Understanding alternative splicing: towards a cellular code

By A. Matlin, F. Clark, Christopher W. J. Smith. Nature reviews. Molecular cell biology, 2005

1,420 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/6e487ab063fc9b945cd2f0c3dfff6655290e3145

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Citations in the corpus

Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data (2011, neutral): “Compared to yeasts, mammalian transcriptomes exhibit substantially more complex patterns of alternative splicing 26 .”
Function of alternative splicing. (2005, positive): “Previous work resulted in an explosion of mechanistical insights into alternative splicing regulation, which has been covered in excellent reviews (Graveley, 2009; Matlin et al., 2005; Li et al., 2007b; Wahl et al., 2009).”
Splicing regulation: from a parts list of regulatory elements to an integrated splicing code. (2008, background): “An important long-term goal in the splicing field is to determine a ‘‘splicing code:’’ a set of rules that can predict the splicing pattern of any primary transcript sequence (Fu 2004; Matlin et al. 2005).”
Analysis and design of RNA sequencing experiments for identifying isoform regulation (2010, methodology): “Under the assumption of a uniform prior on Ψ, it is sufficient to define an estimate for Ψf and transform to get an estimate of Ψ, using the inverse of equation (1).”
Resolving RNA complexity to decipher regulatory rules governing biological networks (2010, neutral): “In general, it is anticipated that the relative amounts of different positive- and negative-acting RNABPs might define a 'cellular RNA-processing code' that dictates the pattern of processing for each pre-mRNA, so that pre-mRNAs with the same set of regulatory elements can be regulated in a coordina”
Alternative Splicing at the Intersection of Biological Timing, Development, and Stress Responses[OPEN] (2013, background): “…cellular conditions is determined by the interaction of additional proteins, globally designated as splicing factors (SFs), that guide spliceosomal components and thereby the spliceosome to the respective splice sites (Matlin et al., 2005; Nilsen and Graveley, 2010; Wachter et al., 2012).”
Expansion of the eukaryotic proteome by alternative splicing (2010, background): “The biochemical mechanisms that control splice-site usage, and therefore alternative splicing, are complex and in large part remain poorly understoo”
Alternative splicing: new insights from global analyses. (2006, background): “cis-acting sequence elements in exons and introns that are important for promoting splice-site recognition and discriminating correct from incorrect pairs of splice sites (Cartegni et al., 2002; Matlin et al., 2005) (Figure 3).”
CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing (2011, neutral): “Alternative splicing decisions are determined by the ability of weak splice sites to effectively compete with strong splice sites for detection by the spliceosom”
Opportunities and challenges Genome-wide analyses of alternative splicing in plants: (2008, positive): “…intronic splicing enhancers (ESEs or ISEs) and exonic or intronic splicing silencers (ESSs or ISSs), are located within the exon or adjacent introns at variable distances from the splice site, and have been identified in several mammalian genes, and direct splice-site choice (Matlin et al. 2005).”
Detection of splice junctions from paired-end RNA-seq data by SpliceMap (2010, background): “This process occurs in over 90% of multi-exon human genes (1,2) and greatly increases the diversity of possible transcripts in the transcriptome.”
Spliceosome structure and function. (2011, background): “For more in-depth reviews of alternative splicing and its regulation the reader is referred to several recent reviews (Chen and Manley 2009; Matlin et al. 2005; Black 2003; Smith and Valcárcel 2000).”