ArticleRNA (New York, N.Y.)2009
Next-generation SELEX identifies sequence and structural determinants of splicing factor binding in human pre-mRNA sequence.
Article in RNA (New York, N.Y.), 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
29 citing papers in PubMed, 48 citations in OpenAlex.
- The role of alternative pre-mRNA splicing in cancer progression.Cancer cell international · 2023Review
- Rationally designed stapled peptides allosterically inhibit PTBP1-RNA-binding.Chemical science · 2023Article
- MDM4 alternative splicing and implication in MDM4 targeted cancer therapies.American journal of cancer research · 2021Review
- Quantitative detection of neurotransmitter using aptamer: From diagnosis to therapeutics.Journal of biosciences · 2020Review
- RNA Expression Profile and Alternative Splicing Signatures of Genistein-Treated Breeder Hens Revealed by Hepatic Transcriptomic Analysis.Oxidative medicine and cellular longevity · 2019Article
- PASSPORT-seq: A Novel High-Throughput Bioassay to Functionally Test Polymorphisms in Micro-RNA Target Sites.Frontiers in genetics · 2018Article
- Widespread intra-dependencies in the removal of introns from human transcripts.Nucleic acids research · 2017Article
- Recognizing RNA structural motifs in HT-SELEX data for ribosomal protein S15.BMC bioinformatics · 2017Article
- High expression of PTBP1 promote invasion of colorectal cancer by alternative splicing of cortactin.Oncotarget · 2017Article
- High-Throughput Assays to Assess the Functional Impact of Genetic Variants: A Road Towards Genomic-Driven Medicine.Clinical and translational science · 2017Review
- A deep learning framework for modeling structural features of RNA-binding protein targets.Nucleic acids research · 2016Article
- New Technologies Provide Quantum Changes in the Scale, Speed, and Success of SELEX Methods and Aptamer Characterization.Molecular therapy. Nucleic acids · 2014Article
- Lineage-specific splicing of a brain-enriched alternative exon promotes glioblastoma progression.The Journal of clinical investigation · 2014Article
- De novo prediction of PTBP1 binding and splicing targets reveals unexpected features of its RNA recognition and function.PLoS computational biology · 2014Article
- New insights into functional roles of the polypyrimidine tract-binding protein.International journal of molecular sciences · 2013Review
- A biophysical model for identifying splicing regulatory elements and their interactions.PloS one · 2013Article
- PTBP1-dependent regulation of USP5 alternative RNA splicing plays a role in glioblastoma tumorigenesis.Molecular carcinogenesis · 2012Article
- Ptbp2 represses adult-specific splicing to regulate the generation of neuronal precursors in the embryonic brain.Genes & development · 2012Article
- Challenges and opportunities for small molecule aptamer development.Journal of nucleic acids · 2012Article
- Frequent gain and loss of intronic splicing regulatory elements during the evolution of vertebrates.Genome biology and evolution · 2012Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
Many splicing factors interact with both mRNA and pre-mRNA. The identification of these interactions has been greatly improved by the development of in vivo cross-linking immunoprecipitation. However, the output carries a strong sampling bias in favor of RNPs that form on more abundant RNA species like mRNA. We have developed a novel in vitro approach for surveying binding on pre-mRNA, without cross-linking or sampling bias. Briefly, this approach entails specifically designed oligonucleotide pools that tile through a pre-mRNA sequence. The pool is then partitioned into bound and unbound fractions, which are quantified by a two-color microarray. We applied this approach to locating splicing factor binding sites in and around approximately 4000 exons. We also quantified the effect of secondary structure on binding. The method is validated by the finding that U1snRNP binds at the 5' splice site (5'ss) with a specificity that is nearly identical to the splice donor motif. In agreement with prior reports, we also show that U1snRNP appears to have some affinity for intronic G triplets that are proximal to the 5'ss. Both U1snRNP and the polypyrimidine tract binding protein (PTB) avoid exonic binding, and the PTB binding map shows increased enrichment at the polypyrimidine tract. For PTB, we confirm polypyrimidine specificity and are also able to identify structural determinants of PTB binding. We detect multiple binding motifs enriched in the PTB bound fraction of oligonucleotides. These motif combinations augment binding in vitro and are also enriched in the vicinity of exons that have been determined to be in vivo targets of PTB.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.