Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements

By L. Lareau, Maki Inada, R. Green, Jordan Wengrod, Steven E. Brenner. Nature, 2007

675 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/719a52055b1e4bfff223c2f5f12e6764d65468c3

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In Molecular Biology

Citations in the corpus

Resolving RNA complexity to decipher regulatory rules governing biological networks (2010, neutral): “; and defining unexpected features, such as ultraconserved elements that mediate nonsense-mediated decay (NMD) of transcripts that encode RNABP”
Rapid report Extensive coupling of alternative splicing of pre-mRNAs of serine⁄arginine (SR) genes with nonsense-mediated decay (2009, background): “Because of this, inhibition of translation has been shown to block NMD (Green et al., 2003; Lareau et al., 2007b; Kurihara et al., 2009).”
Genome-wide mapping of alternative splicing in Arabidopsis thaliana. (2010, background): “Alternatively spliced PTC+ isoforms can be potentially targeted for degradation by the nonsense mediated mRNA decay (NMD) surveillance machinery or regulate the level of functional transcripts by the mechanism of regulated unproductive splicing and translation (RUST).”
TDP‐43 regulates its mRNA levels through a negative feedback loop (2011, background): “…a negative feedback loop has been reported for a number of RNA processing factors including SR proteins SC35 and SF2, and hnRNP members PTB and hnRNP-L (Sureau et al, 2001; Wollerton et al, 2004; Lareau et al, 2007; Ni et al, 2007; Saltzman et al, 2008; Rossbach et al, 2009; Sun et al, 2010).”
Widespread intron retention in mammals functionally tunes transcriptomes (2014, background): “Previous studies have shown that IR functions in the ho- meostatic control of the expression of some RNA processing and export factors (Kalyna et al. 2006; Li et al. 2006; Lareau et al. 2007; Ge and Porse 2013).”
Count-based differential expression analysis of RNA sequencing data using R and Bioconductor (2013, methodology): “Therefore, we emphasize that this protocol is not meant to replace the existing user guides, vignettes and online documentation for the packages and functions described.”
MetaDisorder: a meta-server for the prediction of intrinsic disorder in proteins (2012, methodology): “…[36], PSI-BLAST run in two different modes (with and without masking regions with low sequence complexity) over the culled PDB database [37], PHYRE [38], and PCONS [39] (a consensus method that uses as an input models generated by MODELLER [40] based on alignments from the previously mentioned…”
Quality control of eukaryotic mRNA: safeguarding cells from abnormal mRNA function. (2007, background): “In fact, the pre-mRNA of every known member of the human SR family of splicing regulators contains ultraconserved elements that are alternatively spliced as either exonic cassettes that contain in-frame nonsense codons or introns within the 3 UTR (Lareau et al. 2007).”
Opportunities and challenges Genome-wide analyses of alternative splicing in plants: (2008, neutral): “…conserved AS is observed in both the plant and animal kingdoms, and conserved AS has been used to imply functional significance (Kalyna et al. 2006; Lareau et al. 2007; Irimia et al. 2008; Wang et al. 2008), some cases of conserved AS may reflect conserved sequence features that form mRNA…”