Journal ArticleDOI
The RNA-binding protein repertoire of embryonic stem cells
S. Chul Kwon,Hyerim Yi,Katrin Eichelbaum,Sophia Föhr,Bernd Fischer,Kwon Tae You,Alfredo Castello,Jeroen Krijgsveld,Matthias W. Hentze,Matthias W. Hentze,V. Narry Kim +10 more
TLDR
Two well-known E3 ubiquitin ligases, Trim25 and Trim71, are validated as RBPs, revealing a potential link between RNA biology and protein-modification pathways.Abstract:
A mRNA-interactome capture approach in embryonic stem cells (ESCs) has led to the identification of 283 novel RNA-binding protein (RBP) candidates, of which 68 are preferentially expressed in ESCs. Validation of two known E3 ubiquitin ligases as RBPs reveals an intriguing potential link between RNA biology and protein-modification pathways.read more
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A census of human RNA-binding proteins.
TL;DR: This work presents a census of 1,542 manually curated RBPs that are analysed for their interactions with different classes of RNA, their evolutionary conservation, their abundance and their tissue-specific expression, a critical step towards the comprehensive characterization of proteins involved in human RNA metabolism.
Journal ArticleDOI
m 6 A RNA methylation promotes XIST -mediated transcriptional repression
Deepak P. Patil,Chun-Kan Chen,Brian F. Pickering,Amy Y. M. Chow,Constanza Jackson,Mitchell Guttman,Samie R. Jaffrey +6 more
TL;DR: The long non-coding RNA X-inactive specific transcript (XIST) mediates the transcriptional silencing of genes on the X chromosome and is highly methylated with at least 78 N6-methyladenosine (m6A) residues, revealing a pathway of m6A formation and recognition required for XIST-mediated transcriptional repression.
Journal ArticleDOI
A brave new world of RNA-binding proteins
TL;DR: The RNA targets and molecular and cellular functions of the new RBPs, as well as the possibility that some RBPs may be regulated by RNA rather than regulate RNA, are discussed.
Journal ArticleDOI
RNA mis-splicing in disease
TL;DR: An overview of RNA splicing mechanisms is provided followed by a discussion of disease-associated errors, with an emphasis on recently described mutations that have provided new insights into splicing regulation.
Journal ArticleDOI
Context-dependent control of alternative splicing by RNA-binding proteins
Xiang-Dong Fu,Manuel Ares +1 more
TL;DR: Some of the emerging rules that govern the highly context-dependent and combinatorial nature of alternative splicing regulation are described.
References
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Jiirgen Cox,Matthias Mann +1 more
TL;DR: MaxQuant, an integrated suite of algorithms specifically developed for high-resolution, quantitative MS data, detects peaks, isotope clusters and stable amino acid isotope–labeled (SILAC) peptide pairs as three-dimensional objects in m/z, elution time and signal intensity space and achieves mass accuracy in the p.p.b. range.
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Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments
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Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
Cole Trapnell,Adam Roberts,Loyal A. Goff,Loyal A. Goff,Loyal A. Goff,Geo Pertea,Daehwan Kim,Daehwan Kim,David R. Kelley,David R. Kelley,Harold Pimentel,Steven L. Salzberg,John L. Rinn,John L. Rinn,Lior Pachter +14 more
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Andromeda: a peptide search engine integrated into the MaxQuant environment
Jürgen Cox,Nadin Neuhauser,Annette Michalski,Richard A. Scheltema,Jesper V. Olsen,Matthias Mann +5 more
TL;DR: A novel peptide search engine using a probabilistic scoring model that can handle data with arbitrarily high fragment mass accuracy, is able to assign and score complex patterns of post-translational modifications, and accommodates extremely large databases.