A genomic code for nucleosome positioning

By Eran Segal, Yvonne Fondufe-Mittendorf, Lingyi Chen, A. Thåström, Yair Field, Irene K. Moore, Ji-Ping Wang, Jonathan Widom. Nature, 2006

1,594 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/0973a5d8c44b7e87945f87cd4c7eb25607cf8809

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Citations in the corpus

Dynamic regulation of nucleosome positioning in the human genome. (2008, neutral): “Published results suggest that nucleosomes are stable under these in vitro conditions; both crosslinked (Albert et al., 2007) and noncrosslinked nucleosomes (Segal et al., 2006) show similar preference to the dinucleotide repeat patterns.”
Machine learning in genetics and genomics (2015, background): “Algorithms can similarly be trained to identify splice sites 3 , promoters 4 , enhancers 5 or positioned nucleosomes 6 .”
Pioneer transcription factors: establishing competence for gene expression. (2011, background): “2008) led to the hypothesis that such regions possess sequences that intrinsically destabilize the nucleosome (Segal et al. 2006).”
The Major Architects of Chromatin: Architectural Proteins in Bacteria, Archaea and Eukaryotes (2008, background): “DNA sequences that position nucleosomes far more stably than natural sequences have been engineered, suggesting that nucleosome positioning sequences have evolved to be metastable (Lowary and Widom, 1998; Segal et al., 2006; Henikoff, 2008), allowing modulation of histone-DNA contacts.”
G+C content dominates intrinsic nucleosome occupancy (2009, methodology): “Methods to predict nucleosome positioning and occupancy from sequence have often relied on periodic dinucleotide patterns found in collections of nucleosomal sequences from both in vivo and in vitro experiments[20,21] and these patterns can explain a fraction of nucleosome positions in vivo[22, 23 ]”
Multivalent engagement of chromatin modifications by linked binding modules (2007, background): “Conclusion Large-scale experiments that have examined chromatin modification patterns through evolutionary space suggest a strong conservation of chromatin signatures and nucleosome positioning biase”
Chromatin organization marks exon-intron structure (2009, background): “DNA sequence modulates how and where the DNA is packaged around nucleosomes, a concept embodied in the idea of a 'chromatin code': this information is to a great extent encoded directly within the genome sequenc”
The biology of chromatin remodeling complexes. (2009, background): “First, DNA sequences, such as AT-rich tracts, bend the DNA in a manner disfavorable to nucleosomes (101) and create a nucleosomefree region (NFR) of ∼100 bp located at the transcription start site (TSS), flanked by H2A.”
A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. (2008, methodology): “In the literature, nucleosome positioning has been defined as the ability of sequences in the genome to encode a nucleosome organization, with such features regulating the access of nonhistone proteins to DNA in vivo (e.g., Segal et al. 2006).”
Precise genome-wide mapping of single nucleosomes and linkers in vivo (2018, methodology): “MNase-seq data from [58] nucleosomes would form with similar affinities on every DNA sequence, but during the mapping process involving chromatin digestion by MNase, the nucleosomes from A/T-rich regions are digested faster, and are underrepresented in the sequenced library after extensive digestion”
Mechanisms of Polycomb gene silencing: knowns and unknowns (2009, background): “Potential PcG recruitment cues besides DNA-binding proteins, such as local nucleosome architecture or positionin”