Nonconsensus Protein Binding to Repetitive DNA Sequence Elements Significantly Affects Eukaryotic Genomes
نویسندگان
چکیده
منابع مشابه
Nonconsensus Protein Binding to Repetitive DNA Sequence Elements Significantly Affects Eukaryotic Genomes
Recent genome-wide experiments in different eukaryotic genomes provide an unprecedented view of transcription factor (TF) binding locations and of nucleosome occupancy. These experiments revealed that a large fraction of TF binding events occur in regions where only a small number of specific TF binding sites (TFBSs) have been detected. Furthermore, in vitro protein-DNA binding measurements per...
متن کاملSeminar in Organic & Biophysical Chemistry
Recent in vitro protein-DNA binding measurements indicate that transcription factors (TFs) are bound with wide range of affinities to different DNA sequences that lack known consensus motifs, thus challenging the classical picture of specific protein-DNA binding. Our group has previously demonstrated that repetitive DNA sequence elements characterized by certain symmetries, statistically affect...
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Genome-wide binding preferences of the key components of eukaryotic preinitiation complex (PIC) have been recently measured at high resolution in Saccharomyces cerevisiae by Rhee and Pugh. However, the rules determining the PIC binding specificity remain poorly understood. In this study, we show that nonconsensus protein-DNA binding significantly influences PIC binding preferences. We estimate ...
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Eukaryotic genomes contain large amount of repetitive DNA, most of which is derived from transposable elements (TEs). Progress has been made to develop computational tools for ab initio identification of repeat families, but there is an urgent need to develop tools to automate the annotation of TEs in genome sequences. Here we introduce REPCLASS, a tool that automates the classification of TE s...
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Repetitive DNA elements have been a part of the genomic fauna of eukaryotes perhaps since their very beginnings. Millions of years of coevolution have given repeats central roles in chromosome maintenance and genetic modulation. Here we review the genomes of parasitic protozoa in the context of the current understanding of repetitive elements. Particular reference is made to repeats in five med...
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ژورنال
عنوان ژورنال: PLOS Computational Biology
سال: 2015
ISSN: 1553-7358
DOI: 10.1371/journal.pcbi.1004429