http://www.ploscompbiol.org/article/info%253Adoi%252F10.1371%252Fjournal.pcbi.1000770
Posts Tagged ‘rnaseq’
An Information-Theoretic Machine Learning Approach to Expression QTL Analysis
July 26, 2013An Information-Theoretic Machine Learning Approach to Expression QTL Analysis Tao Huang, Yu-Dong Cai
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0067899
Direct Competition between hnRNP C and U2AF65 Protects the Transcriptome from the Exonization of Alu Elements.
May 6, 2013Direct Competition between hnRNP C and U2AF65 Protects the
Transcriptome from the Exonization of Alu Elements.
Kathi Zarnack, Julian König, Mojca Tajnik, Iñigo Martincorena, Sebastian Eustermann, Isabelle Stévant, Alejandro Reyes, Simon Anders, Nicholas M Luscombe, and Jernej Ule
There are ∼650,000 Alu elements in transcribed regions of the human genome. These elements contain cryptic splice sites, so they are in constant danger of aberrant incorporation into mature transcripts. Despite posing a major threat to transcriptome integrity, little is known about the molecular mechanisms preventing their inclusion. Here, we present a mechanism for protecting the human transcriptome from the aberrant exonization of transposable elements. Quantitative iCLIP data show that the RNA-binding protein hnRNP C competes with the splicing factor U2AF65 at many genuine and cryptic splice sites. Loss of hnRNP C leads to formation of previously suppressed Alu exons, which severely disrupt transcript function. Minigene experiments explain disease-associated mutations in Alu elements that hamper hnRNP C binding. Thus, by preventing U2AF65 binding to Alu elements, hnRNP C plays a critical role as a genome-wide sentinel protecting the transcriptome. The findings have important implications for human evolution and disease.
Cell, 2013 vol. 152 (3) pp. 453-466
http://www.sciencedirect.com/science/article/pii/S0092867412015450
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=23374342&retmode=ref&cmd=prlinks
bio v tech rep
March 11, 2013http://www.nature.com/nbt/journal/v29/n7/abs/nbt.1910.html
discusses (at a very basic level) the issue of tech versus bio reps related class:
RNA studies under fire
March 7, 2013High-profile results challenged over statistical analysis of sequence data http://www.nature.com/news/rna-studies-under-fire-1.10502
“In July 2010, a team led by Catherine Dulac and Christopher Gregg, both then at Harvard University in Cambridge, Massachusetts, published a study in Science estimating that 1,300 mouse genes — an order of magnitude more than previously known — were imprinted.
Now, researchers are arguing that a flawed analysis led Dulac and Gregg to vastly overestimate imprinting in their paper.”
RNA studies under fire : Nature News & Comment
March 7, 2013Expressed pseudogenes in the transcriptional landscape of human cancers.
November 2, 2012http://www.ncbi.nlm.nih.gov/pubmed/22726445
Cell. 2012 Jun 22;149(7):1622-34.
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