Corrigendum: ChEC-seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo
نویسندگان
چکیده
This corrects the article DOI: 10.1038/ncomms15643.
منابع مشابه
ChEC-seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo
Chromatin endogenous cleavage (ChEC) uses fusion of a protein of interest to micrococcal nuclease (MNase) to target calcium-dependent cleavage to specific genomic loci in vivo. Here we report the combination of ChEC with high-throughput sequencing (ChEC-seq) to map budding yeast transcription factor (TF) binding. Temporal analysis of ChEC-seq data reveals two classes of sites for TFs, one displ...
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Transcription factors (TFs) are DNA-binding proteins that regulate gene expression. Sequence-specific TFs recognize DNA via specific amino acid-base hydrogen bonds and contacts that read local DNA shape1. Studying base and shape readout modes of TFs in vivo has been challenging due to technical issues associated with current approaches for mapping TF-binding sites (TFBSs). We recently introduce...
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Interactions of transcription factors (TFs) with DNA comprise a complex interplay between base-specific amino acid contacts and readout of DNA structure. Recent studies have highlighted the complementarity of DNA sequence and shape in modeling TF binding in vitro. Here, we have provided a comprehensive evaluation of in vivo datasets to assess the predictive power obtained by augmenting various ...
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The interaction between transcription factors (TFs) and DNA results from a complex interplay between the DNA structure and nucleotide‐amino acid contacts. We previously developed a sequence‐based flexible hidden Markov model approach for TF binding site (TFBS) prediction, the Transcription Factor Flexible Model (TFFM). We describe a novel approach which builds upon the TFFMs by integrating four...
متن کاملA widespread role of the motif environment in transcription factor binding across diverse protein families.
Transcriptional regulation requires the binding of transcription factors (TFs) to short sequence-specific DNA motifs, usually located at the gene regulatory regions. Interestingly, based on a vast amount of data accumulated from genomic assays, it has been shown that only a small fraction of all potential binding sites containing the consensus motif of a given TF actually bind the protein. Rece...
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عنوان ژورنال:
دوره 8 شماره
صفحات -
تاریخ انتشار 2015