Expansion of the eukaryotic proteome by alternative splicing

By T. Nilsen, Brenton R. Graveley. Nature, 2010

2,105 citations recorded by the source corpus.

The collection of components required to carry out the intricate processes involved in generating and maintaining a living, breathing and, sometimes, thinking organism is staggeringly complex. Where do all of the parts come from? Early estimates stated that about 100,000 genes would be required to make up a mammal; however, the actual number is less than one-quarter of that, barely four times the number of genes in budding yeast. It is now clear that the 'missing' information is in large part provided by alternative splicing, the process by which multiple different functional messenger RNAs, and therefore proteins, can be synthesized from a single gene.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/614327b0a3242ea5226b4caf0a16b87eee70a2ee

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

Citations in the corpus

iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution (2010, background): “In humans, it was recently estimated that 95–100% of all multi-exon transcripts undergo alternative splicin”
Detecting differential usage of exons from RNA-seq data (2012, background): “We are only beginning to understand which part of this diversity is functional (for recent reviews, see, e.g., Nilsen and Graveley 2010; Grabowski 2011).”
Deep learning in bioinformatics (2016, methodology): “[94] utilized DBN in splice junction prediction, a major research avenue in understanding gene expression [112], and proposed a new DBN training method called boosted contrastive divergence for imbalanced data and a new regularization term for sparsity of DNA sequences; their work showed not only si”
Proteogenomics: concepts, applications, and computational strategies (2014, background): “Alternative splicing is a major source of cell-specific and tissue-specific protein variation in higher eukaryotes 20,68 .”
rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data (2014, neutral): “logit ψ ijk ∼Normal μ= logit ψ ij ; σ2 = σij : [2]”
Charting histone modifications and the functional organization of mammalian genomes (2011, background): “In many cases, alternative splicing provides an additional layer of complexity and regulatio”
Alternative Splicing Regulatory Networks: Functions, Mechanisms, and Evolution. (2019, background): “However, it is well established that such data are severely underrepresented for multiple technical reasons that necessitate a careful modelling of false-negative rates (Blencowe, 2017; Nilsen and Graveley, 2010).”
Diverse alternative back-splicing and alternative splicing landscape of circular RNAs (2016, positive): “It is well known that most multiexonic genes undergo alternative splicing to generate multiple (linear) mRNAs (Nilsen and Graveley 2010).”
Complementary sequence-mediated exon circularization. (2014, background): “…complementary sequences and their competition, it would be interesting to identify other cis elements and trans factors that are involved in alternative circularization, as has been done in the study of alternative splicing (Fairbrother et al., 2002; Lovci et al., 2013; Nilsen and Graveley, 2010).”
RNA sequencing: advances, challenges and opportunities (2010, background): “Characterization of alternative splicing patterns Given the importance of alternative splicing patterns in development and the fact that 15–60% of known disease-causing mutations affect splicin”