binding proteins in regulating proliferation and differentiation processes, and we provide a data exploration tool to aid future experimental studies.
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