Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing

By Qun Pan, O. Shai, Leo J. Lee, Brendan J. Frey, Benjamin J. Blencowe. Nature Genetics, 2008

3,892 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/5f4fb0b0d66c43d69f88b014fbf4c390232ac1f9

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In Molecular Biology

Citations in the corpus

Resolving RNA complexity to decipher regulatory rules governing biological networks (2010, positive): “The power of RNA–seq to assess mRNA complexity was highlighted in 2008 by the Blencow”
CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing (2011, positive): “The balance between splice site selection is principally influenced by two variables(5): (1) the availability of splicing factors that detect enhancer or silencer sequences encoded within nascent RNA(4,6) and (2) the rate of RNA polymerase II (pol II) transcription elongation, wherein a slow rate fa”
Genome-wide mapping of alternative splicing in Arabidopsis thaliana. (2010, methodology): “…have relied on Sanger sequencing of expressed sequence tags (ESTs) and cDNAs, high-density DNA microarrays (for review, see Mockler et al. 2005) and most recently ultrahigh-throughput RNA sequencing (RNA-seq) approaches (Mortazavi et al. 2008; Pan et al. 2008; Sultan et al. 2008; Wang et al. 2008).”
The Developmental Transcriptome of Drosophila melanogaster (2010, positive): “37 , 38 , a larger proportion of Drosophila genes encode alternative transcripts than was previously known.”
In silico prediction of splice-altering single nucleotide variants in the human genome (2014, background): “Another limitation is that controlling for potential confounding effects of alternative splicing on in silico predictions remains a major problem for selecting negative variants because alternative splicing is so wide spread (7).”
Epigenetics in alternative pre-mRNA splicing (2011, positive): “Current estimates based on deep sequencing methodologies indicate that more than 90% of human genes undergo alternative splicing (Croft et al., 2000; Pan et al., 2008; Wang et al., 2008).”
Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation (2012, methodology): “Although RNA-Seq can be used to search for novel exons or for splice-variants and isoform-speciﬁc expression (7,12–14), transcript assembly (15) or allele-speciﬁc expression (16,17), our focus in this article is on differential expression for pre-determined genomic features.”
rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data (2014, methodology): “The basic principle in RNA-Seq analysis of alternative splicing is to use RNA-Seq reads mapped to different isoforms to estimate the isoform proportion (3, 4).”
Complexity of the Alternative Splicing Landscape in Plants[C][W][OPEN] (2013, methodology): “AsmoreRNA-seq studies are now being performed with different tissues and individual cell types and under different biotic and abiotic stresses, our knowledge of AS in plants is likely to further increase in the near future.”
From RNA-seq reads to differential expression results (2010, background): “In addition, RNA-seq promises to unravel previously inaccessible complexities in the transcriptome, such as allele-specific expression and novel promoters and isoforms [1-4].”
Expansion of the eukaryotic proteome by alternative splicing (2010, background): “Recent studies using high-throughput sequencing indicate that 95–100p of human pre-mRNAs that contain sequence corresponding to more than one exon are processed to yield multiple mRNA”
The Nuclear-Retained Noncoding RNA MALAT1 Regulates Alternative Splicing by Modulating SR Splicing Factor Phosphorylation (2010, background): “It has recently been estimated that transcripts from more than 95% of human multi-exon-containing genes undergo AS, and the majority of these are variably expressed between different cell and tissue types (Pan et al., 2008; Wang et al., 2008).”