Alternative splicing and evolution: diversification, exon definition and function

By Hadas Keren, Galit Lev-Maor, Gil Ast. 2010

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In Molecular Biology

Citations in the corpus

OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more (2020, background): “Eukaryotic species, especially vertebrates, use alternative splicing, by which a diversity of protein sequences can originate from a single gene by varying combinations of its exons (9).”
Pol III binding in six mammalian genomes shows high conservation among amino acid isotypes, despite divergence in tRNA gene usage (2011, neutral): “RNA polymerase II (pol II), which is responsible for protein-coding mRNA synthesis, has been well-characterized to bind in vivo to many regions not actively transcribed due to stalled polymerase activity 19,20 , alternate transcription start sites 21 , and regulated alternative splicing 22 .”
rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data (2014, background): “RNA sequencing | alternative splicing | exon | isoform | transcriptome A lternative splicing generates tremendous transcriptomic and proteomic complexity in higher eukaryotes (1 – 4).”
A census of human RNA-binding proteins (2014, positive): “alternative splicing and polyadenylation) (Chen and Manley, 2009; Keren et al., 2010).”
Divergence of duplicate genes in exon–intron structure (2012, background): “Second, alternative splicing does not necessarily need the mutation or modification of the genomic sequences, whereas exonization/pseudoexonization requires the creation and/or fixation of a novel start/stop codon (of a gene) or donor/acceptor site (of an intron) (13, 22, 23).”
Alternative Splicing Regulatory Networks: Functions, Mechanisms, and Evolution. (2019, background): “Intronic sequences derived from transposable elements (TEs) are also a particularly common source of cis-acting elements that vary across evolution and can regulate splicing (Gal-Mark et al., 2009; Keren et al., 2010) (Figure 5a).”
Mechanisms and Functions of Long Non-Coding RNAs at Multiple Regulatory Levels (2019, background): “Most of the genes (~95%) in human cells are selectively spliced [54].”
Complexity of the Alternative Splicing Landscape in Plants[C][W][OPEN] (2013, background): “Analysis of the large pool of newly discovered U12-type introns might change this number (Zhu and Brendel, 2003; Basu et al., 2008).”
MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data (2012, background): “Alternative splicing plays critical roles in regulating gene function and activity in higher eukaryotes (1).”
Functional consequences of developmentally regulated alternative splicing (2011, background): “It is likely that a large fraction of mRNA diversity has no detectable function within an organism, although some of it provides fodder for the derivation of functional splice variants on an evolutionary timescal”