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MNase-Seq Analysis for Identifying Stress-Altered Nucleosome Occupancy in Plants
Nucleosome occupancy plays an important role in chromatin compaction, affecting biological processes by hampering the binding of cis-acting elements...
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The esBAF and ISWI nucleosome remodeling complexes influence occupancy of overlap** dinucleosomes and fragile nucleosomes in murine embryonic stem cells
BackgroundNucleosome remodeling factors regulate the occupancy and positioning of nucleosomes genome-wide through ATP-driven DNA translocation. While...
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Simultaneous Measurement of DNA Methylation and Nucleosome Occupancy in Single Cells Using scNOMe-Seq
Single-cell Nucleosome Occupancy and Methylome sequencing (scNOMe-seq) is a multimodal assay that simultaneously measures endogenous DNA methylation...
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General regulatory factors exert differential effects on nucleosome sliding activity of the ISW1a complex
BackgroundChromatin dynamics is deeply involved in processes that require access to DNA, such as transcriptional regulation. Among the factors...
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Dynamic nucleosome organization after fertilization reveals regulatory factors for mouse zygotic genome activation
Chromatin remodeling is essential for epigenome reprogramming after fertilization. However, the underlying mechanisms of chromatin remodeling remain...
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Structure of histone deacetylase complex Rpd3S bound to nucleosome
Crosstalk between histone modifications represents a fundamental epigenetic mechanism in gene regulation. During the transcription elongation...
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Nucleosome density shapes kilobase-scale regulation by a mammalian chromatin remodeler
Nearly all essential nuclear processes act on DNA packaged into arrays of nucleosomes. However, our understanding of how these processes (for...
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Nucleosome-bound NR5A2 structure reveals pioneer factor mechanism by DNA minor groove anchor competition
Gene expression during natural and induced reprogramming is controlled by pioneer transcription factors that initiate transcription from closed...
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NucPosDB: a database of nucleosome positioning in vivo and nucleosomics of cell-free DNA
Nucleosome positioning is involved in many gene regulatory processes happening in the cell, and it may change as cells differentiate or respond to...
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Structural mechanism of synergistic targeting of the CX3CR1 nucleosome by PU.1 and C/EBPα
Pioneer transcription factors are vital for cell fate changes. PU.1 and C/EBPα work together to regulate hematopoietic stem cell differentiation....
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Structural basis of nucleosome deacetylation and DNA linker tightening by Rpd3S histone deacetylase complex
In Saccharomyces cerevisiae , cryptic transcription at the coding region is prevented by the activity of Sin3 histone deacetylase (HDAC) complex...
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NucHMM: a method for quantitative modeling of nucleosome organization identifying functional nucleosome states distinctly associated with splicing potentiality
We develop a novel computational method, NucHMM, to identify functional nucleosome states associated with cell type-specific combinatorial histone...
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Histone H1 binding to nucleosome arrays depends on linker DNA length and trajectory
Throughout the genome, nucleosomes often form regular arrays that differ in nucleosome repeat length (NRL), occupancy of linker histone H1 and...
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Machine learning predicts nucleosome binding modes of transcription factors
BackgroundMost transcription factors (TFs) compete with nucleosomes to gain access to their cognate binding sites. Recent studies have identified...
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Chemical map-based prediction of nucleosome positioning using the Bioconductor package nuCpos
BackgroundAssessing the nucleosome-forming potential of specific DNA sequences is important for understanding complex chromatin organization. Methods...
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ORE-Seq: Genome-Wide Absolute Occupancy Measurement by Restriction Enzyme Accessibilities
Digestion with restriction enzymes is a classical approach for probing DNA accessibility in chromatin. It allows to monitor both the cut and the...
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Sox2 levels regulate the chromatin occupancy of WNT mediators in epiblast progenitors responsible for vertebrate body formation
WNT signalling has multiple roles. It maintains pluripotency of embryonic stem cells, assigns posterior identity in the epiblast and induces...
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MiOS, an integrated imaging and computational strategy to model gene folding with nucleosome resolution
The linear sequence of DNA provides invaluable information about genes and their regulatory elements along chromosomes. However, to fully understand...
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A deformation energy model reveals sequence-dependent property of nucleosome positioning
We present a deformation energy model for predicting nucleosome positioning, in which a position-dependent structural parameter set derived from...
