scholarly journals E2F in vivo binding specificity: Comparison of consensus versus nonconsensus binding sites

2008 ◽  
Vol 18 (11) ◽  
pp. 1763-1777 ◽  
Author(s):  
A. Rabinovich ◽  
V. X. Jin ◽  
R. Rabinovich ◽  
X. Xu ◽  
P. J. Farnham
Keyword(s):  
Binding Sites ◽  
Binding Specificity ◽  
In Vivo Binding

scholarly journals De novo identification of in vivo binding sites from ChIP-chip data

2008 ◽  
Vol 9 (S7) ◽  
Author(s):  
Victor Jin ◽  
Alina Rabinovich ◽  
Henny O'Geen ◽  
Sushma Iyengar ◽  
Peggy Farnham
Keyword(s):  
Binding Sites ◽  
De Novo ◽  
Chip Data ◽  
In Vivo Binding ◽  
Chip Chip

scholarly journals Genome-Wide Mapping of Collier In Vivo Binding Sites Highlights Its Hierarchical Position in Different Transcription Regulatory Networks

PLoS ONE ◽  
2015 ◽  
Vol 10 (7) ◽  
pp. e0133387 ◽  
Author(s):  
Mathilde de Taffin ◽  
Yannick Carrier ◽  
Laurence Dubois ◽  
Laetitia Bataillé ◽  
Anaïs Painset ◽  
...  
Keyword(s):  
Binding Sites ◽  
Regulatory Networks ◽  
In Vivo Binding ◽  
Genome Wide ◽  
Hierarchical Position

scholarly journals Predicting in vivo binding sites of RNA-binding proteins using mRNA secondary structure

RNA ◽  
2010 ◽  
Vol 16 (6) ◽  
pp. 1096-1107 ◽  
Author(s):  
X. Li ◽  
G. Quon ◽  
H. D. Lipshitz ◽  
Q. Morris
Keyword(s):  
Secondary Structure ◽  
Binding Sites ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Mrna Secondary Structure ◽  
In Vivo Binding

scholarly journals Modeling RNA-binding protein specificity in vivo by precisely registering protein-RNA crosslink sites

2018 ◽  
Author(s):  
Huijuan Feng ◽  
Suying Bao ◽  
Sebastien M. Weyn-Vanhentenryck ◽  
Aziz Khan ◽  
Justin Wong ◽  
...  
Keyword(s):  
Binding Sites ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Binding Specificity ◽  
Computational Method ◽  
Sr Protein ◽  
Genome Wide ◽  
Sequence Elements ◽  
Nucleotide Resolution

AbstractRNA-binding proteins (RBPs) regulate post-transcriptional gene expression by recognizing short and degenerate sequence elements in their target transcripts. Despite the expanding list of RBPs with in vivo binding sites mapped genomewide using crosslinking and immunoprecipitation (CLIP), defining precise RBP binding specificity remains challenging. We previously demonstrated that the exact protein-RNA crosslink sites can be mapped using CLIP data at single-nucleotide resolution and observed that crosslinking frequently occurs at specific positions in RBP motifs. Here we have developed a computational method, named mCross, to jointly model RBP binding specificity while precisely registering the crosslinking position in motif sites. We applied mCross to 112 RBPs using ENCODE eCLIP data and validated the reliability of the resulting motifs by genome-wide analysis of allelic binding sites also detected by CLIP. We found that the prototypical SR protein SRSF1 recognizes GGA clusters to regulate splicing in a much larger repertoire of transcripts than previously appreciated.

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