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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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Analyses of Promoter , Enhancer, and Nucleosome Organization in Mammalian Cells by MNase-Seq
MNase-Seq is a genome-wide procedure that allows map** of DNA associated to nucleosomes following micrococcal nuclease digestion. It is a rapid and...
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Genome-Wide Identification of Open Chromatin in Plants Using MH-Seq
Functional cis-regulatory elements (CREs) act as precise transcriptional switches for fine-tuning gene transcription. Identification of CREs is...
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Quantitative MNase-seq accurately maps nucleosome occupancy levels
Micrococcal nuclease (MNase) is widely used to map nucleosomes. However, its aggressive endo-/exo-nuclease activities make MNase-seq unreliable for...
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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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Plant Stress Tolerance Methods and Protocols
This fully updated new edition explores new techniques for studying plant stress. This includes novel methodologies such as MeRIP-seq for identifying...
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Regulation of self-renewal and senescence in primitive mesenchymal stem cells by Wnt and TGFβ signaling
BackgroundThe therapeutic application of multipotent mesenchymal stem cells (MSCs) encounters significant challenges, primarily stemming from their...
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Genome-Wide Profiling of Protein–DNA Interactions with Chromatin Endogenous Cleavage and High-Throughput Sequencing (ChEC-Seq )
Interactions between regulatory proteins and specific genomic regions are critical for all chromatin-based processes, including transcription, DNA...
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Open chromatin analysis in Trypanosoma cruzi life forms highlights critical differences in genomic compartments and developmental regulation at tDNA loci
BackgroundGenomic organization and gene expression regulation in trypanosomes are remarkable because protein-coding genes are organized into...
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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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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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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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Measuring Genome-Wide Nascent Nucleosome Assembly Using ReIN-Map
The successful assembly of nucleosomes following DNA replication is critically important for both the inheritance of epigenetic information and the...
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Ribosome Profiling Methods Adapted to the Study of RNA-Dependent Translation Regulation in Staphylococcus aureus
Noncoding RNAs, including regulatory RNAs (sRNAs), are instrumental in regulating gene expression in pathogenic bacteria, allowing them to adapt to...
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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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Profiling Accessible Chromatin and Nucleosomes in the Mammalian Genome
Genomic DNA wraps around core histones to form nucleosomes, which provides steric constraints on how transcription factors (TFs) can interact with...
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Creating 2D Occupancy Plots Using plot2DO
Chromatin organization and epigenetic marks play a critical role in stem cell pluripotency and differentiation. Chromatin digestion by micrococcal...
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Profiling the Epigenetic Landscape of the Spermatogonial Stem Cell—Part 1: Epigenomics Assays
Epigenomics encompasses analyses of a variety of different epigenetic parameters which, collectively, make up the epigenetic programming that...
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CUT&Tag for Map** In Vivo Protein-DNA Interactions in Plants
Histone post-translational modifications and transcription factors (TFs) play vital roles in regulating gene expression. A comprehensive...
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cBAF generates subnucleosomes that expand OCT4 binding and function beyond DNA motifs at enhancers
The canonical BRG/BRM-associated factor (cBAF) complex is essential for chromatin opening at enhancers in mammalian cells. However, the nature of the...
