Genomic sequence is highly predictive of local nucleosome depletion. [PDF]
PLoS Computational Biology, 2008 The regulation of DNA accessibility through nucleosome positioning is important for transcription control. Computational models have been developed to predict genome-wide nucleosome positions from DNA sequences, but these models consider only nucleosome ...
Guo-Cheng Yuan, Jun S Liu
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FACT, the Bur kinase pathway, and the histone co-repressor HirC have overlapping nucleosome-related roles in yeast transcription elongation. [PDF]
PLoS ONE, 2011 Gene transcription is constrained by the nucleosomal nature of chromosomal DNA. This nucleosomal barrier is modulated by FACT, a conserved histone-binding heterodimer.
Jennifer R Stevens +6 more
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Predicting nucleosome positioning using a duration Hidden Markov Model
BMC Bioinformatics, 2010 Background The nucleosome is the fundamental packing unit of DNAs in eukaryotic cells. Its detailed positioning on the genome is closely related to chromosome functions.
Widom Jonathan +5 more
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BMC Bioinformatics, 2021 Background Nucleosome organization is involved in many regulatory activities in various organisms. However, studies integrating nucleosome organization in mammalian genomes are very limited mainly due to the lack of comprehensive data quality control (QC)
Xiaolan Chen +3 more
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NAP1-assisted nucleosome assembly on DNA measured in real time by single-molecule magnetic tweezers.
PLoS ONE, 2012 While many proteins are involved in the assembly and (re)positioning of nucleosomes, the dynamics of protein-assisted nucleosome formation are not well understood.
Rifka Vlijm +3 more
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Distinct modes of regulation by chromatin encoded through nucleosome positioning signals.
PLoS Computational Biology, 2008 The detailed positions of nucleosomes profoundly impact gene regulation and are partly encoded by the genomic DNA sequence. However, less is known about the functional consequences of this encoding.
Yair Field +7 more
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Cell cycle-specified fluctuation of nucleosome occupancy at gene promoters.
PLoS Genetics, 2006 The packaging of DNA into nucleosomes influences the accessibility of underlying regulatory information. Nucleosome occupancy and positioning are best characterized in the budding yeast Saccharomyces cerevisiae, albeit in asynchronous cell populations or
Gregory J Hogan +2 more
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Defining transcription factor nucleosome binding with Pioneer-seq.
PLoS GeneticsGene expression requires the targeting of transcription factors (TFs) to regulatory sequences often occluded within nucleosomes. To comprehensively examine TF nucleosome binding, we developed Pioneer-Seq.
Maria Tsompana +4 more
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Insights into distinct regulatory modes of nucleosome positioning
BMC Genomics, 2009 Background The nucleosome is the fundamental unit of eukaryotic genomes. Experimental evidence suggests that the genomic DNA sequence and a variety of protein factors contribute to nucleosome positioning in vivo.
Feng Jihua +5 more
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Diversity of eukaryotic DNA replication origins revealed by genome-wide analysis of chromatin structure. [PDF]
PLoS Genetics, 2010 Eukaryotic DNA replication origins differ both in their efficiency and in the characteristic time during S phase when they become active. The biological basis for these differences remains unknown, but they could be a consequence of chromatin structure ...
Nicolas M Berbenetz +2 more
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